DNA barcoding of Oryza: conventional,specific, and super barcodes

Key message

We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.

Abstract

Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world’s population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.

     

Revisiting the phosphotyrosine binding pocket of Fyn SH2 domain led to the identification of novel SH2 superbinders.

Protein engineering through directed evolution is an effective way to obtain proteins with novel functions with the potential applications as tools for diagnosis or therapeutics. Many natural proteins have undergone directed evolution in vitro in the test tubes in the laboratories worldwide, resulting in the numerous protein variants with novel or enhanced functions. we constructed here an SH2 variant library by randomizing 8 variable residues in its phosphotyrosine (pTyr) binding pocket. Selection of this library by a pTyr peptide led to the identification of SH2 variants with enhanced affinities measured by EC50. Fluorescent polarization was then applied to quantify the binding affinities of the newly identified SH2 variants. As a result, three SH2 variants, named V3, V13 and V24, have comparable binding affinities with the previously identified SH2 triple‐mutant superbinder. Biolayer Interferometry assay was employed to disclose the kinetics of the binding of these SH2 superbinders to the phosphotyrosine peptide. The results indicated that all the SH2 superbinders have two‐orders increase of the dissociation rate when binding the pTyr peptide while there was no significant change in their associate rates. Intriguingly, though binding the pTyr peptide with comparable affinity with other SH2 superbinders, the V3 does not bind to the sTyr peptide. However, variant V13 and V24 have cross‐reactivity with both pTyr and sTyr peptides. The newly identified superbinders could be utilized as tools for the identification of pTyr‐containing proteins from tissues under different physiological or pathophysiological conditions and may have the potential in the therapeutics.     

Dynamic Host Immune and Transcriptomic Responses to Respiratory Syncytial Virus Infection in a Vaccination-Challenge Mouse Model

Virologica Sinica - Respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infections in children. Inactivated RSV vaccine was developed in the late 1960’s, but the...     

A Self-Biomineralized Novel Adenovirus Vectored COVID-19 Vaccine for Boosting Immunization of Mice

Virologica Sinica - SARS-CoV-2 has caused more than 3.8 million deaths worldwide, and several types of COVID-19 vaccines are urgently approved for use, including adenovirus vectored vaccines....     

The differential contributions of herkogamy and dichogamy as mechanisms of avoiding self‐interference in four self‐incompatible Epimedium species

Self‐interference is one of the most important selective forces in shaping floral evolution. Herkogamy and dichogamy both can achieve reductions in the extent of self‐interference, but they may have different roles in minimizing self‐interference in a single species. We used four self‐incompatible Epimedium species to explore the roles of herkogamy and dichogamy in avoiding self‐interference and to test the hypothesis that herkogamy and dichogamy may be separated and become selected preferentially in the taxa. Two species (E. franchetii and E. mikinorii) expressed strong herkogamy and weak protogyny (adichogamy), whereas another two species (E. sutchuenense and E. leptorrhizum) expressed slight herkogamy and partial protandry. Field investigations indicated that there was no physical self‐interference between male function and female function regarding pollen removal and pollen deposition in all species. Self‐pollination (autonomous or facilitated) was greater in species with slight herkogamy than in those with strong herkogamy. Artificial pollination treatments revealed that self‐pollination could reduce outcrossed female fertility in all species, and we found evidence that self‐interference reduced seed set in E. sutchuenense and E. leptorrhizum in the field, but not in E. franchetii and E. mikinorii. These results indicate that well‐developed herkogamy is more effective compared with dichogamy in avoiding self‐interference in the four species. In genus Epimedium, herkogamy instead of dichogamy should be selected preferentially and evolved as an effective mechanism for avoiding self‐interference and might not need to evolve linked with dichogamy.     

Immunohistochemical Expression of RAGE and Its Ligand (S100A9) in Cervical Lesions

Altered expressions of receptor for advanced glycation end-products (RAGE) and its ligand (S100A9) are observed in many cancers and play a key role in inflammation-associated cancer. In our previous study, by two-dimensional gel electrophoresis followed by mass spectrometry, the expression of S100A9 protein was found to increase in squamous cervical cancer compared with adjacent normal cervical tissues. Therefore, in the present study we observed the expressions of S100A9 and RAGE in 30 chronic cervicitis, 50 cervical intraepithelial neoplasia (CIN), and 40 squamous cervical cancer (SCC) using immunohistochemical analysis and analyzed the differential expression and possible role of S100A9 and RAGE in cancer development. Immunohistochemical findings were as follows: the expressions of S100A9 and RAGE were demonstrated in chronic cervicitis, CIN, and SCC. Moreover, their expressions were gradually increasing as the tumor progressed. In SCC, the staining scores of S100A9 and RAGE were significantly higher in well-differentiated tumors compared to moderately and poorly differentiated tumors. The expression of S100A9 in epithelial cells exhibited a positive correlation to RAGE expression in chronic cervicitis, CIN, and SCC. There were no significant difference of S100A9 immunoreactivity in stromal cells among chronic cervicitis, CIN, and SCC. Moreover, there was no correlation between S100A9 immunoreactivity in stromal cells of SCC and clinicopathological parameters. Finally, double immunohistochemistry illustrated that RAGE and S100A9 co-express in SCC. In conclusion, RAGE binds its ligand (S100A9), which plays an important role in the development of SCC. In addition, the expressions of S100A9 and RAGE in SCC tumor cells were closely associated with histological differentiation.     

Drug-Loaded Zein Nanofibers Prepared Using a Modified Coaxial Electrospinning Process

This study investigated the preparation of drug-loaded fibers using a modified coaxial electrospinning process, in which only unspinnable solvent was used as sheath fluid. With zein/ibuprofen (IBU) co-dissolving solution and N, N-dimethylformamide as core and sheath fluids, respectively, the drug-loaded zein fibers could be generated continuously and smoothly without any clogging of the spinneret. Field emission scanning electron microscopy and transmission electron microscopy observations demonstrated that the fibers had ribbon morphology with a smooth surface. Their average diameters were 0.94 ± 0.34 and 0.67 ± 0.21 μm when the sheath-to-core flow rate ratios were taken as 0.11 and 0.25, respectively. X-ray diffraction and differential scanning calorimetry verified that IBU was in an amorphous state in all fiber composites. Fourier transform infrared spectra showed that zein had good compatibility with IBU owing to hydrogen bonding. In vitro dissolution tests showed that all the fibers could provide sustained drug release files via a typical Fickian diffusion mechanism. The modified coaxial electrospinning process reported here can expand the capability of electrospinning in generating fibers and provides a new manner for developing novel drug delivery systems.KEYWORDS: coaxial electrospinning, drug-loaded fibers, sheath solvent, sustained release, zein