RNA-Seq Transcriptome Analysis and Evolution of OsEBS, a Gene Involved in Enhanced Spikelet Number per Panicle in Rice.

Spikelet number per panicle (SNP) is one of the most important yield components in rice. Rice ENHANCING BIOMASS AND SPIKELET NUMBER (OsEBS), a gene involved in improved SNP and yield, has been cloned from an accession of Dongxiang wild rice. However, the mechanism of OsEBS increasing rice SNP is poorly understood. In this study, the RNA-Seq technology was used to analyze the transcriptome of wildtype Guichao 2 and OsEBS over-expression line B102 at the heading stage, and analysis of the evolution of OsEBS was also conducted. A total of 5369 differentially expressed genes (DEGs) were identified between Guichao2 and B102, most of which were down-regulated in B102. Analysis of the expression of endogenous hormone-related genes revealed that 63 auxin-related genes were significantly down-regulated in B102. Gene Ontogeny (GO) enrichment analysis showed that the 63 DEGs were mainly enriched in eight GO terms, including auxin-activated signaling pathway, auxin polar transport, auxin transport, basipetal auxin transport, and amino acid transmembrane transport, most of which were directly or indirectly related to polar auxin transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis further verified that the down-regulated genes related to polar auxin transport had important effects on increased SNP. Analysis of the evolution of OsEBS found that OsEBS was involved in the differentiation of indica and japonica, and the differentiation of OsEBS supported the multi-origin model of rice domestication. Indica (XI) subspecies harbored higher nucleotide diversity than japonica (GJ) subspecies in the OsEBS region, and XI experienced strong balancing selection during evolution, while selection in GJ was neutral. The degree of genetic differentiation between GJ and Bas subspecies was the smallest, while it was the highest between GJ and Aus. Phylogenetic analysis of the Hsp70 family in O. sativa, Brachypodium distachyon, and Arabidopsis thaliana indicated that changes in the sequences of OsEBS were accelerated during evolution. Accelerated evolution and domain loss in OsEBS resulted in neofunctionalization. The results obtained from this study provide an important theoretical basis for high-yield rice breeding.

Fast and Precise Temperature Control for Axon Stretch Growth Bioreactor Based on Fuzzy PID Control.

A suitable environment is essential for successful long-term cell culturing in vitro. Too high or too low temperature will affect the growth of cells, so we need to maintain the constant temperature of the cell culture environment. Usually, cells are cultured in a cell incubator, and the constant temperature is provided by the cell incubator. Recently, we have developed a multi-channel axon stretch growth bioreactor for rapid acquisition of autologous nerve tissue. Since the motor and controller are placed in the incubator for a long time, the service life of the equipment will be shortened or even damaged due to high humidity and weak acid environment. In order to enable the axon stretch growth bioreactor to culture cells independently, we designed a constant temperature control system for the device. Firstly, the simulation results show that the fuzzy PID control reduces the overshoot and improves the traditional PID control with large overshoot and low control precision. Then, the two control algorithms were applied to the multi-channel axon stretch growth bioreactor by STM32F4 microcontroller. The experimental data show that the fuzzy PID control algorithm has good control effect and can meet the requirement of constant temperature of cell growth. Finally, nerve cells derived from human pluripotent stem cells were successfully cultured in a cell culture amplification chamber under a constant temperature environment provided by a fuzzy PID controller, and well-developed axons could be seen. In the future, we may transplant stretch growth axons into living organisms to repair nerve damage.

A Nanoparticle-Based Anticaries Vaccine Enhances the Persistent Immune Response To Inhibit Streptococcus mutans and Prevent Caries.

Caries vaccines have been identified as a good strategy for the prevention of caries through the mechanism of inoculation against Streptococcus mutans, which is the main etiological bacterium causing caries. Protein antigen c (PAc) of S. mutans has been administered as an anticaries vaccine but shows relatively weak immunogenicity to elicit a low-level immune response. Here, we report a zeolitic imidazolate framework-8 nanoparticle (ZIF-8 NP)-based adjuvant with good biocompatibility, pH responsiveness, and high loading performance for PAc that was used as an anticaries vaccine. In this study, we prepared a ZIF-8@PAc anticaries vaccine and investigated the immune responses and anticaries efficacy induced by this vaccine in vitro and in vivo. ZIF-8 NPs substantially improved the internalization of PAc in lysosomes for further processing and presentation to T lymphocytes. In addition, significantly higher IgG antibody titers, cytokine levels, splenocyte proliferation indices, and percentages of mature dendritic cells (DCs) and central memory T cells were detected in mice subcutaneously immunized with ZIF-8@PAc than in mice subcutaneously immunized with PAc alone. Finally, rats were immunized with ZIF-8@PAc, and ZIF-8@PAc elicited a strong immune response to inhibit colonization by S. mutans and improve prophylactic efficacy against caries. Based on the results, ZIF-8 NPs are promising as an adjuvant for anticaries vaccine development. IMPORTANCE Streptococcus mutans is the main etiologic bacterium of dental caries, whose protein antigen c (PAc) has been administered as an anticaries vaccine. However, the immunogenicity of PAc is relatively weak. To improve the immunogenicity of PAc, ZIF-8 NP was used as an adjuvant, and the immune responses and protective effect elicited by ZIF-8@PAc anticaries vaccine were evaluated in vitro and in vivo. The findings will help in prevention of dental caries and provide new insight for the development of anticaries vaccine in the future.

Efficient simulations of stretch growth axon based on improved HH model.

OBJECTIVE: According to recent studies, synaptic connections by axons formed can resist stronger mechanical stresses. A large number of nerve tissues with regular growth can be achieved quickly by appropriately managing the pulling pace and force. However, currently there are few studies on the physiological characteristics of stretching growth axons. Until now, there is no mature technology for determining whether the axons can normally transmit neural signals following continuous mechanical stimulation. In this paper, an improved HH model was proposed to investigate the effect of mechanical stimuli on stretched axons and synapses. METHODS: First, we add the link between membrane capacitance and diameter to the standard HH model and the fundamental concept of capacitance. Then, unmyelinated stretch growth axons with different lengths were simulated in this model. RESULTS: After mechanical pulling stimulation, the improved model successfully replicated the generation and propagation of action potentials in several different axon segments. This increase in length accompanying an increase in diameter due to stretch growth. When the stretching growth axon was stimulated again by traction, the membrane capacitance rapidly increased from the constant value and the inward current was large enough to depolarize the membrane and produce an action potential. After stretching, nerve fibers could still receive signals sent by other neuron cells and complete the signal transmission. DISCUSSION: This proposed research can help to optimize stretching axon culture conditions, avoid mechanical force damage to nerve tissue, and achieve a more effective nerve tissue culture process.

Establishment of an efficient early flowering-assisted CRISPR/Cas9 gene-editing system in Arabidopsis.

KEY MESSAGE: Ectopic expression of the florigen FT gene along with the Cas9 cassette promotes fast reproduction of the T1 transgenic plants, and the late-flowering phenotype serves as a convenient marker for transgene-free plants screening in T2 segregation population.

Uridylation and the SKI complex orchestrate the Calvin cycle of photosynthesis through RNA surveillance of TKL1 in Arabidopsis.

RNA uridylation, catalyzed by terminal uridylyl transferases (TUTases), represents a conserved and widespread posttranscriptional RNA modification in eukaryotes that affects RNA metabolism. In plants, several TUTases, including HEN1 SUPPRESSOR 1 (HESO1) and UTP: RNA URIDYLYLTRANSFERASE (URT1), have been characterized through genetic and biochemical approaches. However, little is known about their physiological significance during plant development. Here, we show that HESO1 and URT1 act cooperatively with the cytoplasmic 3'-5' exoribonucleolytic machinery component SUPERKILLER 2 (SKI2) to regulate photosynthesis through RNA surveillance of the Calvin cycle gene TRANSKETOLASE 1 (TKL1) in Arabidopsis. Simultaneous dysfunction of HESO1, URT1, and SKI2 resulted in leaf etiolation and reduced photosynthetic efficiency. In addition, we detected massive illegitimate short interfering RNAs (siRNAs) from the TKL1 locus in heso1 urt1 ski2, accompanied by reduced TKL1/2 expression and attenuated TKL activities. Consequently, the metabolic analysis revealed that the abundance of many Calvin cycle intermediates is dramatically disturbed in heso1 urt1 ski2. Importantly, all these molecular and physiological defects were largely rescued by the loss-of-function mutation in RNA-DEPENDENT RNA POLYMERASE 6 (RDR6), demonstrating illegitimate siRNA-mediated TKL silencing. Taken together, our results suggest that HESO1- and URT1-mediated RNA uridylation connects to the cytoplasmic RNA degradation pathway for RNA surveillance, which is crucial for TKL expression and photosynthesis in Arabidopsis.

OsPDCD5 negatively regulates plant architecture and grain yield in rice.

Plant architecture is an important agronomic trait that affects crop yield. Here, we report that a gene involved in programmed cell death, OsPDCD5, negatively regulates plant architecture and grain yield in rice. We used the CRISPR/Cas9 system to introduce loss-of-function mutations into OsPDCD5 in 11 rice cultivars. Targeted mutagenesis of OsPDCD5 enhanced grain yield and improved plant architecture by increasing plant height and optimizing panicle type and grain shape. Transcriptome analysis showed that OsPDCD5 knockout affected auxin biosynthesis, as well as the gibberellin and cytokinin biosynthesis and signaling pathways. OsPDCD5 interacted directly with OsAGAP, and OsAGAP positively regulated plant architecture and grain yield in rice. Collectively, these findings demonstrate that OsPDCD5 is a promising candidate gene for breeding super rice cultivars with increased yield potential and superior quality.

TCP transcription factors are critical for the coordinated regulation of isochorismate synthase 1 expression in Arabidopsis thaliana.

Salicylic acid (SA) plays an important role in various aspects of plant development and responses to stresses. To elucidate the sophisticated regulatory mechanism of SA synthesis and signaling, we used a yeast one-hybrid system to screen for regulators of isochorismate synthase 1 (ICS1), a gene encoding the key enzyme in SA biosynthesis in Arabidopsis thaliana. A TCP family transcription factor AtTCP8 was initially identified as a candidate regulator of ICS1. The regulation of ICS1 by TCP proteins is supported by the presence of a typical TCP binding site in the ICS1 promoter. The binding of TCP8 to this site was confirmed by in vitro and in vivo assays. Expression patterns of TCP8 and its corresponding gene TCP9 largely overlapped with ICS1 under pathogen attack. A significant reduction in the expression of ICS1 during immune responses was observed in the tcp8 tcp9 double mutant. We also detected strong interactions between TCP8 and SAR deficient 1 (SARD1), WRKY family transcription factor 28 (WRKY28), NAC (NAM/ATAF1,ATAF2/CUC2) family transcription factor 019 (NAC019), as well as among TCP8, TCP9 and TCP20, suggesting a complex coordinated regulatory mechanism underlying ICS1 expression. Our results collectively demonstrate that TCP proteins are involved in the orchestrated regulation of ICS1 expression, with TCP8 and TCP9 being verified as major representatives.

Identification and characterization of OsEBS, a gene involved in enhanced plant biomass and spikelet number in rice.

Common wild rice (Oryza rufipogon Griff.) is an important genetic reservoir for rice improvement. We investigated a quantitative trait locus (QTL), qGP5-1, which is related to plant height, leaf size and panicle architecture, using a set of introgression lines of O. rufipogon in the background of the Indica cultivar Guichao2 (Oryza sativa L.). We cloned and characterized qGP5-1 and confirmed that the newly identified gene OsEBS (enhancing biomass and spikelet number) increased plant height, leaf size and spikelet number per panicle, leading to an increase in total grain yield per plant. Our results showed that the increased size of vegetative organs in OsEBS-expressed plants was enormously caused by increasing cell number. Sequence alignment showed that OsEBS protein contains a region with high similarity to the N-terminal conserved ATPase domain of Hsp70, but it lacks the C-terminal regions of the peptide-binding domain and the C-terminal lid. More results indicated that OsEBS gene did not have typical characteristics of Hsp70 in this study. Furthermore, Arabidopsis (Arabidopsis thaliana) transformed with OsEBS showed a similar phenotype to OsEBS-transgenic rice, indicating a conserved function of OsEBS among plant species. Together, we report the cloning and characterization of OsEBS, a new QTL that controls rice biomass and spikelet number, through map-based cloning, and it may have utility in improving grain yield in rice.

Identification of heterotic loci associated with yield-related traits in Chinese common wild rice (Oryza rufipogon Griff.).

Many rice breeding programs have currently reached yield plateaus as a result of limited genetic variability in parental strains. Dongxiang common wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and serves as an important gene pool for the genetic improvement of rice cultivars. In this study, heterotic loci (HLs) associated with six yield-related traits were identified in wild and cultivated rice and investigated using a set of 265 introgression lines (ILs) of O. rufipogon Griff. in the background of the Indica high-yielding cultivar Guichao 2 (O. sativa L.). Forty-two HLs were detected by a single point analysis of mid-parent heterosis values from test cross F(1) offspring, and 30 (71.5%) of these HLs showed significantly positive effects, consistent with the superiority shown by the F(1) test cross population in the six yield-related traits under study. Genetic mapping of hsp11, a locus responsible for the number of spikelets per panicle, confirmed the utility of these HLs. The results indicate that favorable HLs capable of improving agronomic traits are available. The identification of HLs between wild rice and cultivated rice could lead to a new strategy for the application of heterosis in rice breeding.