Lipofection with Synthetic mRNA as a Simple Method for T-Cell Immunomonitoring.

The quantification of T-cell immune responses is crucial for the monitoring of natural and treatment-induced immunity, as well as for the validation of new immunotherapeutic approaches. The present study presents a simple method based on lipofection of synthetic mRNA in mononuclear cells as a method to determine in vitro T-cell responses. We compared several commercially available transfection reagents for their potential to transfect mRNA into human peripheral blood mononuclear cells and murine splenocytes. We also investigated the impact of RNA modifications in improving this method. Our results demonstrate that antigen-specific T-cell immunomonitoring can be easily and quickly performed by simple lipofection of antigen-coding mRNA in complex immune cell populations. Thus, our work discloses a convenient solution for the in vitro monitoring of natural or therapy-induced T-cell immune responses

Entanglement Entropy of Random Fractional Quantum Hall Systems

The entanglement entropy of the $\nu = 1/3$ and $\nu = 5/2$ quantum Hall states in the presence of short range random disorder has been calculated by direct diagonalization. A microscopic model of electron-electron interaction is used, electrons are confined to a single Landau level and interact with long range Coulomb interaction. For very weak disorder, the values of the topological entanglement entropy are roughly consistent with expected theoretical results. By considering a broader range of disorder strengths, the fluctuation in the entanglement entropy was studied in an effort to detect quantum phase transitions. In particular, there is a clear signature of a transition as a function of the disorder strength for the $\nu = 5/2$ state. Prospects for using the density matrix renormalization group to compute the entanglement entropy for larger system sizes are discussed.Comment: 29 pages, 16 figures; fixed figures and figure captions; revised fluctuation calculation

Improved selectivity of an engineered multi-product terpene synthase

Mutation of the sesquiterpene synthase Cop2 was conducted with a high-throughput screen for the cyclization activity using a non-natural substrate. A mutant of Cop2 was identified that contained three amino acid substitutions. This mutant, 17H2, converted the natural substrate FPP into germacrene D-4-ol with 77% selectivity. This selectivity is in contrast to that of the parent enzyme in which germacrene D-4-ol is produced as 29% and α-cadinol is produced as 46% of the product mixture. The mutations were shown to each contribute to this selectivity, and a homology model suggested that the mutations lie near to the active site though would be unlikely to be targeted for mutation by rational methods. Kinetic comparisons show that 17H2 maintains a k_(cat)/K_M of 0.62 mM^(−1) s^(−1), which is nearly identical to that of the parent Cop2, which had a k_(cat)/K_M of 0.58 mM^(−1) s^(−1)

Ground states and dynamics of population-imbalanced Fermi condensates in one dimension

By using the numerically exact density-matrix renormalization group (DMRG) approach, we investigate the ground states of harmonically trapped one-dimensional (1D) fermions with population imbalance and find that the Larkin-Ovchinnikov (LO) state, which is a condensed state of fermion pairs with nonzero center-of-mass momentum, is realized for a wide range of parameters. The phase diagram comprising the two phases of i) an LO state at the trap center and a balanced condensate at the periphery and ii) an LO state at the trap center and a pure majority component at the periphery, is obtained. The reduced two-body density matrix indicates that most of the minority atoms contribute to the LO-type quasi-condensate. With the time-dependent DMRG, we also investigate the real-time dynamics of a system of 1D fermions in response to a spin-flip excitation.Comment: 20 pages, 15 figures, accepted for publication in New Journal of Physic

Valence Bond States: Link models

An isotropic anti-ferromagnetic quantum state on a square lattice is characterized by symmetry arguments only. By construction, this quantum state is the result of an underlying valence bond structure without breaking any symmetry in the lattice or spin spaces. A detailed analysis of the correlations of the quantum state is given (using a mapping to a 2D classical statistical model and methods in field theory like mapping to the non-linear sigma model or bosonization techniques) as well as the results of numerical treatments (regarding exact diagonalization and variational methods). Finally, the physical relevance of the model is motivated. A comparison of the model to known anti-ferromagnetic Mott-Hubbard insulators is given by means of the two-point equal-time correlation function obtained i) numerically from the suggested state and ii) experimentally from neutron scattering on cuprates in the anti-ferromagnetic insulator phase.Comment: 20 pages, 15 figures; added references, corrected some typos, new sections. Published versio

Quantum Quench from a Thermal Initial State

We consider a quantum quench in a system of free bosons, starting from a thermal initial state. As in the case where the system is initially in the ground state, any finite subsystem eventually reaches a stationary thermal state with a momentum-dependent effective temperature. We find that this can, in some cases, even be lower than the initial temperature. We also study lattice effects and discuss more general types of quenches.Comment: 6 pages, 2 figures; short published version, added references, minor change

High-Throughput Screening for Terpene-Synthase-Cyclization Activity and Directed Evolution of a Terpene Synthase

The development of high-throughput assays can be extremely challenging, yet is essential for many applications in drug discovery and enzyme engineering

Responses to salt stress in Juncus acutus and J. maritimus during seed germination and vegetative plant growth

[EN] Responses to increasing salinity, during seed germination and vegetative plant growth, were studied in two related species of Juncus, J. maritimus and J. acutus. In both species, germination was optimal in the absence of salt, reduced by about 50% in the presence of 200 mM NaCl, and completely inhibited by NaCl concentrations above 300 mM. Previous exposure of the seeds to salt, up to 500 mM NaCl, did not affect the germination capacity in J. acutus, and clearly enhanced it in J. maritimus. A concentration-dependent inhibition of plant growth was observed in the presence of NaCl for both species, together with the parallel accumulation of sodium ions in the leaves, as determined by cation exchange HPLC. Regarding the levels of divalent cations, in J. acutus Ca2+ and Mg2+ increased up to about two-fold in plants treated with 500 mM NaCl, as compared to control plants, whereas in J. maritimus they were three-to four-fold higher than in J. acutus in the absence of salt, and did not change significantly with increasing NaCl concentrations. These results suggest that Ca2+ and Mg2+ participate in defence mechanisms against salt stress, which would be constitutive in J. maritimus and salt-inducible in J. acutus.Boscaiu Neagu, MT.; Ballesteros Amat, G.; Naranjo Olivero, MA.; Vicente Meana, Ó.; Boira Tortajada, H. (2011). Responses to salt stress in Juncus acutus and J. maritimus during seed germination and vegetative plant growth. Plant Biosystems. 145(4):770-777. doi:10.1080/11263504.2011.628446S770777145

Effect of supplemental Ca2+ on NaCl-stressed castor plants (Ricinus communis L.)

Greenhouse experiments were conducted to assess the effects of supplemental Ca2+ in salinised soil on germination and plant growth response of castor plant (Ricinus communis L. Var. Avani-31, Euphorbiaceae). NaCl amounting to 390 g was thoroughly mixed with soil of seven lots, of 100 kg each, to give electrical conductivity of 4.1 dS m–1. Further, Ca(NO3)2 × 4H20 to the quantity of 97.5, 195, 292.5, 390, 487.5, and 585 g was separately mixed with soil of six lots to give 1:0.25, 1:0.50, 1:0.75, 1:1, 1:1.25, and 1:1.50 Na+/Ca2+ ratios, respectively. The soil of the seventh lot contained only NaCl and its Na+/Ca2+ ratio was 1:0. Soil without addition of NaCl and Ca (NO3)2 × 4H20 served as control, with a 0:0 Na+/Ca2+ ratio. Salinity significantly retarded seed germination and plant growth, but the deleterious effects of NaCl on seed germination were ameliorated and plant growth was restored with Ca2+ supply at the critical level (1:0.25 Na+/Ca2+ ratio) to salinised soil. Supply of Ca2+ above the critical level further retarded seed germination and plant growth due to the increased soil salinity. Salt stress reduced N, P, K+ and Ca2+ content in plant tissues, but these nutrients were restored by addition of Ca2+ at the critical level to saline soil. In contrast, Na+ content in plant tissues significantly increased in response to salinity, but significantly decreased with increasing Ca2+ supply to saline soil. The results are discussed in terms of the beneficial effects of Ca2+ supply on the plant growth of Ricinus communis grown under saline conditions

Transcriptional Downregulation of Rice rpL32 Gene under Abiotic Stress Is Associated with Removal of Transcription Factors within the Promoter Region

Background: The regulation of ribosomal proteins in plants under stress conditions has not been well studied. Although a few reports have shown stress-specific post-transcriptional and translational mechanisms involved in downregulation of ribosomal proteins yet stress-responsive transcriptional regulation of ribosomal proteins is largely unknown in plants. Methodology/Principal Findings: In the present work, transcriptional regulation of genes encoding rice 60S ribosomal protein L32 (rpL32) in response to salt stress has been studied. Northern and RT-PCR analyses showed a significant downregulation of rpL32 transcripts under abiotic stress conditions in rice. Of the four rpL32 genes in rice genome, the gene on chromosome 8 (rpL32_8.1) showed a higher degree of stress-responsive downregulation in salt sensitive rice variety than in tolerant one and its expression reverted to its original level upon withdrawal of stress. The nuclear run-on and promoter:reporter assays revealed that the downregulation of this gene is transcriptional and originates within the promoter region. Using in vivo footprinting and electrophoretic mobility shift assay (EMSA), cis-elements in the promoter of rpL32_8.1 showing reduced binding to proteins in shoots of salt stressed rice seedlings were identified. Conclusions: The present work is one of the few reports on study of stress downregulated genes. The data revealed that rpL32 gene is transcriptionally downregulated under abiotic stress in rice and that this transcriptional downregulation i