The Potential Role of Plastome Copy Number as a Quality Biomarker for Plant Products using Real-time Quantitative Polymerase Chain Reaction

Background: Plastids are plant-specific semi-autonomous self-replicating organelles, containing circular DNA molecules called plastomes. Plastids perform crucial functions, including photosynthesis, stress perception and response, synthesis of metabolites, and storage. The plastome and plastid numbers have been shown to be modulated by developmental stage and environmental stimuli and have been used as a biomarker (identification of plant species) and biosensor (an indicator of abiotic and biotic stresses). However, the determination of plastome sequence and plastid number is a laborious process requiring sophisticated equipment. Methods: This study proposes using plastome copy number (PCN), which can be determined rapidly by real-time quantitative polymerase chain reaction (RT-qPCR) as a plant product quality biomarker. This study shows that the PCN log₁₀ and range PCN log₁₀ values calculated from RT-qPCR data, which was obtained for two years from leaves and lint samples of cotton and seed samples of cotton, rice, soybean, maize, and sesame can be used for assessing the quality of the samples. Results: Observation of lower range PCN log₁₀ values for CS (0.31) and CR (0.58) indicated that the PCN showed little variance from the mean PCN log₁₀ values for CS (3.81) and CR (3.85), suggesting that these samples might have encountered ambient environmental conditions during growth and/ or post-harvest storage and processing. This conclusion was further supported by observation of higher range PCN log₁₀ values for RS (3.09) versus RP (0.05), where rice seeds in the RP group had protective hull covering compared to broken hull-less seeds in the RS group. To further support that PCN is affected by external factors, rice seeds treated with high temperatures and pathogens exhibited lower PCN values when compared to untreated seeds. Furthermore, the range PCN log₁₀ values were found to be high for cotton leaf (CL) and lint (Clt) sample groups, 4.11 and 3.63, respectively, where leaf and lint samples were of different sizes, indicating that leaf samples might be of different developmental stage and lint samples might have been processed differently, supporting that the PCN is affected by both internal and external factors, respectively. Moreover, PCN log₁₀ values were found to be plant specific, with oil containing seeds such as SeS (6.49) and MS (5.05) exhibiting high PCN log₁₀ values compared to non-oil seeds such as SS (1.96). Conclusion: In conclusion, it was observed that PCN log₁₀ values calculated from RT-qPCR assays were specific to plant species and the range of PCN log₁₀ values can be directly correlated to the internal and external factors and, therefore might be used as a potential biomarker for assessing the quality of plant products.

Theoretical exploitation of acceptors based on benzobis(thiadiazole) and derivatives for organic NIR-II fluorophores

Small-molecule dyes with fluorescence emission in the second near-infrared (NIR-II) region (1000-1700 nm) have attracted considerable attention in the biomedical and bioimaging fields due to their greater imaging depths, better spatial resolution, and higher signal-to-background ratios. However, currently reported organic NIR-II fluorophores are still limited and there is great demand to develop other novel NIR-II fluorophores besides benzobisthiadiazole (BBT)-based fluorophores. More importantly, there is a lack of an appropriate level of theory capable of providing both efficient and accurate predictions of the electronic structures of organic NIR-II fluorophores. In this work, successful application of time-dependent density functional theory (TDDFT) using optimally-tuned range-separated functionals for calculations of both absorption and fluorescence spectral properties has been demonstrated, compared with the available experimental data. A series of thiadiazole-based acceptors (A) and derivatives based on the D-A-D skeleton are designed coupled with the triphenylamine donor (D). The structure-property relationships for these fluorophores are thus revealed by analyzing their ground (S0) and excited (S1) state geometries, frontier molecular orbitals (HOMO and LUMO), HOMO-LUMO energy gaps, oscillator strengths, hole-electron distributions and fluorescence wavelengths. It is suggested that the existence of a hypervalent structure leading to a much lower LUMO level and accompanying significant hole-electron separation plays a key role in the red-shift of fluorescence emission in the NIR-II region. In addition, the substitution of BBT oligomers and analogues as acceptor cores is an efficient way to achieve both red-shifted fluorescence wavelengths and enhanced oscillator strengths. The present work provides a reliable and efficient theoretical tool for predicting the related electronic and spectral properties of organic fluorophores and future screening out of potential candidates for excellent NIR-II molecular fluorophores.

Dye chemistry with time-dependent density functional theory

In this perspective, we present an overview of the determination of excited-state properties of "real-life" dyes, and notably of their optical absorption and emission spectra, performed during the last decade with time-dependent density functional theory (TD-DFT). We discuss the results obtained with both vertical and adiabatic (vibronic) approximations, choosing relevant examples for several series of dyes. These examples include reproducing absorption wavelengths of numerous families of coloured molecules, understanding the specific band shape of amino-anthraquinones, optimising the properties of dyes used in solar cells, mimicking the fluorescence wavelengths of fluorescent brighteners and BODIPY dyes, studying optically active biomolecules and photo-induced proton transfer, as well as improving the properties of photochromes.

Thiophene-based compounds as fluorescent tags to study mesenchymal stem cell uptake and release of taxanes

Human mesenchymal stem cells (hMSC) are multipotent cells that display the unique ability to home and engraft in tumor stroma. This remarkable tumor tropic property has generated a great deal of interest in many clinical settings. Recently, we showed that hMSC represent an excellent base for cell-mediated anticancer therapy since they are able to internalize paclitaxel (PTX) and to release it in an amount sufficient to inhibit tumor cell proliferation. In order to shed light on the dynamics of drug uptake and release, in the present paper we describe the synthesis of two novel thiophene-based fluorophore-paclitaxel conjugates, namely PTX-F32 and PTX-F35, as tools for in vitro drug tracking. We aimed to study the ability of these novel derivatives to be efficiently internalized by hMSC and, in a properly engineered coculture assay, to be released in the medium and taken up by tumor cells. In order to ensure better stability of the conjugates toward enzymatic hydrolysis, the selected oligothiophenes were connected to the taxol core at the C7 position through a carbamate linkage between PTX and the diamino linker. Antiproliferative experiments on both tumor cells and stromal cells clearly indicate that, in good correlation with the parent compound, cells are sensitive to nanomolar concentrations of the fluorescent conjugates. Moreover, in the coculture assay we were able to monitor, by fluorescence microscopy, PTX-F32 trafficking from hMSC toward glioblastoma U87 tumor cells. Our work paves the way for novel possibilities to perform extensive and high quality fluorescence-based analysis in order to better understand the cellular mechanisms involved in drug trafficking, such as microvescicle/exosome mediated release, in hMSC vehicle cells.

Axial chirality of donor-donor, donor-acceptor, and tethered 1,1'-binaphthyls: a theoretical revisit with dynamics trajectories

The circular dichroism (CD) spectra of (R)-2,2'-dimethoxy-1,1'-binaphthyl (DD) and its untethered and tethered donor-acceptor analogues (DA and DA7-DA9) were investigated experimentally and theoretically. The experimental CD spectra of DD and DA resembled each other in several aspects, displaying a positive-positive-negative Cotton effect pattern in the (1)L(b)-(1)L(a) region and a strong negative couplet at the (1)B(b) band, but significantly differed in transition energy and rotatory strength. The couplet amplitude (A) of the main band was 1.6 times larger in DA than in DD, despite the comparable extinction coefficients and seemingly analogous conformations. An additional positive Cotton effect was observed at the CT (CT) band for donor-acceptor binaphthyl DA. Our theoretical prediction of the CD spectra of binaphthyls involves three sequential first principle quantum mechanics (QM) calculations. Thus, the geometry optimizations of a series of conformers with varying dihedral angles were performed by the dispersion-corrected DFT-D method using the B97-D functional and the TZV2P basis set. The potential curve as a function of the dihedral angle (θ) was obtained by using the SCS-MP2/TZVPP single-point energy calculations with and without application of the solvent correction. The CD spectrum of each conformer was independently calculated by the second-order approximate coupled cluster calculation (CC2 method) using the TZVPP basis sets and the resolution of the identity (RI-J) approximation. The (net) theoretical CD spectrum was obtained by averaging over all possible conformers, where the dynamics trajectories based on the relative SCS-MP2 energies were taken into account. By using 17 possible conformers at θ varying from 50 to 130° by 5° intervals, the experimental CD spectra were successfully reproduced in a quantitative manner, enabling us to characterize properly almost all of the important spectral features and chiroptical properties. The two-state model, reported previously, turned out to have led to the right answer with wrong reasons. The couplet sign and amplitude A are critical functions of θ and can be used not only for (qualitatively) determining the absolute configuration but also for quantitatively analyzing the binaphthyl conformations. The angle dependence of A was already argued in the classical coupled oscillator and exciton chirality theories to provide reasonable structure elucidations but only in a qualitative or semiquantitative manner. Our method is able to predict the A value quantitatively as a function of θ. For tethered binaphthyls DA7-DA9, particular care should be exercised in the conformational assessment based on the classical treatment because the amplitude A was shown to be significantly affected by the existence of the tether itself. In the present method, the couplet amplitude A was nicely related to the dihedral angle θ of DA and DD by the state-of-the-art ab initio calculations, enabling us to gain the quantitative information about the conformation of axially chiral binaphthyls. The Cotton effect at the CT band also serves as a complementary clue for elucidating the conformation of donor-acceptor binaphthyls.

Microwave-assisted synthesis of thiophene fluorophores, labeling and multilabeling of monoclonal antibodies, and long lasting staining of fixed cells

We report the expedient microwave-assisted synthesis of thiophene based 4-sulfo-2,3,5,6,-tetrafluorophenyl esters whose molecular structure was engineered to achieve blue to red bright fluorescence. The reactivity toward monoclonal antibodies of the newly synthesized fluorophores was analyzed in comparison with that of the corresponding N-succinimidyl esters. Single-fluorophore and multiple-fluorophore labeled antibodies were easily prepared with both types of esters. Multiple-fluorophore labeling with blue and orange emitting fluorophores resulted in white fluorescent antibodies. Thiophene based fluorophores displayed unprecedented fluorescence stability in immunostaining experiments. First-principles TD-DFT theoretical calculations helped us to interpret the behavior of fluorescence emission in different environments.