Mapping and Candidate Gene Analysis of the Low-Temperature-Sensitive Albino Gene OsLTSA8 in Rice Seedlings.

Chloroplasts are organelles responsible for photosynthesis in plants, providing energy for growth and development. However, the genetic regulatory mechanisms underlying early chloroplast development in rice remain incompletely understood. In this study, we identified a rice seedling thermosensitive chlorophyll-deficient mutant, osltsa8, and the genetic analysis of two F2 populations suggested that this trait may be controlled by more than one pair of alleles. Through reciprocal F2 populations and QTL-seq technology, OsLTSA8 was mapped to the interval of 24,280,402-25,920,942 bp on rice chromosome 8, representing a novel albino gene in rice. Within the candidate gene region of OsLTSA8, there were 258 predicted genes, among which LOC_Os08g39050, LOC_Os08g39130, and LOC_Os08g40870 encode pentatricopeptide repeat (PPR) proteins. RNA-seq identified 18 DEGs (differentially expressed genes) within the candidate interval, with LOC_Os08g39420 showing homology to the pigment biosynthesis-related genes Zm00001d017656 and Sb01g000470; LOC_Os08g39430 and LOC_Os08g39850 were implicated in chlorophyll precursor synthesis. RT-qPCR was employed to assess the expression levels of LOC_Os08g39050, LOC_Os08g39130, LOC_Os08g40870, LOC_Os08g39420, LOC_Os08g39430, and LOC_Os08g39850 in the wild-type and mutant plants. Among them, the differences in the expression levels of LOC_Os08g39050 and LOC_Os08g39430 were the most significant. This study will contribute to further elucidating the molecular mechanisms of rice chloroplast development.

Comparisons of clinical characteristics, treatments, and outcomes among different pathological subtypes of chondrosarcoma in the spine.

INTRODUCTION: Spinal chondrosarcoma exhibits higher invasiveness and a worse prognosis compared to chondrosarcoma in the extremities. The prognosis and therapeutic plan vary greatly among different pathological subtypes of chondrosarcoma. This study aimed to analyze the differences in clinical characteristics, molecular features, therapeutic effects, and prognostic factors among the subtypes of chondrosarcoma in the spine. METHODS: A retrospective review was conducted on 205 patients with spinal chondrosarcoma. The clinical features and immunohistochemical (IHC) markers were compared among the pathological subtypes of chondrosarcoma grade 1, grade 2, grade 3, mesenchymal chondrosarcoma (MCS), dedifferentiated chondrosarcoma (DCS), and clear cell chondrosarcoma (CCCS). Chondrosarcoma grade 1/2/3 are collectively referred to as conventional chondrosarcoma (CCS) for multivariate survival analysis. Univariate and multivariate analyses were performed to investigate independent prognostic factors for overall survival (OS) and recurrence-free survival (RFS) in patients with spinal chondrosarcoma. Furthermore, independent prognostic factors for OS and RFS were identified in CCS and MCS. RESULTS: MCS patients were younger than the other subtypes. Patients with chondrosarcoma grade 1/2 had better OS than those with chondrosarcoma grade 3, MCS and DCS, while only chondrosarcoma grade 1 patients showed better RFS than chondrosarcoma grade 2/3, MCS and DCS patients. Ki-67 index was higher in chondrosarcoma grade 3, MCS and DCS than chondrosarcoma grade 1/2. The comparison of IHC markers further highlighted the overexpression of P53/MDM2 in MCS and DCS. Gross total resection, including en-bloc and piecemeal resection, significantly improved OS and RFS for CCS patients, while only en-bloc resection significantly improved the prognosis of MCS patients. Chemotherapy appeared to be important for the OS of MCS patients. CONCLUSION: P53/MDM2 pathway was upregulated in MCS and DCS compared to chondrosarcoma grade 1/2. Radical tumor resection is crucial for the treatment of spinal chondrosarcoma, while MCS patients require further comprehensive treatments perioperatively.

Efficacy and safety of laminoplasty combined with C3 laminectomy for patients with multilevel degenerative cervical myelopathy: a systematic review and meta-analysis.

PURPOSE: Laminoplasty (LP) combined with C3 laminectomy (LN) can effectively achieve spinal cord decompression while maintaining the integrity of the posterior ligament-muscle complex, thereby minimizing cervical muscle damage. However, its necessity and safety remain controversial. This study aimed to compare the safety and efficacy of LP and LP combined with C3 LN in the treatment of patients with multilevel degenerative cervical spondylotic myelopathy (DCM). METHODS: A systematic review and meta-analysis of the literature was performed. A search of PubMed, Web of Science, Embase, and the Cochrane Library databases was conducted from inception through December 2023 and updated in February 2024. Search terms included laminoplasty, laminectomy, C3 and degenerative cervical spondylosis. The literature search yielded 14 studies that met our inclusion criteria. Outcomes included radiographic results, neck pain, neurologic function, surgical parameters, and postoperative complications. We also assessed methodologic quality, publication bias, and quality of evidence. RESULTS: Fourteen studies were identified, including 590 patients who underwent LP combined with C3 LN (modified group, MG) compared to 669 patients who underwent LP (traditional group, TG). The results of the study indicated a statistically significant improvement in cervical range of motion (WMD = 3.62, 95% CI: 0.39 to 6.85) and cervical sagittal angle (WMD = 2.07, 95% CI: 0.40 to 3.74) in the MG compared to the TG at the last follow-up (very low-level evidence). The TG had a higher number of patients with complications, especially C2-3 bone fusion. There was no significant difference found in improvement of neck pain, JOA, NDI, cSVA, T1 slope at latest follow-up. CONCLUSION: LP combined with C3 LN is an effective and necessary surgical method for multilevel DCM patients to maintain cervical sagittal balance. However, due to the low quality of evidence in existing studies, more and higher quality research on the technology is needed in the future.

Molecular basis of genetic improvement for key rice quality traits in Southern China.

Grain qualities including milling quality, appearance quality, eating and cooking quality, and nutritional quality are important indicators in rice breeding. Significant achievements in genetic improvement of rice quality have been made. In this study, we analyzed the variation patterns of 16 traits in 1570 rice varieties and found significant improvements in appearance quality and eating and cooking quality, particularly in hybrid rice. Through genome-wide association study and allelic functional nucleotide polymorphisms analysis of quality trait genes, we found that ALK, FGR1, FLO7, GL7/GW7, GLW7, GS2, GS3, ONAC129, OsGRF8, POW1, WCR1, and Wx were associated with the genetic improvement of rice quality traits in Southern China. Allelic functional nucleotide polymorphisms analysis of 13 important rice quality genes, including fragrance gene fgr, were performed using the polymerase chain reaction amplification refractory mutation system technology. The results showed that Gui516, Gui569, Gui721, Ryousi, Rsimiao, Rbasi, and Yuehui9802 possessed multiple superior alleles. This study elucidates the phenotypic changes and molecular basis of key quality traits of varieties in Southern China. The findings will provide guidance for genetic improvement of rice quality and the development of new varieties.

Metabolome and Transcriptome Unveil the Correlated Metabolites and Transcripts with 2-acetyl-1-pyrroline in Fragrant Rice.

Fragrance is a valuable trait in rice varieties, with its aroma significantly influencing consumer preference. In this study, we conducted comprehensive metabolome and transcriptome analyses to elucidate the genetic and biochemical basis of fragrance in the Shangsixiangnuo (SSXN) variety, a fragrant indica rice cultivated in Guangxi, China. Through sensory evaluation and genetic analysis, we confirmed SSXN as strongly fragrant, with an 806 bp deletion in the BADH2 gene associated with fragrance production. In the metabolome analysis, a total of 238, 233, 105 and 60 metabolic compounds exhibited significant changes at the seedling (S), reproductive (R), filling (F), and maturation (M) stages, respectively. We identified four compounds that exhibited significant changes in SSXN across all four development stages. Our analyses revealed a significant upregulation of 2-acetyl-1-pyrroline (2AP), the well-studied aromatic compound, in SSXN compared to the non-fragrant variety. Additionally, correlation analysis identified several metabolites strongly associated with 2AP, including ethanone, 1-(1H-pyrrol-2-yl)-, 1H-pyrrole, and pyrrole. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) analysis highlighted the magenta and yellow modules as particularly enriched in aroma-related metabolites, providing insights into the complex aromatic compounds underlying the fragrance of rice. In the transcriptome analysis, a total of 5582, 5506, 4965, and 4599 differential expressed genes (DEGs) were identified across the four developmental stages, with a notable enrichment of the common pathway amino sugar and nucleotide sugar metabolism in all stages. In our correlation analysis between metabolome and transcriptome data, the top three connected metabolites, phenol-, 3-amino-, and 2AP, along with ethanone, 1-(1H-pyrrol-2-yl)-, exhibited strong associations with transcripts, highlighting their potential roles in fragrance biosynthesis. Additionally, the downregulated expression of the P4H4 gene, encoding a procollagen-proline dioxygenase that specifically targets proline, in SSXN suggests its involvement in proline metabolism and potentially in aroma formation pathways. Overall, our study provides comprehensive insights into the genetic and biochemical mechanisms underlying fragrance production in rice, laying the foundation for further research aimed at enhancing fragrance quality in rice breeding programs.

Utilization of natural alleles for heat adaptability QTLs at the flowering stage in rice.

BACKGROUND: Heat stress threatens rice yield and quality at flowering stage. In this study, average relative seed setting rate under heat stress (RHSR) and genotypes of 284 varieties were used for a genome-wide association study. RESULTS: We identified eight and six QTLs distributed on chromosomes 1, 3, 4, 5, 7 and 12 in the full population and indica, respectively. qHTT4.2 was detected in both the full population and indica as an overlapping QTL. RHSR was positively correlated with the accumulation of heat-tolerant superior alleles (SA), and indica accession contained at least two heat-tolerant SA with average RHSR greater than 43%, meeting the needs of stable production and heat-tolerant QTLs were offer yield basic for chalkiness degree, amylose content, gel consistency and gelatinization temperature. Chalkiness degree, amylose content, and gelatinization temperature under heat stress increased with accumulation of heat-tolerant SA. Gel consistency under heat stress decreased with polymerization of heat-tolerant SA. The study revealed qHTT4.2 as a stable heat-tolerant QTL that can be used for breeding that was detected in the full population and indica. And the grain quality of qHTT4.2-haplotype1 (Hap1) with chalk5, wx, and alk was better than that of qHTT4.2-Hap1 with CHALK5, WX, and ALK. Twelve putative candidate genes were identified for qHTT4.2 that enhance RHSR based on gene expression data and these genes were validated in two groups. Candidate genes LOC_Os04g52830 and LOC_Os04g52870 were induced by high temperature. CONCLUSIONS: Our findings identify strong heat-tolerant cultivars and heat-tolerant QTLs with great potential value to improve rice tolerance to heat stress, and suggest a strategy for the breeding of yield-balance-quality heat-tolerant crop varieties.

Structural ordering governs stiffness and ductile-to-brittle transition in Al-Li alloys.

The trade-off of stiffness and ductility of metals has long plagued materials scientists. To address this issue, atomic structure designs of short-range ordering (SRO) to sub-nanometer and nanometer scales have received much interest in tailoring the atomic environment and electronic interaction between solute and solvent atoms. Taking an example of Al-Li alloy with high specific stiffness and reverse correlation of Young's modulus and melting point, in this work, we investigate the SRO-dependent stiffness and intrinsic ductile-brittle properties by performing a full-configuration strategy containing various structural ordering features. It suggests that the short-range ordered arrangement of Li atoms can effectively enhance the stiffness while keeping ductility, playing a hydrostatic pressure-like role. Our findings present fundamental knowledge to enable high stiffness and ductility for solvent phases with low modulus through designing local short-range ordered cluster structures.

An improved total en bloc spondylectomy for L5 vertebral giant cell tumor through a single-stage posterior approach.

PURPOSE: Although total en bloc spondylectomy (TES) is strongly recommended for spinal giant cell tumor (GCT), it is extremely difficult to excise a L5 neoplasm intactly through the single-stage posterior approach. Given the risk of neurological and vascular injury, intralesional curettage (IC) is usually recommended for the treatment of L5 GCT. In this study, we presented our experience with the use of an improved TES to treat L5 GCT through the single-stage posterior approach. METHODS: This study included 20 patients with L5 GCT who received surgical treatment in our department between September 2010 and April 2021. Of them, seven patients received improved TES without iliac osteotomy, and the other 13 patients received IC (n = 8), sagittal en bloc resection (n = 1), TES with iliac osteotomy (n = 3), and TES with radicotomy (n = 1) as control. RESULTS: The mean operative time was 331.43 ± 92.95 min for improved TES group and 365.77 ± 85.17 min for the control group (p = 0.415), with the mean blood loss of 1142.86 ± 340.87 ml vs. 1969.23 ± 563.30 ml (p = 0.002). Postoperative treatment included bisphosphonates in nine patients and denosumab in 12 patients including one patient who changed from bisphosphonates to denosumab. Three patients who received IC experienced local recurrence, and no relapse was observed in improved TES group. CONCLUSION: Single-stage posterior TES for L5 GCT was previously considered impossible. In this study, we presented our experience with the use of an improved surgical technique for L5 TES through the single-stage posterior approach, which has proved to be superior to the conventional procedures in terms of blood loss control and complication and recurrence rates. LEVEL OF EVIDENCE: IV.

OsTTG1, a WD40 repeat gene, regulates anthocyanin biosynthesis in rice.

Anthocyanins play an important role in the growth of plants, and are beneficial to human health. In plants, the MYB-bHLH-WD40 (MBW) complex activates the genes for anthocyanin biosynthesis. However, in rice, the WD40 regulators remain to be conclusively identified. Here, a crucial anthocyanin biosynthesis gene was fine mapped to a 43.4-kb genomic region on chromosome 2, and a WD40 gene OsTTG1 (Oryza sativa TRANSPARENT TESTA GLABRA1) was identified as ideal candidate gene. Subsequently, a homozygous mutant (osttg1) generated by CRISPR/Cas9 showed significantly decreased anthocyanin accumulation in various rice organs. OsTTG1 was highly expressed in various rice tissues after germination, and it was affected by light and temperature. OsTTG1 protein was localized to the nucleus, and can physically interact with Kala4, OsC1, OsDFR and Rc. Furthermore, a total of 59 hub transcription factor genes might affect rice anthocyanin biosynthesis, and LOC_Os01g28680 and LOC_Os02g32430 could have functional redundancy with OsTTG1. Phylogenetic analysis indicated that directional selection has driven the evolutionary divergence of the indica and japonica OsTTG1 alleles. Our results suggest that OsTTG1 is a vital regulator of anthocyanin biosynthesis, and an important gene resource for the genetic engineering of anthocyanin biosynthesis in rice and other plants.

Surgical efficacy and survival prediction of patients with unspecified malignant bone tumors.

BACKGROUND: The surgical efficacy and prognostic outcomes of patients with unspecific malignant bone tumors (UMBTs) remain unclear. The study is to address: 1) What are the clinicopathological features and prognostic determinants for patients with UMBTs? 2) Can a nomogram be developed for clinicians to predict the short and long-term outcomes for individuals with UMBTs? 3) Does surgery improve outcomes for UMBT patients who received radiotherapy or chemotherapy after balancing the confounding bias? METHODS: 400 UMBT patients were filtrated from the Surveillance, Epidemiology, and End Results database to assess the clinicopathological features, treatments, and factors affecting prognosis. The optimal cutoff values of continuous variables were identified by the x-tile software. Kaplan-Meier method and multivariate Cox proportional hazard modeling were performed to evaluate the independent prognostic factors. Nomogram was further developed by using R software with rms package. The surgical efficacy was further assessed for patients receiving radiotherapy or chemotherapy after performing propensity score matching. RESULTS: The enrolled cohort included 195 (48.8%) female and 205 (51.2%) male patients. The 2- and 5-year cancer-specific survival (CSS) and overall survival (OS) rate were 58.2 ± 3.0%, 46.8 ± 3.2%, and 46.5 ± 2.6%, 34.4 ± 2.5%, respectively. Nomogram was finally developed for CSS and OS according to the identified independent factors: age, tumor extent, primary tumor surgery, tumor size, and pathology grade. For UMBT patients who received radiotherapy or chemotherapy, surgical intervention was associated with better CSS (pr = 0.003, pc = 0.002) and OS (pr = 0.035, pc = 0.002), respectively. CONCLUSIONS: Nomogram was developed for individual UMBT patient to predict short and long-term CSS and OS rate, and more external patient cohorts are warranted for validation. Surgery improves outcomes for UMBT patients who received either radiotherapy or chemotherapy.

KP-10/Gpr54 attenuates rheumatic arthritis through inactivating NF-κB and MAPK signaling in macrophages.

Rheumatoid arthritis (RA) is an autoimmune disease mainly characterized as chronic inflammation of joint. Both genetic and environmental factors play important roles in RA progression. G protein-coupled receptor 54 (GPR54) and Kisspeptins (KPs), the natural GRP54 ligands encoded by Kiss-1 gene are known to play important roles in immune regulation but the precise role of KP-10/GPR54 in RA remains elusive. Kiss1/Gpr54 expression was determined by immunohistochemistry on protein and real-time PCR on RNA from isolated RA-patient synovial tissue and PBMC. Collagen-induced arthritis (CIA) mouse models were used to investigate the effect of KP-10/Gpr54 on the rheumatic arthritis severity in the mice. The signaling pathway involved in KP-10/GPR54 was assessed by western blot and immunofluorescence.In the present study, we demonstrated that GPR54 upregulation in bone marrow-derived macrophages (BMDM) was associated with the severity of RA. In addition, Gpr54-/- increased the inflammatory cytokines induced by lipopolysaccharide (LPS) in BMDM and diseased severity of CIA (n = 10), while KP-10 reduced the LPS-induced inflammatory cytokines in vitro and ameliorated the CIA symptoms in vivo. Furthermore, we demonstrated that KP-10/GPR54 binds to PP2A-C to suppressed LPS induced NF-κB and MAPK signaling in BMDM. All these findings suggest that KP-10/GPR54 may be a novel therapeutic target for the diagnosis and treatment of RA.

Clinical features and surgical treatments of rare gastrointestinal stromal tumor spinal metastases.

OBJECTIVE: To increase our knowledge of the characteristics of rare gastrointestinal stromal tumors (GISTs) spinal metastatic diseases and share our experience of dealing with these diseases. METHODS: A total of 6 patients with spinal cord compression caused by GISTs spinal metastases operated in our department were identified from Oct, 2010 to Oct, 2018. The clinical and operative notes, radiographic images, and pathological reports with histochemistry of all these patients were reviewed. RESULTS: Among these six, four were male. The average age was 57.2 ± 9.0 years-old. The average duration between GISTs resections and diagnosis of spinal metastases was 80.8 ± 91.9 months. Four patients died from their disease during follow-up. The average duration between operation and death was 8.5 ± 4.4 months. CONCLUSIONS: Generally, patients with GISTs spinal metastatic diseases had a poor prognosis. The average survival of these patients did not exceed 12 months. Palliative treatments are recommended mainly to control symptoms.

Deep Learning-Based Congestion Detection at Urban Intersections.

In this paper, a deep learning-based traffic state discrimination method is proposed to detect traffic congestion at urban intersections. The detection algorithm includes two parts, global speed detection and a traffic state discrimination algorithm. Firstly, the region of interest (ROI) is selected as the road intersection from the input image of the You Only Look Once (YOLO) v3 object detection algorithm for vehicle target detection. The Lucas-Kanade (LK) optical flow method is employed to calculate the vehicle speed. Then, the corresponding intersection state can be obtained based on the vehicle speed and the discrimination algorithm. The detection of the vehicle takes the position information obtained by YOLOv3 as the input of the LK optical flow algorithm and forms an optical flow vector to complete the vehicle speed detection. Experimental results show that the detection algorithm can detect the vehicle speed and traffic state discrimination method can judge the traffic state accurately, which has a strong anti-interference ability and meets the practical application requirements.

Apatinib in patients with advanced chordoma: a single-arm, single-centre, phase 2 study.

BACKGROUND: No standard treatment exists for advanced chordoma. Apatinib has been found to have promising efficacy and manageable adverse effects for the treatment of solid tumours. We aimed to investigate the safety and antitumour activity of apatinib in patients with advanced chordoma. METHODS: We did a single-arm, phase 2 study at one tertiary hospital in Shanghai, China. Eligible patients were aged 18-75 years, with histologically confirmed advanced chordoma that was unresectable or resectable only through demolitive surgery, who had previously received surgical treatment, with at least one measurable lesion according to the Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1, evidence of tumour progression on enhanced CT or MRI in the previous 6 months, and an Eastern Cooperative Oncology Group performance status of 0-2. Patients received oral 500 mg apatinib once daily until disease progression or unacceptable toxicity. The co-primary endpoints were progression-free survival and objective response rate according to RECIST 1.1 and Choi criteria by investigator assessment. Progression-free survival was assessed in the intention-to-treat population. Objective response rate was assessed in the per-protocol population, which included all enrolled patients who were compliant with the protocol and had at least one post-baseline assessment. Safety was analysed in all patients with complete safety data. This study is ongoing, but recruitment is complete. This study is registered with Chictr.org.cn, ChiCTR-OIC-17013586. FINDINGS: Between Aug 21, 2017, and May 31, 2019, we screened 32 patients, of whom 30 were enrolled. Median follow-up was 14·2 months (IQR 9·4-19·7). Of the 27 patients included in the per-protocol population, one patient (3·7%; 95% CI 0-11·3) achieved an objective response according to RECIST, and seven patients (25·9%; 8·3-43·6) achieved an objective response according to Choi criteria. Median progression-free survival was 18 months (95% CI 3-34) according to RECIST and 18 months (3-33) according to Choi criteria. The most common treatment-related grade 3 adverse events were hypertension (seven [24%] of 29 patients) and proteinuria (two [7%]). No treatment-related grade 4 adverse events or treatment-related deaths were observed. INTERPRETATION: To our knowledge, this is the first trial of apatinib for the treatment of advanced chordoma. Apatinib shows promising activity and manageable toxicity and thus might be an option for the treatment of advanced chordoma. FUNDING: None.

Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice.

BACKGROUND: Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. RESULTS: This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44-68.71 million readings were obtained, resulting in the alignment of 29,128 and 30,131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis (WGCNA) revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. CONCLUSION: Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.

Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency.

BACKGROUND: Nitrogen (N) is a major nutrient element for crop growth. In plants, the members of the peptide transporter (PTR) gene family may involve in nitrate uptake and transport. Here, we identified PTR gene family in rice and analyzed their expression profile in near-isogenic lines. RESULTS: We identified 96, 85 and 78 PTR genes in Nipponbare, R498 and Oryza glaberrima, and the phylogenetic trees were similar in Asian cultivated rice and African cultivated rice. The number of PTR genes was higher in peanut (125) and soybean (127). The 521 PTR genes in rice, maize, sorghum, peanut, soybean and Arabidopsis could be classified into 4 groups, and their distribution was different between monocots and dicots. In Nipponbare genome, the 25 PTR genes were distributed in 5 segmental duplication regions on chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 10. The PTR genes in rice have 0-11 introns and 1-12 exons, and 16 of them have the NPF (NRT1/PTR family) domain. The results of RNA-seq showed that the number of differentially expressed genes (DEGs) between NIL15 and NIL19 at three stages were 928, 1467, and 1586, respectively. Under low N conditions, the number of differentially expressed PTR genes increased significantly. The RNA-seq data was analyzed using WGCNA to predict the potential interaction between genes. We classified the genes with similar expression pattern into one module, and obtained 25 target modules. Among these modules, three modules may be involved in rice N uptake and utilization, especially the brown module, in which hub genes were annotated as protein kinase that may regulate rice N metabolism. CONCLUSIONS: In this study, we comprehensively analyzed the PTR gene family in rice. 96 PTR genes were identified in Nippobare genome and 25 of them were located on five large segmental duplication regions. The Ka/Ks ratio indicated that many PTR genes had undergone positive selection. The RNA-seq results showed that many PTR genes were involved in rice nitrogen use efficiency (NUE), and protein kinases might play an important role in this process. These results provide a fundamental basis to improve the rice NUE via molecular breeding.

FOXD3 Suppresses Tumor-Initiating Features in Lung Cancer via Transcriptional Repression of WDR5.

The tumor-initiating cells (TICs) are a cell population that can initiate tumor occurrence, mediate drug resistance, and give rise to metastasis. FOXD3 is a forkhead box (Fox) transcription factor family that regulates the pluripotency of embryonic stem cell and tumorigenicity. However, it is unclear whether FOXD3 plays any role in TIC and tumor metastasis. The functional analysis of FOXD3 was performed by oncospheres formation and redifferentiation, drug resistance assay, and cell migration. Global genomic RNA-Seq and ChIP-Seq analysis were used to identify the direct target of FOXD3 in lung cancer. We demonstrated that downregulation of FOXD3 in TICs was positively correlated with higher histologic grades and positive lymph node metastasis. FOXD3 repressed TIC expansion and cell migration, drug resistance, and osteoclasts in vitro and in vivo. Mechanically, we found that FOXD3 represses WDR5, which regulates TIC-related signaling pathway. Moreover, WDR5 were positively correlated with the TIC abundance and tumor progression. Besides, patients with high expression of WDR5 presented a poorer overall survival. FOXD3 may suppress TIC accumulation by repressing the expression of WDR5 in lung cancer. Stem Cells 2019;37:582-592.

Identification and evaluation of reference genes for quantitative real-time PCR analysis in Passiflora edulis under stem rot condition.

Passion fruit (Passiflora edulis), an important tropical and subtropical fruit, has a high edible and medicinal value. Stem rot disease is one of the most important diseases of passion fruit. An effective way for control and prevention of this disease is to identify the genes associated with resistance to this disease. Quantitative real-time PCR (RT-qPCR) has mainly been widely applied to detect gene expression because of its simplicity, fastness, low cost and high sensitivity. One of the requirements for RT-qPCR is the availability of suitable reference genes for normalization of gene expression. However, currently, no Passiflora edulis reference genes have been identified andthus it has hindered the gene expression studies in this plant. The present study aimed to address this issue. We analyzed sixteen candidate reference genes, including nine common (GAPDH, UBQ, ACT1, ACT2, EF-1α-1, EF-1α-2, TUA, NADP, and GBP) and seven novel genes (C13615, C24590, C27182, C10445, C21209, C22199, and C22526), in different tissues (stem, leaf, flower and fruit) of two accessions under stem rot condition. We calculated the expression stability in twenty-four samples using the ΔCt, GeNorm, NormFinder, BestKeeper and RefFinder. The results showed that both C21209 and EF-1α-2 were sufficient to normalize gene expression under stem rot, whereas the commonly used reference genes, GAPDH and UBQ, were the least stable ones. The expression patterns of PeUFC under stem rot condition normalized by stable and unstable reference genes indicated the suitability of using the optimal reference genes. To our knowledge, this is the first systematic study of reference genes in Passiflora edulis, which identified a number of reliable reference genes suitable for gene expression studies in Passiflora edulis by RT-qPCR.

Comparison of Laparoscopic and Open Approach in Treating Gallbladder Cancer.

BACKGROUND: Preliminary study on the feasibility and efficacy of laparoscopic cholecystectomy and radical cholecystectomy in stage Tis-T3 gallbladder cancer (GBC). METHODS: Retrospective analysis of the clinical data of 102 patients with GBC from August 2008 to August 2017 in the Department of Hepatopancreatobiliary Surgery at the Third Affiliated Hospital of Soochow University. The clinical and pathological data of laparoscopic surgery and open surgery were compared. RESULTS: Of 102 patients with GBC, 41 underwent laparoscopic treatment, 12 of whom underwent laparoscopic cholecystectomy, and the others underwent laparoscopic radical cholecystectomy/extended radical cholecystectomy. Sixty-one patients underwent radical cholecystectomy/extended radical cholecystectomy. Based on the individual patient's condition, excision of the extrahepatic biliary tract and cholangioenterostomy were performed. There were no perioperative deaths. There was no significant difference in the operative blood loss (P = 0.732), operative time (P = 0.058), postoperative complications (P = 0.933), R0 margins (P = 0.679), and tumor-related death (P = 0.396) between the laparoscopic group and the laparotomy group. The postoperative activity time (P < 0.001), postoperative eating time (P < 0.001), drainage tube removal time (P < 0.001), and postoperative hospital discharge time (P < 0.001) in the laparoscopic group were all earlier than those in the laparotomy group, and the difference was statistically significant. The number of lymph nodes resected in the laparoscopic group and the laparotomy group was 1-17, average (5 ± 3) and 1-13 average (5 ± 3), respectively, with no statistically significant difference (P = 0.973). The 1-, 3-, and 5-y survival rates in the laparoscopic group were 97.1%, 69.4%, and 51.9%, respectively, and those in the laparotomy group were 94.7%, 64.9%, and 55.7%, respectively; there were no significant difference between the two groups (P = 0.453). In terms of different pathologic T stages, the 5-y survival rates of patients with stage Tis (9 cases), T1a (2 cases), T1b (8 cases), T2 (14 cases), and T3 (8 cases) disease in the laparoscopic group were 100%, 100%, 75%, 48.1%, and 12.5%, respectively, and the 5-y survival rates in patients with stage Tis (4 cases), T1b (9 cases), T2 (32 cases), and T3 (16 cases) disease in the laparotomy group were 100%, 87.5%, 64.7%, and 16%, respectively; there were no significant differences between the two groups. CONCLUSIONS: Laparoscopic treatment of stage Tis-T3 GBC is feasible. Laparoscopic treatment of GBC does not increase the incision metastasis rate on the basis of the intact gallbladder wall. The same survival rates can be achieved with laparoscopic treatment as with open treatment of GBC. In terms of postoperative rehabilitation, laparoscopic treatment has more advantages.

Underwater wireless optical communication system using a 16-QAM modulated 450-nm laser diode based on an FPGA.

An underwater wireless optical communication (UWOC) system with a 450-nm laser diode and a 150-MHz PIN photodiode is presented. The 16-ary quadrature amplitude modulation scheme is employed and realized on a field-programmable gate array (FPGA) to efficiently provide a high data rate. Experimental results show that this system can achieve data rates up to 50 Mbps over a distance of 3 m underwater with a bit error rate (BER) of 7.11×10-4 in artificial seawater at 35‰ salinity, where the attenuation coefficient is 0.481. This BER is below the forward error correction target of 3.8×10-3. Thus, this system can provide reliable high-speed communications over short to moderate distance point-to-point UWOC links.