Practical and reliable FRET/FLIM pair of fluorescent proteins

Background: In spite of a great number of monomeric fluorescent proteins developed in the recent years, the reported fluorescent protein-based FRET pairs are still characterized by a number of disadvantageous features, complicating their use as reporters in cell biology and for high-throughput cell-based screenings. Results: Here we screened some of the recently developed monomeric protein pairs to find the optimal combination, which would provide high dynamic range FRET changes, along with high pH- and photo-stability, fast maturation and bright fluorescence, and reliable detection in any fluorescent imaging system. Among generated FRET pairs, we have selected TagGFP-TagRFP, combining all the mentioned desirable characteristics. On the basis of this highly efficient FRET pair, we have generated a bright, high contrast, pH- and photo-stable apoptosis reporter, named CaspeR3 (Caspase 3 Reporter). Conclusion: The combined advantages suggest that the TagGFP-TagRFP is one of the most efficient green/red couples available to date for FRET/FLIM analyses to monitor interaction of proteins of interest in living cells and to generate FRET-based sensors for various applications. CaspeR3 provides reliable detection of apoptosis, and should become a popular tool both for cell biology studies and high throughput screening assays

Space-Time Evolution of Ultrarelativistic Quantum Dipoles in Quantum Electrodynamics

We discuss space-time evolution of ultrarelativistic quantum dipole in QED. We show that the space-time evolution can be described, in a certain approximation, by means of a regularized wave function, whose parameters are determined by the process of the dipole creation by a local current. We derive using these wave functions the dipole expansion law, that is found to coincide parametrically in the leading order with the one suggested by Farrar, Frankfurt,Liu and Strikman.Comment: 15 page

Coordination of NK cell markers expression and IgG response in hCMV infection

Human cytomegalovirus (hCMV) is a prevalent virus that affects a large proportion of the population worldwide. Natural Killer (NK) cells are essential immune cells that play a crucial role in controlling hCMV infection. Despite the wide spread of hCMV infection, there is still not enough data related to the association between innate and adaptive immunity. This study investigated the coordination between some of the NK cell markers expression and humoral immune response during hCMV infection. Thirty-three samples obtained from different healthy donors were investigated. The anti-hCMV IgG antibody titer was measured in serum samples, and expression of NKG2C, HLA-DR, CD57, KIR2DL2/DL3, and KIR2DL1 were analyzed in CD56+CD3- cells in PBMC samples by flow cytometry. To evaluate the dependence of proportions of different NK cell subsets on IgG titers, cluster analysis was first performed on all the obtained data, resulting in the identification of four main clusters. The identified clusters demonstrated a dependence on the levels of hCMV antibodies, according to which clusters corresponding to seronegative and low-positive were grouped. The results confirmed that hCMV infection leads to an expansion of NK cell populations expressing the NKG2C marker, which correlates with higher levels of IgG response to hCMV. Besides, we identified increased HLA-DR+ and decreased of KIR2DL1+ NK cells proportions in the middle anti-CMV-IgG level group compared to samples obtained from seronegative and low-positive donors. Moreover, the statistically significant negative correlation was found between KIR2DL1+NK cell percentage and anti-CMV IgG antibody titer, while the positive correlation between HLA-DR+NK cell proportion and the IgG level was noticed only without the cluster corresponded to high level of anti-hCMV IgG. In this cohort, we did not find any association between KIR2DL3 and CD57 expression in NK cells and levels of IgG response to hCMV. This may indicate that different subsets of NK cells may have distinct roles in regulating humoral immunity to hCMV. Overall, the results of the study provide valuable insights into the coordination of NK cell marker expression and IgG response in hCMV infection

On inconsistency of experimental data on primary nuclei spectra with sea level muon intensity measurements

For the first time a complete set of the most recent direct data on primary cosmic ray spectra is used as input into calculations of muon flux at sea level in wide energy range $E_\mu=1-3\cdot10^5$ GeV. Computations have been performed with the CORSIKA/QGSJET and CORSIKA/VENUS codes. The comparison of the obtained muon intensity with the data of muon experiments shows, that measurements of primary nuclei spectra conform to sea level muon data only up to several tens of GeV and result in essential deficit of muons at higher energies. As it follows from our examination, uncertainties in muon flux measurements and in the description of nuclear cascades development are not suitable to explain this contradiction, and the only remaining factor, leading to this situation, is underestimation of primary light nuclei fluxes. We have considered systematic effects, that may distort the results of the primary cosmic ray measurements with the application of the emulsion chambers. We suggest, that re-examination of these measurements is required with the employment of different hadronic interaction models. Also, in our point of view, it is necessary to perform estimates of possible influence of the fact, that sizable fraction of events, identified as protons, actually are antiprotons. Study of these cosmic ray component begins to attract much attention, but today nothing definite is known for the energies $>40$ GeV. In any case, to realize whether the mentioned, or some other reasons are the sources of disagreement of the data on primaries with the data on muons, the indicated effects should be thoroughly analyzed

A Search for Sigma^0_5, N^0_5 and Theta^++ Pentaquark States

A high-resolution (sigma_instr. = 1.5 MeV) search for narrow states (Gamma < 10 MeV) with masses of M_x approx 1500-1850 MeV in ep -> e'K^+ X, e'K^- X and e' pi^+ X electroproduction at small angles and low Q^2 was performed. These states would be candidate partner states of the reported Theta^+(1540) pentaquark. No statistically significant signal was observed in any of the channels at 90% C.L. Upper limits on forward production were determined to be between 0.7% and 4.2% of the Lambda(1520) production cross section, depending on the channel and the assumed mass and width of the state.Comment: 5 pages, 5 figures, to appear in Phys. Rev. C, update with responses to referee suggestion

Exploring the pre-immune landscape of antigen-specific T cells

Abstract Background Adaptive immune responses to newly encountered pathogens depend on the mobilization of antigen-specific clonotypes from a vastly diverse pool of naive T cells. Using recent advances in immune repertoire sequencing technologies, models of the immune receptor rearrangement process, and a database of annotated T cell receptor (TCR) sequences with known specificities, we explored the baseline frequencies of T cells specific for defined human leukocyte antigen (HLA) class I-restricted epitopes in healthy individuals. Methods We used a database of TCR sequences with known antigen specificities and a probabilistic TCR rearrangement model to estimate the baseline frequencies of TCRs specific to distinct antigens epitopespecificT-cells. We verified our estimates using a publicly available collection of TCR repertoires from healthy individuals. We also interrogated a database of immunogenic and non-immunogenic peptides is used to link baseline T-cell frequencies with epitope immunogenicity. Results Our findings revealed a high degree of variability in the prevalence of T cells specific for different antigens that could be explained by the physicochemical properties of the corresponding HLA class I-bound peptides. The occurrence of certain rearrangements was influenced by ancestry and HLA class I restriction, and umbilical cord blood samples contained higher frequencies of common pathogen-specific TCRs. We also identified a quantitative link between specific T cell frequencies and the immunogenicity of cognate epitopes presented by defined HLA class I molecules. Conclusions Our results suggest that the population frequencies of specific T cells are strikingly non-uniform across epitopes that are known to elicit immune responses. This inference leads to a new definition of epitope immunogenicity based on specific TCR frequencies, which can be estimated with a high degree of accuracy in silico, thereby providing a novel framework to integrate computational and experimental genomics with basic and translational research efforts in the field of T cell immunology

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key insights into adaptive immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is unclear. In this study, we systematically compared the results of nine commercial and academic TCRseq methods, including six rapid amplification of complementary DNA ends (RACE)-polymerase chain reaction (PCR) and three multiplex-PCR approaches, when applied to the same T cell sample. We found marked differences in accuracy and intra- and inter-method reproducibility for T cell receptor α (TRA) and T cell receptor β (TRB) TCR chains. Most methods showed a lower ability to capture TRA than TRB diversity. Low RNA input generated non-representative repertoires. Results from the 5' RACE-PCR methods were consistent among themselves but differed from the RNA-based multiplex-PCR results. Using an in silico meta-repertoire generated from 108 replicates, we found that one genomic DNA-based method and two non-unique molecular identifier (UMI) RNA-based methods were more sensitive than UMI methods in detecting rare clonotypes, despite the better clonotype quantification accuracy of the latter

Search for the exotic Ξ−−(1860)\Xi^{--}(1860) Resonance in 340GeV/c Σ−\Sigma^--Nucleus Interactions

We report on a high statistics search for the $\Xi^{--}(1860)$ resonance in $\Sigma^-$-nucleus collisions at 340GeV/c. No evidence for this resonance is found in our data sample which contains 676000 $\Xi^-$ candidates above background. For the decay channel $\Xi^{--}(1860) \to \Xi^-\pi^-$ and the kinematic range 0.15$<x_F<$0.9 we find a 3$\sigma$ upper limit for the production cross section of 3.1 and 3.5 $\mu$b per nucleon for reactions with carbon and copper, respectively.Comment: 5 pages, 4 figures, modification of ref. 43 and 4

mKikGR, a Monomeric Photoswitchable Fluorescent Protein

The recent demonstration and utilization of fluorescent proteins whose fluorescence can be switched on and off has greatly expanded the toolkit of molecular and cell biology. These photoswitchable proteins have facilitated the characterization of specifically tagged molecular species in the cell and have enabled fluorescence imaging of intracellular structures with a resolution far below the classical diffraction limit of light. Applications are limited, however, by the fast photobleaching, slow photoswitching, and oligomerization typical for photoswitchable proteins currently available. Here, we report the molecular cloning and spectroscopic characterization of mKikGR, a monomeric version of the previously reported KikGR that displays high photostability and switching rates. Furthermore, we present single-molecule imaging experiments that demonstrate that individual mKikGR proteins can be localized with a precision of better than 10 nanometers, suggesting their suitability for super-resolution imaging