Characterization of Variant RNAs Encapsidated during Bromovirus Infection by High-Throughput Sequencing.

Previously, we described the RNA recombinants accumulating in tissues infected with the bromoviruses BMV (Brome mosaic virus) and CCMV (Cowpea chlorotic mottle virus). In this work, we characterize the recombinants encapsidated inside the purified virion particles of BMV and CCMV. By using a tool called the Viral Recombination Mapper (ViReMa) that detects recombination junctions, we analyzed a high number of high-throughput sequencing (HTS) short RNA sequence reads.

Shared graft-versus-leukemia minor histocompatibility antigens in DISCOVeRY-BMT.

T-cell responses to minor histocompatibility antigens (mHAs) mediate graft-versus-leukemia (GVL) effects and graft-versus-host disease (GVHD) in allogeneic hematopoietic cell transplantation. Therapies that boost T-cell responses improve allogeneic hematopoietic cell transplant (alloHCT) efficacy but are limited by concurrent increases in the incidence and severity of GVHD. mHAs with expression restricted to hematopoietic tissue (GVL mHAs) are attractive targets for driving GVL without causing GVHD.

Observation of structural relaxation during exciton self-trapping via excited-state resonant impulsive stimulated Raman spectroscopy.

We detect the change in vibrational frequency associated with the transition from a delocalized to a localized electronic state using femtosecond vibrational wavepacket techniques. The experiments are carried out in the mixed-valence linear chain material [Pt(en)2][Pt(en)2Cl2]⋅(ClO4)4 (en = ethylenediamine, C2H8N2), a quasi-one-dimensional system with strong electron-phonon coupling. Vibrational spectroscopy of the equilibrated self-trapped exciton is carried out using a multiple pulse excitation technique: an initial pump pulse creates a population of delocalized excitons that self-trap and equilibrate, and a time-delayed second pump pulse tuned to the red-shifted absorption band of the self-trapped exciton impulsively excites vibrational wavepacket oscillations at the characteristic vibrational frequencies of the equilibrated self-trapped exciton state by the resonant impulsive stimulated Raman mechanism, acting on the excited state.

Femtosecond dynamics of exciton localization: self-trapping from the small to the large polaron limit.

We use femtosecond vibrational wavepacket techniques to time-resolve the coupled electronic and vibrational dynamics of exciton self-trapping in a series of materials in which the relative strength of the electron-phonon coupling can be compositionally tuned from the small to the large polaron limit. Transient absorption experiments are carried out in the quasi-one-dimensional halide-bridged mixed-valence transition metal linear chain complexes [Pt(en)2][Pt(en)2X2]⋅(ClO4)4 (en=ethylenediamine, C2H8N2) with X=Cl, Br and I. In each complex, we detect the formation of the self-trapped exciton through the appearance of its characteristic red-shifted optical absorption, and find that self-trapping occurs on a time scale of the order of a single vibrational period of the optical phonon mode that dominates the self-trapping dynamics.

Vibrational spectroscopy of structurally relaxed self-trapped excitons via excited-state resonant impulsive stimulated Raman spectroscopy.

We probe the vibrational modes of the equilibrated self-trapped exciton (STE) in the mixed-valence linear chain material [Pt(en)(2)][Pt(en)(2)Br(2)]·(ClO(4))(4) using resonantly enhanced impulsive stimulated Raman excitation of the excited electronic state. In these measurements, excitons are created by photoexcitation of the optical intervalence charge transfer band, and after a delay to allow self-trapping and equilibration, the metastable STE is impulsively excited and probed within its red-shifted absorption band. The pump-pump-probe response reveals wavepacket oscillations at a frequency of 125 cm(-1) that are assigned to a Raman-active mode of the STE having Br-Pt-Br symmetric stretching character.

CS-US interval determines the transition from overshadowing to potentiation with flavor compounds.

The present series of five flavor aversion experiments with rat subjects examined compound conditioning at varying CS-US intervals. Using a taste-taste design, Experiments 1A and 1B demonstrated overshadowing at a 0-min CS-US interval and potentiation at a 120-min CS-US interval, and these effects occurred with both tastes of the compound. Experiment 2 showed that the aversion to a single element is reduced when the CS-US interval is increased to 120 min, but the aversion for a compound taste is not.

Femtosecond spectroscopy of optical excitations in single-walled carbon nanotubes: evidence for exciton-exciton annihilation.

Frequency-resolved femtosecond transient absorption spectra and kinetics measured by optical excitation of the second and first electronic transitions of the (8,3) single-walled carbon nanotube species reveal a unique mutual response between these transitions. Based on the analysis of the spectra, kinetics, and their distinct amplitude dependence on the pump intensity observed at these transitions, we conclude that these observations originate from both the excitonic origin of the spectrum and nonlinear exciton annihilation.

Femtosecond vibrational dynamics of self-trapping in a quasi-one-dimensional system.

We have directly time resolved the lattice motions associated with the formation of the self-trapped exciton in the quasi-one-dimensional system [Pt(en)(2)] [Pt(en)2Br2];(PF6)(4) ( en = ethylene-diamine, C2H8N2), using femtosecond impulsive excitation techniques. A strongly damped, low-frequency wave packet modulation at approximately 110 cm(-1) accompanies the formation of the self-trapped exciton on a approximately 200 fs time scale following excitation of the intervalence charge-transfer transition. Coherent oscillations at the ground state vibrational frequency and its harmonics are also detected.

The S0 state of photosystem II induced by hydroxylamine: differences between the structure of the manganese complex in the S0 and S1 states determined by X-ray absorption spectroscopy.

Hydroxylamine at low concentrations causes a two-flash delay in the first maximum flash yield of oxygen evolved from spinach photosystem II (PSII) subchloroplast membranes that have been excited by a series of saturating flashes of light. Untreated PSII membrane preparations exhibit a multiline EPR signal assigned to a manganese cluster and associated with the S2 state when illuminated at 195 K, or at 273 K in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). We used the extent of suppression of the multiline EPR signal observed in samples illuminated at 195 K to determine the fraction of PSII reaction centers set back to a hydroxylamine-induced S0-like state, which we designate S0*.

The S3 state of photosystem II: differences between the structure of the manganese complex in the S2 and S3 states determined by X-ray absorption spectroscopy.

O2-evolving photosystem II (PSII) membranes from spinach have been cryogenically stabilized in the S3 state of the oxygen-evolving complex. The cryogenic trapping of the S3 state was achieved using a double-turnover illumination of dark-adapted PSII preparations maintained at 240 K. A double turnover of PSII was accomplished using the high-potential acceptor, Q400, which is the high-spin iron of the iron-quinone acceptor complex.

Low-potential iron-sulfur centers in photosystem I: an X-ray absorption spectroscopy study.

We have measured the X-ray absorption spectra of Fe in photosystem I (PS I) preparations from spinach and a thermophilic cyanobacterium, Synechococcus sp., to characterize structures of the Fe complexes that function as electron acceptors in PS I. These acceptors include centers A and B, which are probably typical [4Fe-4S] ferredoxins, and X.

Characterization of the manganese O2-evolving complex and the iron-quinone acceptor complex in photosystem II from a thermophilic cyanobacterium by electron paramagnetic resonance and X-ray absorption spectroscopy.

The Mn donor complex in the S1 and S2 states and the iron-quinone acceptor complex (Fe2+-Q) in O2-evolving photosystem II (PS II) preparations from a thermophilic cyanobacterium, Synechococcus sp., have been studied with X-ray absorption spectroscopy and electron paramagnetic resonance (EPR). Illumination of these preparations at 220-240 K results in formation of a multiline EPR signal very similar to that assigned to a Mn S2 species observed in spinach PS II, together with g = 1.

Comparison of the structure of the manganese complex in the S1 and S2 states of the photosynthetic O2-evolving complex: an x-ray absorption spectroscopy study.

A Mn-containing enzyme complex is involved in the oxidation of H2O to O2 in algae and higher plants. X-ray absorption spectroscopy is well suited for studying the structure and function of Mn in this enzyme complex. Results of X-ray K-edge and extended X-ray absorption fine structure (EXAFS) studies of Mn in the S1 and S2 states of the photosynthetic O2-evolving complex in photosystem II preparations from spinach are presented in this paper.

Structure of the manganese complex of photosystem II upon removal of the 33-kilodalton extrinsic protein: an X-ray absorption spectroscopy study.

The structure of the Mn complex of photosystem II (PSII) was studied by X-ray absorption spectroscopy. Oxygen-evolving spinach PSII membranes containing 4-5 Mn/PSII were treated with 0.8 M CaCl2 to extract the 33-, 24-, and 16-kilodalton (kDa) extrinsic membrane proteins.

Assignment of the g = 4.1 EPR signal to manganese in the S2 state of the photosynthetic oxygen-evolving complex: an X-ray absorption edge spectroscopy study.

X-ray absorption spectroscopy at the Mn K-edge has been utilized to study the origin of the g = 4.1 EPR signal associated with the Mn-containing photosynthetic O2-evolving complex. Formation of the g = 4.