PHOSPHATE1-mediated phosphate translocation from roots to shoots regulates floral transition in plants.

Phosphorus nutrition has been known to influence floral transition in plants for a long time, but the underlying mechanism is unclear. Arabidopsis PHOSPHATE1 (PHO1) plays a critical role in phosphate translocation from roots to shoots, but whether and how it regulates floral transition is unknown. Here, we show that knockout mutation of PHO1 delays flowering under both long-day and short-day conditions. The late flowering of pho1 mutants can be partially rescued by Pi supplementation in rosettes or shoot apices. Grafting assay indicates that the late flowering of pho1 mutants is resulted from impaired phosphate translocation from roots to shoots. Knockout mutation of SPX1 and SPX2, two negative regulators of phosphate starvation response, partially rescues the late flowering of pho1 mutants. PHO1 is epistatic to PHO2, a negative regulator of PHO1, in flowering time regulation. Loss of PHO1 represses the expression of some floral activators, including FT encoding florigen, and induces the expression of some floral repressors in shoots. Genetic analyses indicate that at least jasmonic acid signaling is partially responsible for the late flowering of pho1 mutants. In addition, we find rice PHO1;2, the homology of PHO1, plays a similar role in floral transition. These results suggest that PHO1 integrates phosphorus nutrition and flowering time and could be used as a potential target in modulating phosphorus nutrition-mediated flowering time in plants.

Forecast of peak infection and estimate of excess deaths in COVID-19 transmission and prevalence in Taiyuan City, 2022 to 2023.

In this paper, with the method of epidemic dynamics, we assess the spread and prevalence of COVID-19 after the policy adjustment of prevention and control measure in December 2022 in Taiyuan City in China, and estimate the excess population deaths caused by COVID-19. Based on the transmission mechanism of COVID-19 among individuals, a dynamic model with heterogeneous contacts is established to describe the change of control measures and the population's social behavior in Taiyuan city. The model is verified and simulated by basing on reported case data from November 8th to December 5th, 2022 in Taiyuan city and the statistical data of the questionnaire survey from December 1st to 23rd, 2022 in Neijiang city. Combining with reported numbers of permanent residents and deaths from 2017 to 2021 in Taiyuan city, we apply the dynamic model to estimate theoretical population of 2022 under the assumption that there is no effect of COVID-19. In addition, we carry out sensitivity analysis to determine the propagation character of the Omicron strain and the effect of the control measures. As a result of the study, it is concluded that after adjusting the epidemic policy on December 6th, 2022, three peaks of infection in Taiyuan are estimated to be from December 22nd to 31st, 2022, from May 10th to June 1st, 2023, and from September 5th to October 13th, 2023, and the corresponding daily peaks of new cases can reach 400 000, 44 000 and 22 000, respectively. By the end of 2022, excess deaths can range from 887 to 4887, and excess mortality rate can range from 3.06% to 14.82%. The threshold of the infectivity of the COVID-19 variant is estimated 0.0353, that is if the strain infectivity is above it, the epidemic cannot be control with the previous normalization measures.

SHORT-ROOT stabilizes PHOSPHATE1 to regulate phosphate allocation in Arabidopsis.

The coordinated distribution of inorganic phosphate (Pi) between roots and shoots is an important process that plants use to maintain Pi homeostasis. SHORT-ROOT (SHR) is well characterized for its function in root radial patterning. Here we demonstrate a role of SHR in controlling Pi allocation from root to shoot by regulating PHOSPHATE1 in the root differentiation zone. We recovered a weak mutant allele of SHR in Arabidopsis that accumulates much less Pi in the shoot and shows a constitutive Pi starvation response under Pi-sufficient conditions. In addition, Pi starvation suppresses SHR protein accumulation and releases its inhibition on the HD-ZIP III transcription factor PHB. PHB accumulates and directly binds the promoter of PHOSPHATE2 to upregulate its transcription, resulting in PHOSPHATE1 degradation in the xylem-pole pericycle cells. Our findings reveal a previously unrecognized mechanism of how plants regulate Pi translocation from roots to shoots.

An Agrobacterium-mediated transient expression method contributes to functional analysis of a transcription factor and potential application of gene editing in Chenopodium quinoa.

KEY MESSAGE: An efficient Agrobacterium-mediated transient expression method was developed, which contributed to the functional characterization of the transcription factor CqPHR1, and demonstrates the potential application of gene editing in quinoa. Chenopodium quinoa is a crop expected to ensure global food security in future due to its high resistance to multiple abiotic stresses and nutritional value. We cloned one of the paralogous genes of the Arabidopsis homolog PHR1 (PHOSPHATE STARVATION RESPONSE 1) in quinoa-inbred lines by reverse genetic approach. Overexpression of CqPHR1 driven by the constitutive CaMV 35S promoter in Arabidopsis phr1 mutant can complement its phenotypes, including the induction of phosphate starvation-induced (PSI) genes and anthocyanin accumulation in leaves. By Agrobacterium-mediated gene transient expression, we found that CqPHR1 localized in the nucleus of quinoa cells, and overexpression of CqPHR1 in quinoa cells promoted PSI genes expression, which further revealed the function of CqPHR1 as a transcription factor. We have also shown that the transient expression system can be used to express Cas9 protein in various quinoa-inbred lines and perform effective gene editing in quinoa tissue. The method developed in this study will be useful for verifying the effectiveness of gene-editing systems in quinoa cells and has potential application in the generation of gene-edited quinoa with heritable traits.

Mechanism of phosphate sensing and signaling revealed by rice SPX1-PHR2 complex structure.

Phosphate, a key plant nutrient, is perceived through inositol polyphosphates (InsPs) by SPX domain-containing proteins. SPX1 an inhibit the PHR2 transcription factor to maintain Pi homeostasis. How SPX1 recognizes an InsP molecule and represses transcription activation by PHR2 remains unclear. Here we show that, upon binding InsP6, SPX1 can disrupt PHR2 dimers and form a 1:1 SPX1-PHR2 complex. The complex structure reveals that SPX1 helix α1 can impose a steric hindrance when interacting with the PHR2 dimer. By stabilizing helix α1, InsP6 allosterically decouples the PHR2 dimer and stabilizes the SPX1-PHR2 interaction. In doing so, InsP6 further allows SPX1 to engage with the PHR2 MYB domain and sterically block its interaction with DNA. Taken together, our results suggest that, upon sensing the surrogate signals of phosphate, SPX1 inhibits PHR2 via a dual mechanism that attenuates dimerization and DNA binding activities of PHR2.

Regulation of Ammonium Cellular Levels is An Important Adaptive Trait for the Euhalophytic Behavior of Salicornia europaea.

Salinization of agricultural land is a devastating phenomenon which will affect future food security. Understanding how plants survive and thrive in response to salinity is therefore critical to potentiate tolerance traits in crop species. The halophyte Salicornia europaea has been used as model system for this purpose. High salinity causes NH4+ accumulation in plant tissues and consequent toxicity symptoms that may further exacerbate those caused by NaCl. In this experiment we exposed Salicornia plants to five concentrations of NaCl (0, 1, 10, 50 and 200 mM) in combination with two concentrations of NH4Cl (1 and 50 mM). We confirmed the euhalophytic behavior of Salicornia that grew better at 200 vs. 0 mM NaCl in terms of both fresh (+34%) and dry (+46%) weights. Addition of 50 mM NH4Cl to the growth medium caused a general growth reduction, which was likely caused by NH4+ accumulation and toxicity in roots and shoots. When plants were exposed to high NH4Cl, high salinity reduced roots NH4+ concentration (-50%) compared to 0 mM NaCl. This correlates with the activation of the NH4+ assimilation enzymes, glutamine synthetase and glutamate dehydrogenase, and the growth inhibition was partially recovered. We argue that NH4+ detoxification is an important trait under high salinity that may differentiate halophytes from glycophytes and we present a possible model for NH4+ detoxification in response to salinity.

A group of SUVH methyl-DNA binding proteins regulate expression of the DNA demethylase ROS1 in Arabidopsis.

DNA methylation is typically regarded as a repressive epigenetic marker for gene expression. Genome-wide DNA methylation patterns in plants are dynamically regulated by the opposing activities of DNA methylation and demethylation reactions. In Arabidopsis, a DNA methylation monitoring sequence (MEMS) in the promoter of the DNA demethylase gene ROS1 functions as a methylstat that senses these opposing activities and regulates genome DNA methylation levels by adjusting ROS1 expression. How DNA methylation in the MEMS region promotes ROS1 expression is not known. Here, we show that several Su(var)3-9 homologs (SUVHs) can sense DNA methylation levels at the MEMS region and function redundantly to promote ROS1 expression. The SUVHs bind to the MEMS region, and the extent of binding is correlated with the methylation level of the MEMS. Mutations in the SUVHs lead to decreased ROS1 expression, causing DNA hypermethylation at more than 1,000 genomic regions. Thus, the SUVHs function to mediate the activation of gene transcription by DNA methylation.

A method for the further assembly of targeted unigenes in a transcriptome after assembly by Trinity.

RNA-sequencing has been widely used to obtain high throughput transcriptome sequences in various species, but the assembly of a full set of complete transcripts is still a significant challenge. Judging by the number of expected transcripts and assembled unigenes in a transcriptome library, we believe that some unigenes could be reassembled. In this study, using the nitrate transporter (NRT) gene family and phosphate transporter (PHT) gene family in Salicornia europaea as examples, we introduced an approach to further assemble unigenes found in transcriptome libraries which had been previously generated by Trinity. To find the unigenes of a particular transcript that contained gaps, we respectively selected 16 NRT candidate unigene pairs and 12 PHT candidate unigene pairs for which the two unigenes had the same annotations, the same expression patterns among various RNA-seq samples, and different positions of the proteins coded as mapped to a reference protein. To fill a gap between the two unigenes, PCR was performed using primers that mapped to the two unigenes and the PCR products were sequenced, which demonstrated that 5 unigene pairs of NRT and 3 unigene pairs of PHT could be reassembled when the gaps were filled using the corresponding PCR product sequences. This fast and simple method will reduce the redundancy of targeted unigenes and allow acquisition of complete coding sequences (CDS).

Note: Inter-satellite laser range-rate measurement by using digital phase locked loop.

This note presents an improved high-resolution frequency measurement system dedicated for the inter-satellite range-rate monitoring that could be used in the future's gravity recovery mission. We set up a simplified common signal test instead of the three frequencies test. The experimental results show that the dominant noises are the sampling time jitter and the thermal drift of electronic components, which can be reduced by using the pilot-tone correction and passive thermal control. The improved noise level is about 10(-8) Hz/Hz(1/2)@0.01Hz, limited by the signal-to-noise ratio of the sampling circuit.

Validation of suitable reference genes for gene expression analysis in the halophyte Salicornia europaea by real-time quantitative PCR.

Real-time quantitative polymerase chain reaction (RT-qPCR), a reliable technique for quantifying gene expression, requires stable reference genes to normalize its data. Salicornia europaea, a stem succulent halophyte with remarkable salt resistance and high capacity for ion accumulation, has not been investigated with regards to the selection of appropriate reference genes for RT-qPCR. In this study, the expression of 11 candidate reference genes, GAPDH (Glyceraldehyde 3-phosphate dehydrogenase), Actin, α-Tub (α-tubulin), ß-Tub (ß-tubulin), EF1-α (Elongation factor 1-α), UBC (Ubiquitin-conjugating enzyme), UBQ (Polyubiquitin), CYP (Cyclophilin), TIP41 (TIP41-like protein), CAC (Clathrin adaptor complexes), and DNAJ (DnaJ-like protein), was analyzed in S. europaea samples, which were classified into groups according to various abiotic stresses (NaCl, nitrogen, drought, cold and heat), tissues and ages. Three commonly used software programs (geNorm, NormFinder and BestKeeper) were applied to evaluate the stability of gene expression, and comprehensive ranks of stability were generated by aggregate analysis. The results show that the relatively stable genes for each group are the following: (1) CAC and UBC for whole samples; (2) CAC and UBC for NaCl stress; (3) Actin and α-Tub for nitrogen treatment; (4) Actin and GAPDH for drought stress; (5) α-Tub and UBC for cold stress; (6) TIP41 and DNAJ for heat stress; (7) UBC and UBQ for different tissues; and (8) UBC and Actin for various developmental stages. These genes were validated by comparing transcriptome profiles. Using two stable reference genes was recommended in the normalization of RT-qPCR data. This study identifies optimal reference genes for RT-qPCR in S. europaea, which will benefit gene expression analysis under these conditions.

[Assembling of an ammonium transporter gene in Salicornia europaea by expression pattern analysis of Unigene in transcriptome].

RNA-seq can help us quickly obtain the whole transcriptome sequences of species under different conditions. Many Unigenes that are assembled by raw reads always do not contain complete open reading frame (ORF). In addition, it also has some redundancy in transcriptome library. Some Unigenes in the library, although belong to one transcript, cannot be assembled without overlapping. We found five incomplete Unigenes annotated ammonium transporter (AMT) from Salicornia europaea transcriptome, in which two Unigenes (Uni4 and Uni5) had identical expression patterns across four transcriptomes. The two Unigenes may come from one transcript. Analyzing the Unigene position of transcript by NCBI blastx, we found that Uni4 and Uni5 respectively located in 5' end and 3' end compared with the reference transcript, and an unknown gap of 120 bp may exist in a hypothetic transcript to which Uni4 and Uni5 both belong. To verify the hypothesis, single forward primer and single reverse primers were respectively designed on Uni4 and Uni5, and a fragment with about 800 bp was generated by PCR. Then it was sequenced and aligned with Uni4 and Uni5. Finally, we assembled a sequence with 1 667 bp, which contains a complete ORF (1 482 bp, coding 494 amino acids). It belongs to amt1 subfamily and was named Seamt1 via the phylogenetic analysis. It was pointed by bioinformatics tools that SeAMT1 protein conformed to the AMT characteristics of other species. This work clustered expression pattern to explore the Unigenes of one transcript, and the feasibility of this method was validated through the other two groups of Unigenes. The handy method will benefit extension and assembling of Unigene in transcriptome, it also helps achieve the complete ORF and gene function.

Global transcriptome profiling of Salicornia europaea L. shoots under NaCl treatment.

BACKGROUND: Soil salinity is a major abiotic stress that limits agriculture productivity worldwide. Salicornia europaea is well adapted to extreme saline environments with more than 1,000 mM NaCl in the soil, so it could serve as an important model species for studying halophilic mechanisms in euhalophytes. To obtain insights into the molecular basis of salt tolerance, we present here the first extensive transcriptome analysis of this species using the Illumina HiSeq™ 2000. PRINCIPAL FINDINGS: A total of 41 and 39 million clean reads from the salt-treated (Se200S) and salt-free (SeCKS) tissues of S. europaea shoots were obtained, and de novo assembly produced 97,865 and 101,751 unigenes, respectively. Upon further assembly with EST data from both Se200S and SeCKS, 109,712 high-quality non-redundant unigenes were generated with a mean unigene size of 639 bp. Additionally, a total of 3,979 differentially expressed genes (DEGs) were detected between the Se200S and SeCKS libraries, with 348 unigenes solely expressed in Se200S and 460 unigenes solely expressed in SeCKS. Furthermore, we identified a large number of genes that are involved in ion homeostasis and osmotic adjustment, including cation transporters and proteins for the synthesis of low-molecular compounds. All unigenes were functionally annotated within the COG, GO and KEGG pathways, and 10 genes were validated by qRT-PCR. CONCLUSION: Our data contains the extensive sequencing and gene-annotation analysis of S. europaea. This genetic knowledge will be very useful for future studies on the molecular adaptation to abiotic stress in euhalophytes and will facilitate the genetic manipulation of other economically important crops.

Physicochemical properties of A- and B-starch granules isolated from hard red and soft red winter wheat.

Large A- and small B-starch granules separated from hard red and soft red winter wheat grains were investigated for their morphological, structural, and physicochemical properties. A-granules displayed a disk or lenticular shape, and B-granules showed a spherical or polygonal shape according to SEM. XRD analysis showed that both A- and B-granules had A-type crystallinity. A-granules contained a higher amount of amylose and a lower protein content and amylopectin/amylose ratio than B-granules. A-type granules exhibited a higher hydrolysis extent and swelling power and a lower iodine affinity than did B-granules. A-granules showed a higher peak, trough, breakdown and final viscosity, and gelatinization enthalpy than did B-granules, while B-granules exhibited a higher gelatinization temperature. The study demonstrated that the A- and B-granules separated from both hard red and soft red winter wheat grains exhibited a similar structure and very different physicochemical properties.

Effect of nitrogen and sulfur fertilization on accumulation characteristics and physicochemical properties of A- and B-wheat starch.

The effects of nitrogen (N) fertilization at the rates of 0 and 230 kg hm(-2) combined with selected sulfur (S) fertilization rates of 0, 46, 56, 77, and 115 kg hm(-2) on A- and B-wheat starch granule accumulation, composition, and thermal and pasting properties were investigated. Scanning electron micrographs revealed that A- and B-starch granules accumulation during grain filling can be influenced significantly by N and S fertilization, and B-granules tend to be more sensitive to S fertilization than A-starch granules. The doses of nitrogen and sulfur fertilization on starch properties were not positively correlated; higher concentration of fertilizers failed to cause a higher effects. N230S46 and N230S56 treatment resulted in the higher peak viscosity, trough viscosity, breakdown viscosity, final and setback viscosity, and gelatinization temperature (To, Tp, Tc) according to differential scanning calorimeter (DSC) and rapid visco analyzer (RVA), respectively.