Comprehensive Analyses of Four PhNF-YC Genes from Petunia hybrida and Impacts on Flowering Time

Nuclear Factor Y (NF-Y) is a class of heterotrimeric transcription factors composed of three subunits: NF-A, NF-YB, and NF-YC. NF-YC family members play crucial roles in various developmental processes, particularly in the regulation of flowering time. However, their functions in petunia remain poorly understood. In this study, we isolated four PhNF-YC genes from petunia and confirmed their subcellular localization in both the nucleus and cytoplasm. We analyzed the transcript abundance of all four PhNF-YC genes and found that PhNF-YC2 and PhNF-YC4 were highly expressed in apical buds and leaves, with their transcript levels decreasing before flower bud differentiation. Silencing PhNF-YC2 using VIGS resulted in a delayed flowering time and reduced chlorophyll content, while PhNF-YC4-silenced plants only exhibited a delayed flowering time. Furthermore, we detected the transcript abundance of flowering-related genes involved in different signaling pathways and found that PhCO, PhGI, PhFBP21, PhGA20ox4, and PhSPL9b were regulated by both PhNF-YC2 and PhNF-YC4. Additionally, the transcript abundance of PhSPL2, PhSPL3, and PhSPL4 increased only in PhNF-YC2-silenced plants. Overall, these results provide evidence that PhNF-YC2 and PhNF-YC4 negatively regulate flowering time in petunia by modulating a series of flowering-related genes.

Genome-Wide Characterization of Chrysanthemum indicum Nuclear Factor Y, Subunit C Gene Family Reveals the Roles of CiNF-YCs in Flowering Regulation

Nuclear Factor Y, Subunit C (NF-YC) transcription factors are conserved in most plants, and play essential roles in plant growth and development, especially in flowering regulation. Chrysanthemums are important commercial plants, and their market value is strongly impacted by flowering time. Until now, no details regarding the NF-YC family in the Chrysanthemum genus have been available. In this study, five NF-YC genes were cloned from Chrysanthemum indicum. Multiple alignments showed that CiNF-YCs had the highly conserved characteristic regions. Phylogenetic analyses identified a pair of paralogue NF-YC proteins in chrysanthemums. Gene structure and conserved motifs were also analyzed for functional understanding. According to the results of the expression experiments, CiNF-YC1 and CiNF-YC5 were mainly expressed in leaves or flowers, and their expression levels varied greatly from the seedling to flower bud differentiation stage. Arabidopsis overexpressing CiNF-YC1 and CiNF-YC3 showed significantly delayed flowering, accompanied by other morphological alterations. RT-qPCR analysis revealed that genes associated with photoperiod, vernalization, aging, and gibberellin pathways were downregulated in CiNF-YC1-OX lines, relative to the wild type, whereas in CiNF-YC3-OX lines, only SHORT VEGETATIVE PHASE (AtSVP), the key factor in the ambient temperature pathway, was upregulated. Taken together, these findings suggest that CiNF-YC1 and CiNF-YC3 negatively regulate flowering in Arabidopsis via different flowering pathways.

Insights into the trihelix transcription factor responses to salt and other stresses in Osmanthus fragrans

BACKGROUND

Osmanthus fragrans is an evergreen plant with high ornamental and economic values. However, they are easily injured by salt stress, which severely limits their use in high salinity areas. The trihelix transcription factor (TF) family, as one of the earliest discovered TF families in plants, plays an essential part in responses to different abiotic stresses, and it has potential functions in improving the salt-tolerance capability of O. fragrans.

RESULTS

In this study, 56 trihelix genes (OfGTs) were first identified in O. fragrans and then divided into five subfamilies in accordance with a phylogenetic tree analysis. The OfGTs were found to be located randomly on the 20 O. fragrans chromosomes, and an analysis of gene replication events indicated that the OfGT gene family underwent strong purification selection during the evolutionary process. The analysis of conserved motifs and gene structures implied that the OfGT members in the same subfamily have similar conserved motifs and gene structures. A promoter cis-elements analysis showed that all the OfGT genes contained multiple abiotic and hormonal stress-related cis-elements. The RNA-seq data suggested that the OfGTs have specific expression patterns in different tissues, and some were induced by salt stress. The qRT-PCR analysis of 12 selected OfGTs confirmed that OfGT1/3/21/33/42/45/46/52 were induced, with OfGT3/42/46 being the most highly expressed. In addition, OfGT42/OfGT46 had a co-expression pattern under salt-stress conditions. OfGT3/42/46 were mainly localized in the nuclei and exhibited no transcriptional activities based on the analysis of the subcellular localization and transcriptional activity assay. Furthermore, the expression levels of most of the selected OfGTs were induced by multiple abiotic and hormonal stresses, and the expression patterns of some OfGTs were also highly correlated with gibberellic acid and methyl jasmonate levels. Remarkably, the transient transformation results showed lower MDA content and increased expression of ROS-related genes NbAPX in transgenic plants, which implying OfGT3/42/46 may improve the salt tolerance of tobacco.

CONCLUSIONS

The results implied that the OfGT genes were related to abiotic and hormonal stress responses in O. fragrans, and that the OfGT3/42/46 genes in particular might play crucial roles in responses to salt stress. This study made a comprehensive summary of the OfGT gene family, including functions and co-expression patterns in response to salt and other stresses, as well as an evolutionary perspective. Consequently, it lays a foundation for further functional characterizations of these genes.

Gene expression profiles for a prognostic immunoscore in gastric cancer

Background

Increasing evidence has indicated an association between immune infiltration in gastric cancer and clinical outcome. However, reliable prognostic signatures, based on systematic assessments of the immune landscape inferred from bulk tumour transcriptomes, have not been established. The aim was to develop an immune signature, based on the cellular composition of the immune infiltrate inferred from bulk tumour transcriptomes, to improve the prognostic predictions of gastric cancer.

Methods

Twenty‐two types of immune cell fraction were estimated based on large public gastric cancer cohorts from the Gene Expression Omnibus using CIBERSORT. An immunoscore based on the fraction of immune cell types was then constructed using a least absolute shrinkage and selection operator (LASSO) Cox regression model.

Results

Using the LASSO model, an immunoscore was established consisting of 11 types of immune cell fraction. In the training cohort (490 patients), significant differences were found between high‐ and low‐immunoscore groups in overall survival across and within subpopulations with an identical TNM stage. Multivariable analysis revealed that the immunoscore was an independent prognostic factor (hazard ratio 1·92, 95 per cent c.i. 1·54 to 2·40). The prognostic value of the immunoscore was also confirmed in the validation (210) and entire (700) cohorts.

Conclusion

The proposed immunoscore represents a promising signature for estimating overall survival in patients with gastric cancer.

Immunoscore predicts prognosis

Lung cancer in systemic lupus erythematosus

BACKGROUND

Evidence points to a link between systemic lupus erythematosus (SLE) and an increased risk of lung cancer. Our objective was to provide a brief report of the lung cancer cases from an SLE cohort, with respect to demographics, histology, and exposures to smoking and immunosuppressive medications.

METHODS

Data were obtained from a multi-site international cohort study of over 9500 SLE patients from 23 centres. Cancer cases were ascertained through linkage with regional tumor registries.

RESULTS

We analyzed information on histology subtype for 30 lung cancer cases that had occurred across five countries. Most (75%) of these 30 cases were female, with a median age of 61 (range 27-91) years. In eight cases, the histological type was not specified. In the remainder, the most common histological type reported was adenocarcinoma (N=8; two of the adenocarcinomas were bronchoalveolar carcinoma) followed by small cell carcinoma (N=6), and squamous cell carcinoma (N=6) with one case each of large cell carcinoma and carcinoid tumor. Most (71%) of the lung cancer cases were smokers; only the minority (20%) had been previously exposed to immunosuppressive agents.

CONCLUSIONS

The histological distribution of the lung cancers from the SLE sample appeared similar to that of lung cancer patients in the general population, though the possibility of a higher proportion of more uncommon tumors (such as bronchoalveolar and carcinoid) cannot be excluded. A large proportion of the cancer cases were smokers, which is also not surprising. However, only a minority appeared to have been exposed to immunosuppressive agents. A large case-cohort study currently in progress should help shed light on the relative importance of these exposures in lung cancer risk for SLE patients.

Clinical pathways--can they be used in trauma care. An analysis of their ability to fit the patient

This study prospectively evaluated the appropriateness and ability of clinical pathways to fit trauma patients in five key conditions, severe head injury, fractured ribs, fractured pelvis, fractured femur and blunt abdominal trauma, who were admitted to a single Level 1 Trauma Centre, between February and July 1999. Each pathway consisted of 14 elements of care divided into observable outcomes. Failure to achieve an outcome resulted in a variance or deviation from the pathway, which was assessed by the number of non-applicable variances. Appropriateness of clinical pathways was assessed by the applicability index (the number of non-applicable variances divided by the potential variances). Critical mismatches occurred when non-applicable variances exceeded 50% of potential variances. 146 patients, with the mean age 41.9 years (S.D. 20.7), mean ISS 11.1 (S.D. 10.7) were enrolled; 18 with severe head injury, 59 with fractured ribs, 13 with fractured pelvis, 20 with fractured femur and 36 with blunt abdominal trauma. Critical mismatch occurred in seven patients. Applicability indexes were 87 for head, 93 for ribs, 92 for blunt abdominal trauma, 91 for femur and 92 for the pelvic pathway. Patient assessment, pain management, skin integrity and patient education were the most appropriate key elements of care, discharge planning, patient satisfaction, treatment and activity were least applicable. This study identified, for the first time, that clinical pathways are clinically appropriate for major trauma conditions.

[Assessment of the effects of dipyridamole and dobutamine on coronary microcirculation using myocardial contrast echocardiography]

OBJECTIVES

To evaluate the effects of dipyridamole and dobutamine on myocardial blood flow (MBF) and myocardial blood volume (MBV), and their ability to detect non-flow-limiting coronary stenoses with myocardial contrast echocardiography (MCE).

METHODS

Thirteen closed-chest dogs were studied at 7-10 days after placement of ameroid constrictors around proximal coronary arteries and their branches. MBF was measured with radiolabeled microspheres and myocardial plateau video intensity (VI, which indicates relative MBV) and microbubble velocity (beta) were measured with MCE at rest, after dipyridamole (0.56 mg/kg), and during peak dobutamine dose (30-40 micrograms.kg-1.min-1).

RESULTS

The effects of both agents on MBF were similar in abnormal and normal segments. Plateau VI increased more and beta increased less with dobutamine than dipyridamole (P < 0.05), but the plateau VI ratios and beta ratios between abnormal and normal segments were almost identical during both drugs (P < NS), resulting in similar perfusion defects. Excellent linear relations were found between the plateau VI ratio or beta ratio and MBF (derived from radiolabeled microspheres) ratio from abnormal and normal beds during dipyridamole and dobutamine.

CONCLUSION

Although the effect of dipyridamole and dobutamine on MBV is different, they unmask MBF reserve to a similar extent. Thus, the quantification of stenosis severity is identical using both agents with MCE.

Potential advantage of flash echocardiography for digital subtraction of B-mode images acquired during myocardial contrast echocardiography

Optimal assessment of myocardial perfusion with contrast echocardiography by using B-mode imaging often requires image alignment and background subtraction, which are time consuming and need extensive expertise. Flash echocardiography is a new technique in which primary images are gated to the electrocardiogram and secondary images are obtained by transmitting ultrasound pulses in rapid succession after each primary image. Myocardial opacification is seen in the primary image and not in the secondary images because of ultrasound-induced bubble destruction. Because the interval between the primary and first few secondary images is very short, cardiac motion between these images should be minimal. Therefore we hypothesized that 1 or more secondary images could be subtracted from the primary image without the need for image alignment. The ability of ultrasound to destroy microbubbles was assessed by varying the sampling rate, line density, and mechanical index in 6 open-chest dogs. The degree of translation between images was quantified in the x and y directions with the use of computer cross-correlation. At sampling rates of 158 Hz or less and a mechanical index of more than 0.6, videointensity rapidly declined to baseline levels by 25 ms. Significant translation between images was noted only at intervals of more than 112 ms. It is concluded that flash echocardiography can be used for digital subtraction of baseline from contrast-enhanced B-mode images without image alignment. Background subtraction is therefore feasible on-line, potentially eliminating the need for off-line image processing in the future.