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At least 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Near surface defects: Cause of deficit between internal and external open-circuit voltage in solar cells

The presence of interface recombination in a complex multilayered thin-film solar structure causes a disparity between the internal open-circuit voltage (V OC,in ), measured by photoluminescence, and the external open-circuit voltage (V OC,ex ) i.e. an additional V OC deficit. Higher V OC,ex value aim require a comprehensive understanding of connection between V OC deficit and interface recombination. Here, a deep near-surface defect model at the absorber/buffer interface is developed for copper indium di-selenide solar cells grown under Cu excess conditions to explain the disparity between V OC ,in and V OC,ex . The model is based on experimental analysis of admittance spectroscopy and deep-level transient spectroscopy, which show the signature of deep acceptor defect. Further, temperature-dependent current-voltage measurements confirm the presence of near surface defects as the cause of interface recombination. The numerical simulations show strong decrease in the local V OC ,in near the absorber/buffer interface leading to a V OC deficit in the device. This loss mechanism leads to interface recombination without a reduced interface bandgap or Fermi level pinning. Further, these findings demonstrate that the V OC ,in measurements alone can be inconclusive and might conceal the information on interface recombination pathways, establishing the need for complementary techniques like temperature dependent current voltage measurements to identify the cause of interface recombination in the devices.

14 SOLAR ENERGY↗
DOE OSTI2023

Efficacy of antivirals and mRNA vaccination against an XBF clinical isolate

Recombination events occur frequently in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in genetic diversity. Because these events contribute to altered host immune evasion and antiviral susceptibility, it is crucial to evaluate the efficacy of COVID-19 vaccines and antivirals against recombinant variants. As of March 2023, XBB.1.5, a recombinant sublineage of XBB, is currently the dominant form globally (Fig. S1A, Supplementary Appendix). XBB emerged as a result of recombination between two BA.2 descendants, BJ.1 and BM.1.1.1 (a progeny of BA.2.75). We and other groups have shown that XBB.1.5 is resistant to several therapeutic monoclonal antibodies and effectively evades humoral immunity elicited by natural infection or COVID-19 vaccination.1, 2, 3 By March 30, 2023, an additional recombinant variant, XBF, had been sampled 8966 times in 47 countries and territories in GISAID, reaching it highest prevalence in Australia and New Zealand (Fig. S2, Supplementary Appendix). XBF is still increasing in frequency, although the prevalence of XBB.1.5 appears to be increasing at a faster pace in most regions (Fig. S1B, Supplementary Appendix). XBF is a recombinant of BA.5.2.3 (a descendant of BA.5) and CJ.1 (a descendant of BA.2.75) and, like CJ.1, has an additional three substitutions (R346T, F486P, and F490S) in the receptor-binding domain (RBD) of the consensus form of its spike protein compared to baseline BA.2.75 (Fig. S3A, Supplementary Appendix). CJ.1 and its related sublineage CJ.1.1 did not expand as extensively as XBF, being sampled in GISAID only 1589 and 142 times respectively. CJ.1 was found circulating in many countries, but most commonly sampled in South Korea, where it is still increasing and has currently reached about 5% of the sampled population. CJ.1.1 was most frequently sampled in Malaysia and Singapore, but remained rare in both nations, peaking at about 1% of the sample in December of 2022. Despite the importance of these related variants, we have no information about the antiviral efficacy and immunity induced by COVID-19 vaccines against a clinical isolate of XBF.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Electron Mobility and Trapping in Ferrihydrite Nanoparticles

Iron is the most abundant transition metal in the Earth's crust, and naturally occurring iron oxide minerals play a commanding role in environmental redox reactions. Although iron oxide redox reactions are well studied, their precise mechanisms are not fully understood. Recent work has shown that these involve electron transfer pathways within the solid, suggesting that overall reaction rates could be dependent on electron mobility. Initial ultrafast spectroscopy studies of iron oxide nanoparticles sensitized by fluorescein derivatives supported a model for electron mobility based on polaronic hopping of electron charge carriers between iron sites, but the constitutive relationships between hopping mobilities and interfacial charge transfer processes has remained obscured. We developed a coarse-grained lattice Monte Carlo model to simulate the collective mobilities and lifetimes of these photoinjected electrons with respect to recombination with adsorbed dye molecules for the essential nanophase ferrihydrite, and tested predictions made by the simulations using pump-probe spectroscopy. We acquired optical transient absorption spectra as a function of particle size and under a variety of solution conditions, and used cryogenic transmission electron microscopy to determine the aggregation state of the nanoparticles. We observed biphasic electron recombination kinetics over timescales that spanned picoseconds to microseconds, the slower regime of which was fit with a stretched exponential decay function. The recombination rates were weakly affected by nanoparticle size and aggregation state, suspension pH, and the injection of multiple electrons per nanoparticle. We conclude that electron mobility indeed limits the rate of interfacial electron transfer in these systems with the slowest processes relating to escape from deep traps, the presence of which outweighs the influence of environmental factors such as pH-dependent surface charge.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2015

Size and Temperature Dependence of Electron Transfer between CdSe Quantum Dots and a TiO 2 Nanobelt

Understanding charge transfer reactions between quantum dots (QD) and metal oxides is fundamental for improving photocatalytic, photovoltaic and electronic devices. The complexity of these processes makes it difficult to find an optimum QD size with rapid charge injection and low recombination. We combine time-domain density functional theory with nonadiabatic molecular dynamics to investigate the size and temperature dependence of the experimentally studied electron transfer and charge recombination at CdSe QD-TiO 2 nanobelt (NB) interfaces. The electron injection rate shows strong dependence on the QD size, increasing for small QDs. The rate exhibits Arrhenius temperature dependence, with the activation energy of the order of millielectronvolts. The charge recombination process occurs due to coupling of the electronic subsystem to vibrational modes of the TiO 2 NB. Inelastic electron-phonon scattering happens on a picosecond time scale, with strong dependence on the QD size. Our simulations demonstrate that the electron-hole recombination rate decreases significantly as the QD size increases, in excellent agreement with experiments. The temperature dependence of the charge recombination rates can be successfully modeled within the framework of the Marcus theory through optimization of the electronic coupling and the reorganization energy. Our simulations indicate that by varying the QD size, one can modulate the photoinduced charge separation and charge recombination, fundamental aspects of the design principles for high efficiency devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

A traditional evolutionary history of foot-and-mouth disease viruses in Southeast Asia challenged by analyses of non-structural protein coding sequences

Recombination of rapidly evolving RNA-viruses provides an important mechanism for diversifcation, spread, and emergence of new variants with enhanced ftness. Foot-and-mouth disease virus (FMDV) causes an important transboundary disease of livestock that is endemic to most countries in Asia and Africa. Maintenance and spread of FMDV are driven by periods of dominance of specifc viral lineages. Current understanding of the molecular epidemiology of FMDV lineages is generally based on the phylogenetic relationship of the capsid-encoding genes, with less attention to the process of recombination and evolution of non-structural proteins. In this study, the putative recombination breakpoints of FMDVs endemic to Southeast Asia were determined using full-open reading frame sequences. Subsequently, the lineages’ divergence times of recombination-free genome regions were estimated. These analyses revealed a close relationship between two of the earliest endemic viral lineages that appear unrelated when only considering the phylogeny of their capsid proteins. Contrastingly, one lineage, named O/CATHAY, known for having a particular host predilection (pigs) has evolved independently. Additionally, intra-lineage recombination occurred at diferent breakpoints compared to the inter-lineage process. These results provide new insights about FMDV recombination patterns and the evolutionary interdependence of FMDV serotypes and lineages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Pb dimerization greatly accelerates charge losses in MAPbI 3 : Time-domain ab initio analysis

Metal halide perovskites constitute a new type of semiconducting materials with long charge carrier lifetimes and efficient light-harvesting. The performance of perovskite solar cells and related devices is limited by nonradiative charge and energy losses, facilitated by defects. Combining nonadiabatic molecular dynamics and time-domain density functional theory, we demonstrate that charge losses depend strongly on the defect chemical state. By considering an extra Pb atom in CH 3 NH 3 PbI 3 , which is a common defect in lead halide perovskites, we investigate its influence on charge trapping and recombination. In a chemically inert form as a Pb interstitial, the extra Pb atom has only a mild influence on charge recombination. However, if the extra Pb atom binds to a native Pb atom to form a dimer, the charge trapping and recombination are greatly accelerated because the Pb-dimer creates a localized midgap trap state that couples strongly to the perovskite valence band edge. Holes disappear from the valence band two orders of magnitude faster than in the pristine perovskite and recombine with conduction band electrons one order of magnitude faster. The simulations identify the phonon modes involved in the nonradiative charge trapping and recombination and highlight the importance of rapid decoherence within the electronic subsystem for long carrier lifetimes. The detailed atomistic analysis of the charge trapping and recombination mechanisms enriches the understanding of defect properties and provides theoretical guidance for improving perovskite performance.

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

Measurement of the conduction band spin-orbit splitting in $\mathrm{WSe_2}$ and $\mathrm{WS_2}$ monolayers

We have investigated charge tunable devices based on $\mathrm{WSe_2}$ and $\mathrm{WS_2}$monolayers encapsulated in hexagonal boron nitride. In addition to the well-known radiative recombination of neutral and charged excitons, stationary photoluminescence measurements highlight a weaker-intensity optical transition that appears when the monolayer is electrostatically doped with electrons. We have carried out a detailed characterization of this photoluminescence line based on its doping dependence, its variation as a function of the optical excitation power, its polarization characteristics, and its g factor measured under longitudinal magnetic field. We interpret this luminescence peak as an impurity-assisted radiative recombination of the intervalley negatively charged exciton (triplet trion). In addition to the standard direct recombination, the triplet trion has a second recombination channel triggered by elastic scattering off the short-range impurity potential. The energy difference between the emitted photons from these two possible recombination processes of the same triplet trion is simply the single-particle conduction band spin-orbit splitting Δ c . We measure Δ c = 12 ± 0.5 meV for the $\mathrm{WSe_2}$ monolayer and Δ c = 12 ± 1 meV for the $\mathrm{WS_2}$ monolayer. Here, these results demonstrate the importance of second-order exciton recombination processes in transition-metal dichalcogenide structures.

2-dimensional systems↗
NASA NTRS1985

I-V-T analysis of radiation damage in high efficiency Si solar cells

A detailed analysis of current-voltage characteristics of N(+)-P/P solar cells indicate that there is a combination of different mechanisms which results in an enhancement in the dark current and in turn deteriorates the photovoltaic performance of the solar cells after 1 MeV e(-) irradiation. The increase in the dark current is due to three effects, i.e., bulk recombination, space charge recombination by deep traps and space charge recombination through shallow traps. It is shown that the increase in bulk recombination current is about 2 to 3 orders of magnitude whereas space charge recombination current due to shallow traps increases only by an order or so and no space charge recombination through deep traps was observed after irradiation. Thus, in order to improve the radiation hardness of these devices, bulk properties should be preserved.

Banerjee, S.↗
NASA NTRS1986

Requirements for high-efficiency solar cells

Minimum recombination and low injection level are essential for high efficiency. Twenty percent AM1 efficiency requires a dark recombination current density of 2 x 10 to the minus 13th power A/sq cm and a recombination center density of less than 10 to the 10th power /cu cm. Recombination mechanisms at thirteen locations in a conventional single crystalline silicon cell design are reviewed. Three additional recombination locations are described at grain boundaries in polycrystalline cells. Material perfection and fabrication process optimization requirements for high efficiency are outlined. Innovative device designs to reduce recombination in the bulk and interfaces of single crystalline cells and in the grain boundary of polycrystalline cells are reviewed.

Sah, C. T.↗
NASA NTRS1986

The asymmetric profile of the H76 alpha line emission from MWC349

MWC349 is an emission-line star found by Merrill, Humason and Burwell (1932). Braes, Habing and Schoenmaker (1972) discovered that it is a strong radio source. The radio emission originates in a massive ionized wind that is expanding with a velocity of about 50 km s(-1). Its continuum spectrum fits well a nu(0.6) power law from the cm wavelengths to the far-IR. Radio recombination line emission from the envelope of MWC349 was first detected by Altenhoff, Strittmatter and Wendker (1981). We have obtained good signal-to-noise ratio, Very Large Array observations of the H76 alpha radio recombination line from the ionized wind of MWC349. Our data reveal that the profile is markedly asymmetric, with a steep rise on the blue side. This asymmetry could be due to non-LTE effects in the formation and transfer of the line or to intrinsic asymmetries in the envelope. Our analysis suggests that most probably the peculiar profile is caused by a non-LTE enhancement of the line emission from the side of the envelope nearer to the observer. This asymmetry has the opposite sense than that observed in optical and IR recombination lines, where a different effect (absorption of the stellar continuum by the gas in the wind between the star and the observer) is known to be dominant, leading to the classic P Cygni profile. We propose that the profiles of the radio recombination lines from ionized stellar winds will have this characteristic shape, while optical and IR recombination lines are characterized by P Cygni-like profiles. Unfortunately, at present the detection of radio recombination lines from ionized stellar winds is only feasible for MWC349 and a few other objects.

Rodriquez, L. F.↗
NASA NTRSDate not supplied

Analysis of Thermoradiative Thermal Energy Conversion

The thermoradiative cell is a new method for converting heat energy to electrical power, first detailed by Strandberg in 2015. The cell is a p-n junction semiconductor device, similar to a photovoltaic cell but thermodynamically operating in the reverse direction, converting the thermal dark current into electrical power while radiating waste heat to space. The power and efficiency can be calculated as a function of bandgap in the Shockley-Queisser detailed-balance limit, in which the thermal emissivity of the cell is due to the recombination of electron-hole pairs, and all other recombination losses are ignored. The current produced is directly proportional to the recombination radiation. The fundamental loss mechanism for the thermoradiative cell is the energy carried by the infrared radiation into space from band-to-band recombination of carriers injected across the junction. In an ideal cell, to maximize the efficiency, the emission energy of these photons would precisely equal the bandgap. This can be achieved, for example, using dielectric filters or meta-material filters to recycle emission at other wavelengths back into the cell. The voltage is proportional to the external bias. These two constraints allow optimization of the optimum bias point for maximum power. Unlike photovoltaic cells, the maximum power operating point is not the same as the maximum efficiency point, and higher efficiency can be achieved at a higher (negative) bias in the ideal case. Incorporating non-ideal losses, however, shifts the maximum efficiency point toward lower bias. Unlike in photovoltaic cells, non-radiative recombination (e.g., Auger losses) will reduce the output current, but will not reduce the conversion efficiency, since the recombination energy is retained in the cell in the form of heat. Since a thermoradiative cell operates by radiating directly to space, the current produced by themoradiative cells will increase as Stefan-Boltzmann radiation; roughly the fourth power of the temperature. Thus, the power produced is highest at high operating temperatures, and, unlike conventional thermal conversion, increasing radiator temperature increases, the efficiency. Thus, the choice of technology will be toward semiconductors resistant to degradation at high temperature.

Thermoradiative↗
DOE OSTI2015

Designing Passivating, Carrier-Selective Contacts for Photovoltaic Devices

"The first step towards building a high-efficiency solar cell is to develop an absorber with few recombination-active defects. Many photovoltaic technologies have already achieved this (monocrystalline Si, III-V materials grown on lattice-matched substrates, perovskites, polycrystalline CdTe and CIGS); those that have not (a-Si:H, organics) have been limited to low open-circuit voltage. The second step is to develop contacts that both inhibit surface recombination and allow for low-resistance collection of either only electrons or only holes. For most photovoltaic technologies, this step is both more difficult and less explored than the first, and we are unaware of a prescribed methodology for selecting materials for contacts to solar cells. We elucidate a unified, conceptual understanding of contacts within which existing contacting schemes can be interpreted and future contacting schemes can be imagined. Whereas a split of the quasi-Fermi levels of holes and electrons is required in the absorber of any solar cell to generate a voltage, carriers are eventually collected through a metallic wire in which no such quasi-Fermi-level split exists. We define a contact to be all layers between the bulk of the absorber and the recombination-active interface through which carriers are extracted. The quasi-Fermi levels must necessarily collapse at this interface, and thus the transition between maximal quasi-Fermi-level splitting (in the absorber) and no splitting occurs entirely in the contact. Depending on the solar cell architecture, the contact will usually extend from the surface of the absorber to the surface of a metal or transparent conductive oxide layer, and may include deposited or diffused doped layers (e.g., as in crystalline and thin-film Si cells) and heterostructure buffer layers (e.g., the CdS layer in a CdTe device). We further define a passivating contact as one that enables high quasi-Fermi-level splitting in the absorber (large “internal” voltage), where “high” is relative to the splitting dictated by bulk recombination. Finally, we define a carrier-selective contact as one that enables a high “external” voltage measured across the contacts, where “high” is relative to the internal voltage. With these definitions, passivating contacts are those that allow only electrons, only holes, or neither electrons or holes to transport from the absorber to any position in the contact that has recombination-active defects. An excellent example of this is a SiNx layer on a Si wafer: the layer removes dangling bonds at the wafer surface (where there are both electrons and holes) and does not allow either carrier type to travel to its outermost surface, where there are undoubtedly defects. Carrier-selective contacts are then passivating contacts that also allow for low-impedance flow of either electrons or holes (but not both) to the recombination-active, extracting interface. The most common example is a heavily doped layer that establishes an electric field at the absorber surface, which then “filters” the carriers that may pass to the contact according to the sign of their charge.

14 SOLAR ENERGY↗
DOE OSTI2022

Feedback between radiation and transport in photovoltaics

By building on the generalized Hovel model, this work develops an analytical solution to unify photon recycling, light trapping, and carrier transport in solar cells. Enhanced transport due to photon recycling diffusion is considered. While photon recycling diffusion is often negligible, it can significantly support transport in cases where charge diffusion is low but radiative efficiency is high. Next, the diffusion equation is solved to determine carrier collection for planar and textured cells. Results elucidate novel features in the external quantum efficiency (EQE) curve that occur for textured cells with high absorption and limited transport. Then, the effect of limited transport on the radiative recombination of solar cells is investigated in detail. While the traditional treatment of detailed balance uses the applied voltage to calculate a cell's radiative recombination, the present approach uses the spatially resolved quasi-Fermi-level splitting (QFLS). Further, the discrepancy between the models is shown to be inconsequential to performance for cells with low radiative recombination (Si) or with high mobilities (lowly doped GaAs). However, for cells with high radiative recombination and low mobility (highly doped GaAs, polycrystalline CdTe, and thin-film perovskites), incorporating variation in QFLS in the determination of radiative recombination can become necessary for accurate photovoltaic modeling.

14 SOLAR ENERGY↗
DOE OSTI2014

Study of nitrogen flowing afterglow with mercury vapor injection

The reaction kinetics in nitrogen flowing afterglow with mercury vapor addition was studied by optical emission spectroscopy. The DC flowing post-discharge in pure nitrogen was created in a quartz tube at the total gas pressure of 1000 Pa and discharge power of 130 W. The mercury vapors were added into the afterglow at the distance of 30 cm behind the active discharge. The optical emission spectra were measured along the flow tube. Three nitrogen spectral systems – the first positive, the second positive, and the first negative, and after the mercury vapor addition also the mercury resonance line at 254 nm in the spectrum of the second order were identified. The measurement of the spatial dependence of mercury line intensity showed very slow decay of its intensity and the decay rate did not depend on the mercury concentration. In order to explain this behavior, a kinetic model for the reaction in afterglow was developed. This model showed that the state Hg(6 {sup 3}P{sub 1}), which is the upper state of mercury UV resonance line at 254 nm, is produced by the excitation transfer from nitrogen N{sub 2}(A{sup 3}Σ{sup +}{sub u}) metastables to mercury atoms. However, the N{sub 2}(A{sup 3}Σ{sup +}{sub u}) metastables are also produced by the reactions following the N atom recombination, and this limits the decay of N{sub 2}(A{sup 3}Σ{sup +}{sub u}) metastable concentration and results in very slow decay of mercury resonance line intensity. It was found that N atoms are the most important particles in this late nitrogen afterglow, their volume recombination starts a chain of reactions which produce excited states of molecular nitrogen. In order to explain the decrease of N atom concentration, it was also necessary to include the surface recombination of N atoms to the model. The surface recombination was considered as a first order reaction and wall recombination probability γ = (1.35 ± 0.04) × 10{sup −6} was determined from the experimental data. Also sensitivity analysis was applied for the analysis of kinetic model in order to reveal the main control parameters in the model.

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

Multiple-carrier-lifetime model for carrier dynamics in InGaN/GaN LEDs with a non-uniform carrier distribution

Here we introduce a multiple-carrier-lifetime model (MCLM) for light-emitting diodes (LEDs) with non-uniform carrier distribution, such as in multiple-quantum-well (MQW) structures. By employing the MCLM, we successfully explain the modulation response of V-pit engineered MQW LEDs, which exhibit an S 21 roll-off slower than –20 dB/decade. Using the proposed model and employing a gradient descent method, we extract effective recombination and escape lifetimes by averaging the carrier behavior across the quantum wells. Our results reveal slower effective carrier recombination and escape in MQW LEDs compared with LEDs emitting from a single QW, indicating the advantages of lower carrier density achieved through V-pit engineering. Notably, the effective carrier recombination time is more than one order of magnitude lower than the effective escape lifetime, suggesting that most carriers in the quantum wells recombine, while the escape process remains weak. To ensure the reliability and robustness of the MCLM, we subject it to a comprehensive threefold validation process. This work confirms the positive impact of spreading carriers into several quantum wells through V-pit engineering. In addition, the MCLM is applicable to other LEDs with a non-uniform carrier distribution, such as micro-LEDs with significant surface recombination and non-uniform lateral carrier profiles.

42 ENGINEERING↗
DOE OSTI2013

THE DISCREPANT KINEMATICS OF ORLs AND CELs IN NGC 7009 AS A FUNCTION OF IONIZATION STRUCTURE

We present spatially and velocity-resolved echelle spectroscopy for NGC 7009 obtained with the UVES spectrograph at the European Southern Observatory's Very Large Telescope. Our objective is to analyze the kinematics of emission lines excited by recombination and collisions with electrons to determine whether similarities or differences could be useful in elucidating the well-known abundance discrepancy derived from them. We construct position-velocity maps for recombination, fluorescence, charge transfer, and collisionally excited lines. We find a plasma component emitting in the C II, N II, O II, and Ne II recombination lines whose kinematics are discrepant: they are incompatible with the ionization structure derived from all other evidence and the kinematics derived from all of these lines are unexpectedly very similar. We find direct evidence for a recombination contribution to [N II] {lambda}5755. Once taken into account, the electron temperatures from [N II], [O III], and [Ne III] agree at a given position and velocity. The electron densities derived from [O II] and [Ar IV] are consistent with direct imaging and the distribution of hydrogen emission. The kinematics of the C II, N II, O II, and Ne II lines does not coincide with the kinematics of the [O III] and [Ne III] forbidden emission, indicating that there is an additional plasma component to the recombination emission that arises from a different volume from that giving rise to the forbidden emission from the parent ions within NGC 7009. Thus, the chemical abundances derived from either type of line are correct only for the plasma component from which they arise. Apart from [N II] {lambda}5755, we find no anomaly with the forbidden lines usually used to determine chemical abundances in ionized nebulae, so the abundances derived from them should be reliable for the medium from which they arise.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

Organellar Inheritance in the Green Lineage: Insights from Ostreococcus tauri

Along the green lineage (Chlorophyta and Streptophyta), mitochondria and chloroplast are mainly uniparentally transmitted and their evolution is thus clonal. The mode of organellar inheritance in their ancestor is less certain. The inability to make clear phylogenetic inference is partly due to a lack of information for deep branching organisms in this lineage. Here, we investigate organellar evolution in the early branching green alga Ostreococcus tauri using population genomics data from the complete mitochondrial and chloroplast genomes. The haplotype structure is consistent with clonal evolution in mitochondria, while we find evidence for recombination in the chloroplast genome. The number of recombination events in the genealogy of the chloroplast suggests that recombination, and thus biparental inheritance, is not rare. Consistent with the evidence of recombination, we find that the ratio of the number of nonsynonymous to the synonymous polymorphisms per site is lower in chloroplast than in the mitochondria genome. We also find evidence for the segregation of two selfish genetic elements in the chloroplast. These results shed light on the role of recombination and the evolutionary history of organellar inheritance in the green lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Using the Endogenous CRISPR-Cas System of Heliobacterium modesticaldum To Delete the Photochemical Reaction Center Core Subunit Gene

In Heliobacterium modesticaldum , as in many Firmicutes , deleting genes by homologous recombination using standard techniques has been extremely difficult. The cells tend to integrate the introduced plasmid into the chromosome by a single recombination event rather than perform the double recombination required to replace the targeted locus. Transformation with a vector containing only a homologous recombination template for replacement of the photochemical reaction center gene pshA produced colonies with multiple genotypes, rather than a clean gene replacement. To address this issue, we required an additional means of selection to force a clean gene replacement. In this study, we report the genetic structure of the type I-A and I-E CRISPR-Cas systems from H. modesticaldum , as well as methods to leverage the type I-A system for genome editing. In silico analysis of the CRISPR spacers revealed a potential consensus protospacer adjacent motif (PAM) required for Cas3 recognition, which was then tested using an in vivo interference assay. Introduction of a homologous recombination plasmid that carried a miniature CRISPR array targeting sequences in pshA (downstream of a naturally occurring PAM sequence) produced nonphototrophic transformants with clean replacements of the pshA gene with ~80% efficiency. Mutants were confirmed by PCR, sequencing, optical spectroscopy, and growth characteristics. This methodology should be applicable to any genetic locus in the H. modesticaldum genome. The heliobacteria are the only phototrophic members of the largely Gram-positive phylum Firmicutes , which contains medically and industrially important members, such as Clostridium difficile and Clostridium acetobutylicum . Heliobacteria are of interest in the study of photosynthesis because their photosynthetic system is unique and the simplest known. Since their discovery in the early 1980s, work on the heliobacteria has been hindered by the lack of a genetic transformation system. The problem of introducing foreign DNA into these bacteria has been recently rectified by our group; however, issues still remained for efficient genome editing. The significance of this work is that we have characterized the endogenous type I CRISPR-Cas system in the heliobacteria and leveraged it to assist in genome editing. Using the CRISPR-Cas system allowed us to isolate transformants with precise replacement of the pshA gene encoding the main subunit of the photochemical reaction center.

59 BASIC BIOLOGICAL SCIENCES↗