OsNAC103, a NAC Transcription Factor, Positively Regulates Leaf Senescence and Plant Architecture in Rice

Leaf senescence, the last stage of leaf development, is essential for crop yield by promoting nutrition relocation from senescence leaves to new leaves and seeds. NAC (NAM/ATAF1/ATAF2/CUC2) proteins, one of the plant-specific transcription factors, widely distribute in plants and play important roles in plant growth and development. Here, we identified a new NAC member OsNAC103 and found that it plays critical roles in leaf senescence and plant architecture in rice. OsNAC103 mRNA levels were dramatically induced by leaf senescence as well as different phytohormones such as ABA, MeJA and ACC and abiotic stresses including dark, drought and high salinity. OsNAC103 acts as a transcription factor with nuclear localization signals at the N terminal and a transcriptional activation signal at the C terminal. Overexpression of OsNAC103 promoted leaf senescence while osnac103 mutants delayed leaf senescence under natural condition and dark-induced condition, meanwhile, senescence-associated genes (SAGs) were up-regulated in OsNAC103 overexpression (OsNAC103-OE) lines, indicating that OsNAC103 positively regulates leaf senescence in rice. Moreover, OsNAC103-OE lines exhibited loose plant architecture with larger tiller angles while tiller angles of osnac103 mutants decreased during the vegetative and reproductive growth stages due to the response of shoot gravitropism, suggesting that OsNAC103 can regulate the plant architecture in rice. Taken together, our results reveal that OsNAC103 plays crucial roles in the regulation of leaf senescence and plant architecture in rice.

MicroRNA-206 Contributes to the Progression of Preeclampsia by Suppressing the Viability and Mobility of Trophocytes via the Inhibition of AGTR1

The development of preeclampsia (PE) is associated with the impaired trophoblast motility. MicroRNAs (miRs) contribute to the modulation of trophoblast invasion. In the current study, the role of miR-206/AGTR1 in the TNF-alpha-induced invasion defect of trophoblasts was explored. The levels of miR-206 and ATGR1 in clinical placenta tissues were investigated. Trophoblasts were treated with TNF-alpha, and the levels of miR-206 and ATGR1 were modulated. Changes in cell viability, invasion, and inflammation in trophoblasts were detected. The level of miR-206 was induced, while the level of AGTR1 was suppressed in placenta tissues. In in vitro assays, TNF-alpha suppressed viability, induced inflammatory response, inhibited invasion, upregulated miR-206, and down-regulated AGTR1. The inhibited expression of miR-206 or the overexpression of AGTR1 counteracted the effects of TNF-alpha, indicating the key role of the miR-206/AGTR1 in progression of PE. Collectively, miR-206 suppressed viability, induced inflammatory response, and decreased invasion of trophoblasts by inhibiting AGTR1.

OsFTL12, a member of FT-like family, modulates the heading date and plant architecture by florigen repression complex in rice

FLOWERING LOCUS T (FT), a florigen in Arabidopsis, plays critical roles in floral transition. Among 13 FT-like members in rice, OsFTL2 (Hd3a) and OsFTL3 (RFT1), two rice homologues of FT, have been well characterized to act as florigens to induce flowering under short-day (SD) and long-day (LD) conditions, respectively, but the functions of other rice FT-like members remain largely unclear. Here, we show that OsFTL12 plays an antagonistic function against Hd3a and RFT1 to modulate the heading date and plant architecture in rice. Unlike Hd3a and RFT1, OsFTL12 is not regulated by daylength and highly expressed in both SD and LD conditions, and delays the heading date under either SD or LD conditions. We further demonstrate that OsFTL12 interacts with GF14b and OsFD1, two key components of the florigen activation complex (FAC), to form the florigen repression complex (FRC) by competing with Hd3a for binding GF14b. Notably, OsFTL12-FRC can bind to the promoters of the floral identity genes OsMADS14 and OsMADS15 and suppress their expression. The osmads14 osmads15 double mutants could not develop panicles and showed erect leaves. Taken together, our results reveal that different FT-like members can fine-tune heading date and plant architecture by regulating the balance of FAC and FRC in rice.

SDG712, a Putative H3K9-Specific Methyltransferase Encoding Gene, Delays Flowering through Repressing the Expression of Florigen Genes in Rice

SET domain group (SDG) proteins have been identified to be involved in histone modification and participate in diverse biological processes. Rice contains 41 SDG genes, however, most of which have not been functionally characterized. Here, we report the identification and functional investigation of rice SDG712 gene. Phylogenic analysis revealed that SDG712 belongs to the H3K9-specific SDG subclade. SDG712 is highly expressed in leaves during reproductive growth stage with obvious circadian rhythmic pattern. Mutation of SDG712 promotes rice flowering, while overexpression of SDG712 delays rice flowering. Gene expression analysis suggested that SDG712 acts downstream of Hd1, while acts upstream of Ehd1, Hd3a and RFT1. Subcellular localization assay demonstrated that SDG712 is localized in the nucleus. Chromatin immunoprecipitation (ChIP) assay showed that the H3K9me2 levels at Hd3a and RFT1 loci were increased in SDG712 overexpression transgenic plants, indicating that SDG712 may mediate the H3K9 di-methylation on these loci to repress rice flowering. Taken together, our findings demonstrated that SDG712 is a negative flowering regulatory gene in rice, and it delays flowering through repressing key flowering regulator gene Ehd1 and the florigen genes Hd3a and RFT1.

TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs

Background

In plants, microRNAs (miRNAs) are pivotal regulators of plant development and stress responses. Different computational tools and web servers have been developed for plant miRNA target prediction; however, in silico prediction normally contains false positive results. In addition, many plant miRNA target prediction servers lack information for miRNA-triggered phased small interfering RNAs (phasiRNAs). Creating a comprehensive and relatively high-confidence plant miRNA target database is much needed.

Results

Here, we report TarDB, an online database that collects three categories of relatively high-confidence plant miRNA targets: (i) cross-species conserved miRNA targets; (ii) degradome/PARE (Parallel Analysis of RNA Ends) sequencing supported miRNA targets; (iii) miRNA-triggered phasiRNA loci. TarDB provides a user-friendly interface that enables users to easily search, browse and retrieve miRNA targets and miRNA initiated phasiRNAs in a broad variety of plants. TarDB has a comprehensive collection of reliable plant miRNA targets containing previously unreported miRNA targets and miRNA-triggered phasiRNAs even in the well-studied model species. Most of these novel miRNA targets are relevant to lineage-specific or species-specific miRNAs. TarDB data is freely available at http://www.biosequencing.cn/TarDB.

Conclusions

In summary, TarDB serves as a useful web resource for exploring relatively high-confidence miRNA targets and miRNA-triggered phasiRNAs in plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07680-5.

PRMdb: A Repository of Predicted RNA Modifications in Plants

Evidence is mounting that RNA modifications play essential roles in posttranscriptional regulation of gene expression. So far, over 150 RNA modifications catalyzed by distinct enzymes have been documented. In plants, genome-wide identification of RNA modifications is largely limited to the model species Arabidopsis thaliana, while lacking in diverse non-model plants. Here, we present PRMdb, a plant RNA modification database, based on the analysis of thousands of RNA-seq, degradome-seq and small RNA-seq data from a wide range of plant species using the well-documented tool HAMR (high-throughput analysis of modified ribonucleotide). PRMdb provides a user-friendly interface that enables easy browsing and searching of the tRNA and mRNA modification data. We show that PRMdb collects high-confidence RNA modifications including novel RNA modification sites that can be validated by genomic PCR and reverse transcription PCR. In summary, PRMdb provides a valuable web resource for deciphering the epitranscriptomes in diverse plant species and will facilitate functional studies of RNA modifications in plants. RPMdb is available via http://www.biosequencing.cn/PRMdb/.

Expression of long non-coding RNA linc-ITGB1 in breast cancer and its influence on prognosis and survival

OBJECTIVE

Long noncoding RNA linc-ITGB1 (linc-ITGB1) was reported to serve as a tumor promoter in breast cancer (BC). However, the clinical significance of linc-ITGB1 has not been reported. The present study aimed to determine the relationship between linc-ITGB1 expression and clinicopathological features and survival.

PATIENTS AND METHODS

qRT-PCR was used to quantify the expression levels of linc-ITGB1 in BC and adjacent non-cancerous breast tissues. The X2 test was performed to determine the associations between linc-ITGB expression and the clinicopathological characters. The overall survival time (OS) and disease-free survival (DFS) were collected by follow-up and analyzed by Kaplan-Meier analysis. Multivariate Cox regression analysis was used to identify the independent risk factors for BC.

RESULTS

The results showed that linc-ITGB1 levels were lower in tumor tissues of BC patients in comparison to adjacent non-cancerous breast tissues (p < 0.001). Linc-ITGB1 expression was significantly associated with lymph node metastasis, pathological differentiation and TNM stage (all p < 0.05). Furthermore, Kaplan-Meier analysis demonstrated that high-linc-ITGB1 expression level was associated with poorer OS (p = 0.006) and DFS (p = 0.003). Cox proportional hazards risk analysis demonstrated that linc-ITGB1 was an independent predictor for both OS (p = 0.004) and DFS (p = 0.002) in BC.

CONCLUSIONS

These results indicated, for the first time, that linc-ITGB1 be a potential biomarker in the prognosis of BC.

Impact of liver fibrosis on prognosis following liver resection for hepatitis B-associated hepatocellular carcinoma

BACKGROUND

This study aims to evaluate the impact of liver fibrosis severity on prognosis following liver resection among HBV-HCC patients.

METHODS

Data were extracted from a prospective database of 189 HBV-HCC patients treated at Mount Sinai between 1995 and 2008. Fibrosis staging of each surgical resection specimen using the modified Ishak method was performed by a single liver pathologist.

RESULTS

A wide range of Ishak fibrosis stage was observed among this patient population, with 29% having established cirrhosis (Ishak stage 6). Ishak stage 6 was independently associated with poor overall and recurrence-free survival. In patients with Ishak stage 1-5, Ishak stage did not affect survival; rather, tumour size was associated with poor overall survival, and tumour size, histologic activity index and serum AFP>20 ng ml(-1) were associated with poor recurrence-free survival. In patients with Ishak stage 6, poorly differentiated histology and tumour size were associated with poor overall survival, and tumour size was associated with poor recurrence-free survival.

CONCLUSION

HBV-HCC develops with varying degrees of underlying liver fibrosis; however, progressive liver fibrosis does not affect the outcomes following resection until cirrhosis is reached. Established cirrhosis, as defined histologically by Ishak stage 6, is an independent predictor of poor overall and recurrence-free survival among these patients.

OsCD1 encodes a putative member of the cellulose synthase-like D sub-family and is essential for rice plant architecture and growth

The cell wall plays important roles in plant architecture and morphogenesis. The cellulose synthase-like super-families were reported to contain glycosyltransferases motif and are required for the biosynthesis of cell wall polysaccharides. Here, we describe a curled leaf and dwarf mutant, cd1, in rice, which exhibits multiple phenotypic traits such as the reduction of plant height and leaf width, curled leaf morphology and a decrease in the number of grains and in the panicle length. Map-based cloning indicates that a member of the cellulose synthase-like D (CSLD) group is a candidate for OsCD1. RNAi transgenic plants with the candidate CSLD gene display a similar phenotype to the cd1 mutant, suggesting that OsCD1 is a member of the CSLD sub-family. Furthermore, sequence analysis indicates that OsCD1 contains the common D,D,D,QXXRW motif, which is a feature of the cellulose synthase-like super-family. Analysis of OsCD1 promoter with GUS fusion expression shows that OsCD1 exhibits higher expression in young meristem tissues such as fresh roots, young panicle and stem apical meristem. Cell wall composition analysis reveals that cellulose content and the level of xylose are significantly reduced in mature culm owing to loss of OsCD1 function. Take together, the work presented here is useful for expanding the understanding of cell wall biosynthesis.

Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice

Tiller number is highly regulated by controlling the formation of tiller bud and its subsequent outgrowth in response to endogenous and environmental signals. Here, we identified a rice mutant htd2 from one of the 15,000 transgenic rice lines, which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not affect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud. To isolate the htd2 gene, a map-based cloning strategy was employed and 17 new insertions-deletions (InDels) markers were developed. A high-resolution physical map of the chromosomal region around the htd2 gene was made using the F(2) and F(3) population. Finally, the gene was mapped in 12.8 kb region between marker HT41 and marker HT52 within the BAC clone OSJNBa0009J13. Cloning and sequencing of the target region from the mutant showed that the T-DNA insertion caused a 463 bp deletion between the promoter and first exon of an esterase/lipase/thioesterase family gene in the 12.8 kb region. Furthermore, transgenic rice with reduced expression level of the gene exhibited an enhanced tillering and dwarf phenotype. Accordingly, the esterase/lipase/thioesterase family gene (TIGR locus Os03g10620) was identified as the HTD2 gene. HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a significantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway. The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway.

The effect of the crosstalk between photoperiod and temperature on the heading-date in rice

Photoperiod and temperature are two important environmental factors that influence the heading-date of rice. Although the influence of the photoperiod on heading has been extensively reported in rice, the molecular mechanism for the temperature control of heading remains unknown. This study reports an early heading mutant derived from tissue culture lines of rice and investigates the heading-date of wild type and mutant in different photoperiod and temperature treatments. The linkage analysis showed that the mutant phenotype cosegregated with the Hd1 locus. Sequencing analysis found that the mutant contained two insertions and several single-base substitutions that caused a dramatic reduction in Hd1mRNA levels compared with wild type. The expression patterns of Hd1 and Hd3a were also analyzed in different photoperiod and temperature conditions, revealing that Hd1 mRNA levels displayed similar expression patterns for different photoperiod and temperature treatments, with high expression levels at night and reduced levels in the daytime. In addition, Hd1 displayed a slightly higher expression level under long-day and low temperature conditions. Hd3a mRNA was present at a very low level under low temperature conditions regardless of the day-length. This result suggests that suppression of Hd3a expression is a principle cause of late heading under low temperature and long-day conditions.

Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China

The Chinese genebank contains 23,587 soybean landraces collected from 29 provinces. In this study, a representative collection of 1,863 landraces were assessed for genetic diversity and genetic differentiation in order to provide useful information for effective management and utilization. A total of 1,160 SSR alleles at 59 SSR loci were detected including 97 unique and 485 low-frequency alleles, which indicated great richness and uniqueness of genetic variation in this core collection. Seven clusters were inferred by STRUCTURE analysis, which is in good agreement with a neighbor-joining tree. The cluster subdivision was also supported by highly significant pairwise Fst values and was generally in accordance with differences in planting area and sowing season. The cluster HSuM, which contains accessions collected from the region between 32.0 and 40.5 degrees N, 105.4 and 122.2 degrees E along the central and downstream parts of the Yellow River, was the most genetically diverse of the seven clusters. This provides the first molecular evidence for the hypotheses that the origin of cultivated soybean is the Yellow River region. A high proportion (95.1%) of pairs of alleles from different loci was in LD in the complete dataset. This was mostly due to overall population structure, since the number of locus pairs in LD was reduced sharply within each of the clusters compared to the complete dataset. This shows that population structure needs to be accounted for in association studies conducted within this collection. The low value of LD within the clusters can be seen as evidence that much of the recombination events in the past have been maintained in soybean, fixed in homozygous self-fertilizing landraces.

Association of asymptomatic oral candidal carriage, oral candidiasis and CD4+ lymphocyte count in HIV-positive patients in China

OBJECTIVES

To compare the prevalence of asymptomatic oral candidal carriage in healthy volunteers with human immunodeficiency virus (HIV)-positive patients in China, as well as to investigate the relationship between CD4+ lymphocyte count and oral candidal colonization or oral candidiasis.

METHODS

Oral candidal carriage and oral candidiasis were investigated in 101 patients with HIV-infection seen at Youan Hospital, Beijing, China. Two hundred and seventeen healthy volunteers were involved as a control. Culture from saliva was used to test for the presence of oral Candida. CD4+ lymphocyte count was measured by flow cytometry. All data were analyzed statistically by SAS.

RESULTS

Asymptomatic oral candidal carriage rate (28.6%) in HIV-positive group was similar to that in the healthy group (18.0%; P = 0.07). No significant difference in CD4+ lymphocyte count was found between oral Candida carriers and non-carriers among HIV-positive subjects (P = 0.89). However, the frequency of oral candidiasis increased with the decrease in CD4+ lymphocyte count (P < 0.0001), and pseudomembranous candidiasis was predominant in HIV-positive patients with CD4+ <200 cells microl(-1) (66.7%).

CONCLUSIONS

In HIV-positive subjects, asymptomatic oral candidal colonization is not related to CD4+ lymphocyte count of blood, and the carriage rate is similar to that in the healthy population. Oral candidiasis is more likely to be observed in HIV-positive patients who have a low CD4+ lymphocyte count.

[Representativeness of Northeast China spring soybeans and their genetic diversity at SSR loci]

A total of 283 accessions were selected from the total 3 226 Northeast China spring soybeans, which represented > 80% of the whole based on their qualitative and quantitative traits. The representative samples were analyzed by 61 SSR loci, and a total of 534 alleles were detected, ranging 2 - 16 alleles per locus, with an average of 8.75 alleles per locus. Among the accessions, the Simpson diversity index (SDI) for each locus ranged from 0.406 to 0.886, with a mean of 0.704, which was relatively lower since there were dominant alleles at most of loci in the representative samples. 35 accessions had specific alleles, which distributed among 29 loci. The differentiation coefficient was lower than 9.27% in 61 loci among the three provinces of Northeast China, which might be caused by lots of common alleles shared among these provinces. The genetic diversity in Jilin and Liaoning provinces was nearly equal, but was higher than that in Heilongjiang Province. The landraces of the representative samples at 61 loci had a higher genetic diversity than that of the released cultivars. The genetic diversity appeared within and between the provinces could be used to broaden the genetic base of modern cultivars, and also, the landraces were the major source for soybean breeding because of their high genetic diversity.

Cigarette smoking, salivary/gingival crevicular fluid cotinine and periodontal status. A 10-year longitudinal study

BACKGROUND, AIMS

The primary purpose of this study was to determine the association of salivary and gingival crevicular fluid (GCF) cotinine levels with periodontal disease status in smokers and non-smokers.

METHODS

147 male smokers and 30 male non-smokers were included in the current longitudinal study. The 177 individuals were part of a group of 200 subjects (89%) seen 10 years previously for a baseline survey. Oral hygiene indices, probing depth and attachment loss were recorded. Salivary and GCF cotinine levels of 58 smokers were determined by means of ELISA.

RESULTS

Results indicated that no significant difference was found in subjects who smoked, when compared to subjects who did not smoke with respect to plaque accumulation and calculus deposits. Smokers, however, had fewer gingival bleeding sites. Cigarette smoking was associated with a greater increase in probing depth and attachment loss, as well as greater tooth loss at an earlier age. There was greater tooth loss in smokers than non-smokers (p < 0.001). 11 smokers became edentulous, while only 1 non-smoker lost all his teeth within 10 years. The degree of periodontal tissue breakdown was different in each age group with greater periodontal deterioration as age increased. All smokers had detectable salivary and GCF cotinine. Mean GCF cotinine was about 4x higher than mean salivary cotinine levels. Individuals who smoked > or = 20 pack years when compared to <20 pack years, had significantly higher saliva and GCF cotinine levels (p < or = 0.05).

CONCLUSION

Neither salivary cotinine nor GCF cotinine was significantly correlated with probing depth, attachment loss and tooth loss (p > 0.05).

Ten-year incidence of dental caries in adult and elderly Chinese

Only very few longitudinal studies on dental caries are available in adults and elderly. Therefore, the aim of the present study was to describe the patterns of lesion progression in a group of adult and elderly Chinese followed over a 10-year period of time. In 1984, 587 persons aged 20-80 years were examined and by 1994, 440 of these were still available and re-examined by the same two examiners. All restorations, periodontal conditions and dental caries were recorded for all teeth and surfaces. Only caries data are reported here. Dental caries on coronal surfaces was classified as sound, non-cavitated, cavitated without or with pulp involvement or filled. On root surfaces, lesions were classified as sound, active caries or restored. Prior to analysis of the data, a series of drop-out analyses was carried out showing that most of the drop-outs were above 60 years of age at baseline, and death of participants was the major drop-out reason. A total of 2,114 teeth were lost, 36% of which had a deep dentin lesion at baseline. The distribution of persons according to number of new lesions/restorations over 10 years was highly skewed in all age groups, the prevalence increasing with age. Molars had the highest risk of becoming carious/restored over the 10-year period, and a remarkably low proportion of teeth had the same caries diagnosis after 10 years, indicative of lesion progression. When comparing the 1984 DFT/DMFT with the figures for 1994, there were no statistically significant differences indicating that the period and cohort effects cancel out each other. There was a significant increase with age of the number of new DFT. It can be concluded that dental caries is a major health problem in contemporary adult and elderly Chinese populations, and that caries incidence increases with old age.

[A socioepidemiological survey of the oral health status and needs for dental care among elderly population in China]

The purpose of this surrey is to study the prevalence of dental disease and the needs of dental treatment, so as to develop effective programs in improving dental care in the elderly, 475 residents are selected by means of a systematic stratified sampling procedure. The aged people have poor dental health knowledge and habits. Major problems for getting their dental care include: 1. difficult to get registration; 2. long time waiting before seeing a dentist; 3. the actual needs for dental treatment are more than what expected by the elderly themselves. The study reveals that many problems are existed in terms of oral health status and dental care among the elderly, which calls for more attention.

In vivo hydrogen-1 magnetic resonance spectroscopy study of human intracranial tumors

OBJECTIVE

To investigate the metabolic changes, pathological state and histological types of intracranial tumors with hydrogen-1 magnetic resonance spectroscopy (H-1 MRS).

METHODS

Thirteen patients with intracranial tumors were studied with localized proton magnetic resonance spectroscopy (H-1MRS), in vivo. All spectra were obtained with a 2.0 T whole body MR imaging system.

RESULTS

All the spectra of these tumors exhibited high ratios of choline (Cho)/creatine (Cr) and Cho/N-acetyl aspartate (NAA), and histologically different tumors showed obvious variations in the metabolite ratios. Significant differences of Cho/Cr ratio were found between meningiomas and astrocytomas by statistical evaluation. The spectra obtained after operation were remarkably different from those before operation.

CONCLUSION

H-1 MRS can serve as a non-invasive clinical test for therapeutic and prognostic uses for intracranial tumors.