The identification of microRNAs in the whitespotted bamboo shark (Chiloscyllium plagiosum) liver by Illumina sequencing

MicroRNAs are indispensable players in the regulation of a broad range of biological processes. Here, we report the first deep sequencing of the whitespotted bamboo shark (Chiloscyllium plagiosum) liver. We mapped 91 miRNAs in the Callorhinchus milii genome that have previously been described in the Danio rerio, Fugu rubripes, Oryzias latipes, Xenopus laevis, Xenopus tropicalis, Homo sapiens, and Mus musculus. In addition, 156 new putative candidate (PC) C. plagiosum miRNAs were identified. From these 247 miRNAs, 39 miRNA clusters were identified, and the expression of these clustered miRNAs was observed to vary significantly. A total of 7 candidate miRNAs were selected for expression confirmation by stem-loop RT-PCR. This study resulted in the addition of a significant number of novel miRNA sequences to GenBank and laid the foundation for further understanding of the function of miRNAs in the regulation of C. plagiosum liver development.     

The calcium sensor PeCBL1, interacting with PeCIPK24/25 and PeCIPK26, regulates Na+/K+ homeostasis in Populus euphratica

Key message

This paper is the first to directly link two types of ion channel regulation pathway into an emerging and complex CBL–CIPK signal system in wooden plant.

Abstract

In Arabidopsis thaliana, the calcineurin b-like (CBL) 1 gene has been shown to be necessary in response to abiotic stresses. In this study, we identified CBL1 in the woody plant Populus euphratica, designated as PeCBL1. Heterologous expression of PeCBL1 could build the resistance of sensitive phenotypes to low K⁺ stress in the corresponding Arabidopsis cbl1/cbl9 mutant, and display a salt-sensitive phenotype compared with the mutant. Protein interaction analysis showed that PeCBL1 can interact with PeCIPK24, 25 and 26, and form different complexes of PeCBL–PeCIPK. To further investigate the mechanism of PeCBL1, we analyzed the fluxes of K⁺ and Na⁺ in roots of the wild-type Arabidopsis, cbl1/9 mutant, and PeCBL1 transgenic plants under low K⁺ stress and high Na⁺ stress. These analyses revealed that, compared to the cbl1/9 mutant, the PeCBL1 transgenic plant roots exhibited a higher capacity to absorb K⁺ after exposure to low K⁺ stress, and a lower capacity to discharge Na⁺ after exposure to salt stress. The results suggest that CBL1 interacts with CIPK24, CIPK25 and CIPK26 to regulate Na⁺/K⁺ homeostasis in Populus euphratica.     

Structure-based affinity maturation of a chimeric anti-ricin antibody C4C13

Ricin is a highly lethal toxin. Anti-ricin chimeric monoclonal antibody (mAb) C4C13 was prepared in our lab; however, its binding affinity was much weaker than that of the parent antibody 4C13. In this study, based on the computer-guided homology modeling and conformational optimization methods, the 3-D structure of C4C13 variable regions Fv was constructed and optimized. Using molecular docking and dynamics simulation methods, the 3-D complex structure of ricin and C4C13 Fv was obtained. Considering the orientation property, surface electrostatic distribution, residues chemical andphysical character and intermolecular hydrogen bond, the binding mode and key residues were predicted. According to C4C13 Fv fragment and ricin complementary binding surface, electrostatic attraction periphery and van der Waals interaction interface, three mutants (i.e., M1 (N^H102F, W^H103Y); M2 (W^H103Y) and M3 (R^L90G)) were designed, in which M1 and M2 were predicted to possess higher antigen-binding activity than C4C13, while M3 was weaker. The relative affinity assays by ELISA showed that M1 and M2 mutations had higher affinity (9.6 and 18.3?nmol/L) than C4C13 (130?nmol/L) and M3 had weaker affinity (234.5?nmol/L) than C4C13. The results showed that the modeling complex structure of the antigen (ricin) and antibody (C4C13) is reasonable. Our work offered affinity maturated antibodies by site mutations, which were beneficial for valuable anti-ricin antibody design and preparation in future.     

Digestion-after-shuffling: a method for combinatorial library construction

We have developed a convenient method for family shuffling of amino acid sequences, termed digestion-after-shuffling. After DNA shuffling of homologous genes, plasmid mixture is extracted from a library and used for several double digestions with restriction enzymes. For each double digestion, two restriction enzymes are selected, corresponding to the single restriction sites of different parental genes. After digestions, fragments with expected sizes are obtained by gel purification and religated to construct recombinant plasmids. Thus, the obtained genes should be chimeras and have at least two restriction sites originating from different parental sequences.     

Altered nucleic acid partitioning during phenol extraction or silica adsorption by guanidinium and potassium salts

Nucleic acids were found to partition into the phenol phase during phenol extraction in the presence of guanidinium at certain concentrations under acidic conditions. The guanidinium-concentration-dependent nucleic acid partitioning patterns were analogous to those of the nucleic acid adsorption/partitioning onto silica mediated by guanidinium, which implied that phenol and silica interact with nucleic acids through similar mechanisms. A competition effect was observed in which the nucleic acids that had partitioned into the phenol phase or onto the silica solid phase could be recovered to the aqueous phases by potassium in a molecular weight–salt concentration-dependent manner (the higher molecular weight nucleic acids needed higher concentrations of potassium to be recovered, and vice versa). Methods were developed based on these findings to isolate total RNA from Escherichia coli. By controlling the concentrations of guanidinium and potassium salts used before phenol extraction or silica adsorption, we can selectively recover total RNA but not the high molecular weight genomic DNA in the aqueous phases. Genomic DNA-free total RNA obtained by our methods is suitable for RT-PCR or other purposes. The methods can also be adapted to isolate small RNAs or RNA in certain molecular weight ranges by changing the salt concentrations used.     

A novel mechanical loading model for studying the distributions of strain and mechano-growth factor expression

Mechano-growth factor (MGF), an insulin-like growth factor-I (IGF-I) splice variant, often serves as an important local tissue repair factor in response to the mechanical environment. However, there is no model for exhibiting the MGF expression in a series of strain distribution up to now. In this study, a novel mechanical loading model containing different stresses and strains simultaneously was developed to examine the MGF expression. The strain distributions were predicted by finite element modeling. The MC3T3-E1 cells on a silicone membrane with a central circular hole were exposed to a variable strain environment through stretching. The finite element analysis showed that, when the strain reached the magnitude of 10%, the strain concentration near the circular hole displayed along with the vertical stretch direction, while the minimum strain appeared in the parallel stretch direction. Furthermore, the results showed that MGF expression decreased gradually from high to low strain regions by immunocytochemistry. Meanwhile, the proliferation of osteoblasts increased significantly in the high strain region. In conclusion, this mechanical loading model can present the different distributions of the strain of osteoblasts in vitro. MGF expression and osteoblast proliferation have a high correlation with the levels of strain.     

Single-molecule imaging revealed enhanced dimerization of transforming growth factor β type II receptors in hypertrophic cardiomyocytes

Transforming growth factor β (TGF-β) signaling plays an important role in the pathogenesis of cardiac hypertrophy. However, the molecular mechanism of TGF-β signaling during the process of cardiac remodeling remains poorly understood. In the present study, by employing single-molecule fluorescence imaging approach, we demonstrated that in neonatal rat cardiomyocytes, TGF-β type II receptors (TβRII) existed as monomers at the low expression level, and dimerized upon TGF-β1 stimulation. Importantly, for the first time, we found the increased dimerization of TβRII in hypertrophic cardiomyocytes comparing to the normal cardiomyocytes. The enhanced TβRII dimerization was correlated with the enhanced Smad3 phosphorylation levels. These results provide new information on the mechanism of TGF-β signaling in cardiac remodeling.