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At least 919 records · Page 51

Elevated Expression of a Functional Suf Pathway in Escherichia coli BL21(DE3) Enhances Recombinant Production of an Iron-Sulfur Cluster-Containing Protein

Structural and spectroscopic analysis of iron-sulfur [Fe-S] cluster-containing proteins is often limited by the occupancy and yield of recombinantly produced proteins. In this work, we report that Escherichia coli BL21(DE3), a strain routinely used to overproduce [Fe-S] cluster-containing proteins, has a nonfunctional Suf pathway, one of two E. coli [Fe-S] cluster biogenesis pathways. We confirmed that BL21(DE3) and commercially available derivatives carry a deletion that results in an in-frame fusion of sufA and sufB genes within the sufABCDSE operon. We show that this fusion protein accumulates in cells but is inactive in [Fe-S] cluster biogenesis. Restoration of an intact Suf pathway combined with enhanced suf operon expression led to a remarkable (~3-fold) increase in the production of the [4Fe-4S] cluster-containing BchL protein, a key component of the dark-operative protochlorophyllide oxidoreductase complex. These results show that this engineered “SufFeScient” derivative of BL21(DE3) is suitable for enhanced large-scale synthesis of an [Fe-S] cluster-containing protein.

59 BASIC BIOLOGICAL SCIENCES↗

Structure and Receptor Binding Preferences of Recombinant Hemagglutinins from Avian and Human H6 and H10 Influenza A Virus Subtypes

During 2013, three new avian influenza A virus subtypes, A(H7N9), A(H6N1), and A(H10N8), resulted in human infections. While the A(H7N9) virus resulted in a significant epidemic in China across 19 provinces and municipalities, both A(H6N1) and A(H10N8) viruses resulted in only a few human infections. This study focuses on the major surface glycoprotein hemagglutinins from both of these novel human viruses. The detailed structural and glycan microarray analyses presented here highlight the idea that both A(H6N1) and A(H10N8) virus hemagglutinins retain a strong avian receptor binding preference and thus currently pose a low risk for sustained human infections. Human infections with zoonotic influenza virus subtypes continue to be a great public health concern. Here, we report detailed structural analysis and glycan microarray data for recombinant hemagglutinins from A(H6N1) and A(H10N8) viruses, isolated from human infections in 2013, and compare them with hemagglutinins of avian origin. This is the first structural report of an H6 hemagglutinin, and our results should further the understanding of these viruses and provide useful information to aid in the continuous surveillance of these zoonotic influenza viruses.

59 BASIC BIOLOGICAL SCIENCES↗

Epstein-Barr Virus Epitope–Major Histocompatibility Complex Interaction Combined with Convergent Recombination Drives Selection of Diverse T Cell Receptor α and β Repertoires

Recognition modes of individual T cell receptors (TCRs) are well studied, but factors driving the selection of TCR repertoires from primary through persistent human virus infections are less well understood. Using deep sequencing, we demonstrate a high degree of diversity of Epstein-Barr virus (EBV)-specific clonotypes in acute infectious mononucleosis (AIM). Only 9% of unique clonotypes detected in AIM persisted into convalescence; the majority (91%) of unique clonotypes detected in AIM were not detected in convalescence and were seeming replaced by equally diverse “de novo” clonotypes. The persistent clonotypes had a greater probability of being generated than nonpersistent clonotypes due to convergence recombination of multiple nucleotide sequences to encode the same amino acid sequence, as well as the use of shorter complementarity-determining regions 3 (CDR3s) with fewer nucleotide additions (i.e., sequences closer to germ line). Moreover, the two most immunodominant HLA-A2-restricted EBV epitopes, BRLF1 109 and BMLF1 280 , show highly distinct antigen-specific public (i.e., shared between individuals) features. In fact, TCRα CDR3 motifs played a dominant role, while TCRβ played a minimal role, in the selection of TCR repertoire to an immunodominant EBV epitope, BRLF1. This contrasts with the majority of previously reported repertoires, which appear to be selected either on TCRβ CDR3 interactions with peptide/major histocompatibility complex (MHC) or in combination with TCRα CDR3. Understanding of how TCR-peptide-MHC complex interactions drive repertoire selection can be used to develop optimal strategies for vaccine design or generation of appropriate adoptive immunotherapies for viral infections in transplant settings or for cancer.

59 BASIC BIOLOGICAL SCIENCES↗

Crystallization and preliminary X-ray diffraction analysis of recombinant phosphoribosylpyrophosphate synthetase from the Thermophilic thermus thermophilus strain HB27

Phosphoribosylpyrophosphate synthetases (PRPP synthetases) are among the key enzymes essential for vital functions of organisms and are involved in the biosynthesis of purine and pyrimidine nucleotides, coenzymes, and the amino acids histidine and tryptophan. These enzymes are used in biotechnology for the combined chemoenzymatic synthesis of natural nucleotide analogs. Recombinant phosphoribosylpyrophosphate synthetase I from the thermophilic strain HB27 of the bacterium Thermus thermophilus (T. th HB27) has high thermal stability and shows maximum activity at 75°Ð¡, due to which this enzyme holds promise for biotechnological applications. In order to grow crystals and study them by X-ray crystallography, an enzyme sample, which was produced using a highly efficient producer strain, was purified by affinity and gel-filtration chromatography. The screening of crystallization conditions was performed by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown by the counter-diffusion method through a gel layer. These crystals were used to collect the X-ray diffraction data set at the SPring-8 synchrotron radiation facility (Japan) to 3-Å resolution. The crystals belong to sp. gr. P2{sub 1} and have the following unitcell parameters: a = 107.7 Å, b = 112.6 Å, c = 110.2 Å, α = γ = 90°, β = 116.6°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the enzyme at 3.0-Å resolution.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Crystallization and preliminary X-ray diffraction study of recombinant adenine phosphoribosyltransferase from the thermophilic bacterium Thermus thermophilus strain HB27

Adenine phosphoribosyltransferase (APRT) belongs to the type I phosphoribosyltransferase family and catalyzes the formation of adenosine monophosphate via transfer of the 5-phosphoribosyl group from phosphoribosyl pyrophosphate to the nitrogen atom N9 of the adenine base. Proteins of this family are involved in a salvage pathway of nucleotide synthesis, thus providing purine base utilization and maintaining the optimal level of purine bases in the body. Adenine phosphoribosyltransferase from the extremely thermophilic Thermus thermophilus strain HB27 was produced using a highly efficient E. coli producer strain and was then purified by affinity and gel-filtration chromatography. This enzyme was successfully employed as a catalyst for the cascade biosynthesis of biologically important nucleotides. The screening of crystallization conditions for recombinant APRT from T. thermophilus HB27 was performed in order to determine the enzyme structure by X-ray diffraction. The crystallization conditions, which were found by the vapor-diffusion technique, were then optimized to apply the counter-diffusion technique. The crystals of the enzyme were grown by the capillary counter-diffusion method. The crystals belong to sp. gr. P12{sub 1}1 and have the following unitcell parameters: a = 69.86 Å, b = 82.16 Å, c = 91.39 Å, α = γ = 90°, β = 102.58°. The X-ray diffraction data set suitable for the determination of the APRT structure at 2.6 Å resolution was collected from the crystals at the SPring-8 synchrotron facility (Japan).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Estimation of the Density of the Self-Interacting Dark-Matter Component within a Clump with Allowance for Recombination

The model of dark matter featuring a component in the form of free particles and antiparticles (a, ā ) possessing self-interaction of the Coulomb type is considered. Darkmattermay form small-scale clumps where the annihilation of particles a and ā is enhanced. This annihilation may lead to observable effects (in cosmic rays, for example) and/or to the destruction of these clumps. However, there is an ambiguity in describing the annihilation (via recombination) of very slow particles, which may include a and ā in clumps. The effect of annihilation (in terms of the residual number of free particles a and ā in clumps) is estimated within two approaches (simplified quantum-mechanical and classical) at chosen parameter values.

79 ASTRONOMY AND ASTROPHYSICS↗

CXSFIT Code Application to Process Charge-Exchange Recombination Spectroscopy Data at the T-10 Tokamak

The applicability of the CXSFIT code to process experimental data from Charge-eXchange Recombination Spectroscopy (CXRS) diagnostics at the T-10 tokamak is studied with a view to its further use for processing experimental data at the ITER facility. The design and operating principle of the CXRS diagnostics are described. The main methods for processing the CXRS spectra of the 5291-Å line of C{sup 5+} ions at the T-10 tokamak (with and without subtraction of parasitic emission from the edge plasma) are analyzed. The method of averaging the CXRS spectra over several shots, which is used at the T-10 tokamak to increase the signal-to-noise ratio, is described. The approximation of the spectrum by a set of Gaussian components is used to identify the active CXRS line in the measured spectrum. Using the CXSFIT code, the ion temperature in ohmic discharges and discharges with auxiliary electron cyclotron resonance heating (ECRH) at the T-10 tokamak is calculated from the CXRS spectra of the 5291-Å line. The time behavior of the ion temperature profile in different ohmic heating modes is studied. The temperature profile dependence on the ECRH power is measured, and the dynamics of ECR removal of carbon nuclei from the T-10 plasma is described. Experimental data from the CXRS diagnostics at T-10 substantially contribute to the implementation of physical programs of studies on heat and particle transport in tokamak plasmas and investigation of geodesic acoustic mode properties.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Radiative Recombination, Carrier Capture at Traps, and Photocurrent Relaxation in PbSnTe:In with a Composition Close to Band Inversion

Based on the notions that PbSnTe:In is a direct-gap semiconductor, the radiative-recombination lifetime is calculated, and the photocurrent relaxation and dependences of the instantaneous electron and hole lifetime are calculated under the assumption that PbSnTe:In is a disordered structure containing capture centers. These calculations explain such experimentally observed peculiarities of PbSnTe:In as a high photosensitivity in a wide wavelength range, pinning of the Fermi level, and long-term photocurrent relaxation. Calculations are also compared with experimental data and the possible parameters of photodetectors are evaluated.

36 MATERIALS SCIENCE↗

Molecular Reaction Imaging of a Surface Recombination Process Explains Performance Variation Among Smooth MoS 2 Photoelectrodes

Transition metal dichalcogenides (TMD) such as WSe 2 and MoS 2 are highly efficient and stable light absorbers in TMD∣I − ,I 3 − ∣Pt liquid junction solar cells. It is generally accepted that TMD crystals with a large fraction of exposed edge sites exhibit lower power conversion efficiencies (PCEs) than apparently smooth crystals. However, one open question is why does the PCE vary significantly from one crystal to another? Answering this critical question could lead to robust syntheses for high quality and uniform TMD samples. In this work, we apply nanoscale photoelectrochemical microscopy techniques to study n-type TMD nanoflake∣I − ,I 3 − ∣Pt cells. Using a combination of near-diffraction-limited photocurrent mapping and molecular reaction imaging techniques, we reveal a previously hidden surface recombination process: photogenerated holes in hidden p-type domains travel micron-scale distances parallel to the solid/liquid interface and preferentially react with iodide at step-edges. The overall efficiency of the nanoflake, as evidenced from whole nanoflake-level photoelectrochemical measurements, is dictated by the size, efficiency, and location of n- and p-type domains. Furthermore, these results provide a unifying view of efficiency losses in smooth TMD photoelectrodes and open the possibility to design electrode architectures that leverage the long-range lateral charge transport property for photoelectrocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection

Background: In many applications, a family of nucleotide or protein sequences classified into several subfamilies has to be modeled. Profile Hidden Markov Models (pHMMs) are widely used for this task, modeling each subfamily separately by one pHMM. However, a major drawback of this approach is the difficulty of dealing with subfamilies composed of very few sequences. One of the most crucial bioinformatical tasks affected by the problem of small-size subfamilies is the subtyping of human immunodeficiency virus type 1 (HIV-1) sequences, i.e., HIV-1 subtypes for which only a small number of sequences is known. Results: To deal with small samples for particular subfamilies of HIV-1, we introduce a novel model-based information sharing protocol. It estimates the emission probabilities of the pHMM modeling a particular subfamily not only based on the nucleotide frequencies of the respective subfamily but also incorporating the nucleotide frequencies of all available subfamilies. To this end, the underlying probabilistic model mimics the pattern of commonality and variation between the subtypes with regards to the biological characteristics of HI viruses. In order to implement the proposed protocol, we make use of an existing HMM architecture and its associated inference engine. Conclusions: We apply the modified algorithm to classify HIV-1 sequence data in the form of partial HIV-1 sequences and semi-artificial recombinants. Thereby, we demonstrate that the performance of pHMMs can be significantly improved by the proposed technique. Moreover, we show that our algorithm performs significantly better than Simplot and Bootscanning.

59 BASIC BIOLOGICAL SCIENCES↗

Colossal Photon Bunching Driven by Phonon Recombination Dynamics

We report photon bunching g(2)(0) ≈ 49 due to phonon sidebands in spectrally filtered cathodoluminescence from NV centers in diamond. The result is consistent with fast, phonon-mediated recombination dynamics, and supported by a stochastic model.

Feldman, Matthew A.↗

General algorithm for characterization of donor-acceptor pair recombination processes in solid-state materials

Radiative recombination processes can occur in solid-state systems through the pairing of donor and acceptor defects of the lattice. Recently, donor-acceptor pairs (DAP) have been proposed as promising candidates for quantum applications, and their signature has been observed in emerging low-dimensional materials. Therefore, the identification of such processes is gaining interest and requires methods to efficiently and reliably characterize them. Here, we introduce a general algorithm to identify DAP processes starting from the experimental photoluminescence (PL) emission spectrum and basic material parameters, including the lattice structure and dielectric constant. The algorithm recognizes possible DAP transitions from the emission pattern in the spectrum and returns the characteristic energy of the DAP transition and the separation between the donor and acceptor sites. By testing the algorithm on the photoluminescence spectrum of hexagonal boron nitride (hBN), we show that our method is robust against experimental errors and adds new capabilities to the investigation toolbox of semiconductors and their optical properties.

36 MATERIALS SCIENCE↗

Detection of Homologous Recombination Events in Bacterial Genomes

We study the detection of mutations, sequencing errors, and homologous recombination events (HREs) in a set of closely related microbial genomes. We base the model on single nucleotide polymorphisms (SNPs) and break the genomes into blocks to handle the rearrangement problem. Then we apply a dynamic programming algorithm to model whether changes within each block are likely a result of mutations, sequencing errors, or HREs. Results from simulation experiments show that we can detect 31%–61% of HREs and the precision of our detection is about 48%–90% depending on the rates of mutation and missing data. The HREfinder software for predicting HREs in a set of whole genomes is available as open source (http:// sourceforge.net/projects/hrefinder/).

59 BASIC BIOLOGICAL SCIENCES↗

Efficacy of commercial recombinant HVT vaccines against a North American clade 2.3.4.4b H5N1 highly pathogenic avian influenza virus in chickens

The outbreak of clade 2.3.4.4b H5 highly pathogenic avian influenza (HPAI) in North America that started in 2021 has increased interest in applying vaccination as a strategy to help control and prevent the disease in poultry. Two commercially available vaccines based on the recombinant herpes virus of turkeys (rHVT) vector were tested against a recent North American clade 2.3.4.4b H5 HPAI virus isolate: A/turkey/Indiana/22-003707-003/2022 H5N1 in specific pathogen free white leghorn (WL) chickens and commercial broiler chickens. One rHVT-H5 vaccine encodes a hemagglutinin (HA) gene designed by the computationally optimized broadly reactive antigen method (COBRA-HVT vaccine). The other encodes an HA gene of a clade 2.2 virus (2.2-HVT vaccine). There was 100% survival of both chicken types COBRA-HVT vaccinated groups and in the 2.2-HVT vaccinated groups there was 94.8% and 90% survival of the WL and broilers respectively. Compared to the 2.2-HVT vaccinated groups, WL in the COBRA-HVT vaccinated group shed significantly lower mean viral titers by the cloacal route and broilers shed significantly lower titers by the oropharyngeal route than broilers. Virus titers detected in oral and cloacal swabs were otherwise similar among both vaccine groups and chicken types. To assess antibody-based tests to identify birds that have been infected after vaccination (DIVA-VI), sera collected after the challenge were tested with enzyme-linked lectin assay-neuraminidase inhibition (ELLA-NI) for N1 neuraminidase antibody detection and by commercial ELISA for detection of antibodies to the NP protein. As early as 7 days post challenge (DPC) 100% of the chickens were positive by ELLA-NI. ELISA was less sensitive with a maximum of 75% positive at 10DPC in broilers vaccinated with 2.2-HVT. Both vaccines provided protection from challenge to both types of chickens and ELLA-NI was sensitive at identifying antibodies to the challenge virus therefore should be evaluated further for DIVA-VI.

60 APPLIED LIFE SCIENCES↗

Genotyping by Sequencing of 393 Sorghum bicolor BTx623 × IS3620C Recombinant Inbred Lines Improves Sensitivity and Resolution of QTL Detection

We describe a genetic map with a total of 381 bins of 616 genotyping by sequencing (GBS)- based SNP markers in a F6-F8 recombinant inbred line (RIL) population of 393 individuals derived from crossing S. bicolor BTx623 to S. bicolor IS3620C, a guinea line substantially diverged from BTx623. Five segregation distorted regions were found with four showing enrichment for S. bicolor alleles, suggesting possible selection during formation of this RIL population. A quantitative trait locus (QTL) study with this number of individuals, tripled relative to prior studies of this cross, provided resources, validated previous findings, and demonstrated improved power to detect plant height and flowering time related QTL relative to other published studies. An unexpected low correlation between flowering time and plant height permitted us to separate QTL for each trait and provide evidence against pleiotropy. Ten non- random syntenic regions conferring QTL for the same trait suggest that those QTL may represent alleles at genes functioning in the same manner since the 96 million year ago genome duplication that created these syntenic relationships, while syntenic regions conferring QTL for different trait may suggest sub-functionalization after duplication. Collectively, this study provides resources for marker-assisted breeding, as well as a framework for fine mapping and subsequent cloning of major genes for important traits such as plant height and flowering time in sorghum.

54 ENVIRONMENTAL SCIENCES↗

Distinguishing Bulk and Surface Recombination By Measuring and Modeling Ultrafast Carrier Dynamics

Distinguishing Bulk and Surface Recombination By Measuring and Modeling Ultrafast Carrier Dynamics The combination of modeling with TRTS and TRPL under multiple excitation conditions improves accuracy and precision of parameter estimation. Ultrafast carrier dynamics can link materials, processing, and device performance to direct the design of more efficient solar cells.

14 SOLAR ENERGY↗

Diagnosing and overcoming recombination and resistive losses in non-silicon solar cells using a silicon-inspired characterization platform

This project aimed to generate the characterization tools needed for accurate and systematic loss analysis in non-silicon photovoltaic solar cell technologies and, through the use of these tools and analysis techniques, contribute to the development of a novel class of hetero-contacts to II-VI absorbers, with the final goal of demonstrating record-breaking CdSeTe devices. CdSeTe solar cells provide a prime example of the potential impact of the techniques we proposed to develop and implement: record poly-CdSeTe cells have bandgap-voltage deficits (W oc ) of approximately 550 mV, as compared with below 400 mV for all other mature PV technologies. Similarly, these record CdSeTe devices have FFs below 80%, when other mature cells are near or above 85%. Frustratingly, a systematic identification of the origin of these sub-par performances—for example recombination or resistive losses—has been lacking, thus slowing down the development of these technologies. Similarly, it is often asserted that CdSeTe cells need a better back (hole) contact. Although most believe this is true, no one knew—at the start of this project—how high the V oc and FF could be for a given cell if it had a perfect back contact. Such characterization techniques and loss analysis methods exist and are routinely performed on c-Si solar cells (e.g. injection-dependent lifetime, Suns-V oc , transfer length method, etc). Over the years, they have been instrumental in the development of silicon devices that operate at 91% of their theoretical (Auger) limit. Lifetime testing, and the associated reconstruction of the implied-J-V curve, can moreover be performed at every cell-processing step, thus allowing a direct peek into the impact of that step on cell performance. Therefore, adapting these techniques and tools to non-Si devices would greatly improve their learning rate. In this project, we developed a Suns-ERE technique—the equipment, methodology, and know-how—to measure the implied-J-V curve, the pseudo-J-V curve, and the actual J-V curve of a thin-film solar cell, allowing an accurate assessment of the quality of the bulk material and its surface passivation, the selectivity of the contact, and its resistivity. We used this technique to show that the absorber of present CdSeTe solar cells is capable of achieving 1 V Voc,, that passivation layers exist (e.g., Al2O3) that can support such high voltages, and that the barrier is identifying contact layers that are both passivating and carrier-selective. The characterization platform created in this project and the understanding generated using it will accelerate the progress of non-silicon PV technologies. In particular, the project will contribute to CdSeTe solar cells with Voc > 1 V and cell efficiency > 24%. Such cells provide a pathway to module-level efficiencies >23%. As CdSeTe presently competes with silicon on module cost (in $\$ $/W) and yet has significantly more room for efficiency gains, the potential for LCOE reduction is particularly large. For example, CdTe modules with an efficiency of 21% would allow an LCOE below $\$ $0.04kWh -1 in average US climates.

14 SOLAR ENERGY↗