Characterization of the ddt1 Mutant in Rice and Its Impact on Plant Height Reduction and Water Use Efficiency.

Rice (Oryza sativa L.), a fundamental global staple, nourishes over half of the world's population. The identification of the ddt1 mutant in rice through EMS mutagenesis of the indica cultivar Shuhui527 revealed a dwarf phenotype, characterized by reduced plant height, smaller grain size, and decreased grain weight. Detailed phenotypic analysis and map-based cloning pinpointed the mutation to a single-base transversion in the LOC_Os03g04680 gene, encoding a cytochrome P450 enzyme, which results in a premature termination of the protein. Functional complementation tests confirmed LOC_Os03g04680 as the DDT1 gene responsible for the observed phenotype. We further demonstrated that the ddt1 mutation leads to significant alterations in gibberellic acid (GA) metabolism and signal transduction, evidenced by the differential expression of key GA-related genes such as OsGA20OX2, OsGA20OX3, and SLR1. The mutant also displayed enhanced drought tolerance, as indicated by higher survival rates, reduced water loss, and rapid stomatal closure under drought conditions. This increased drought resistance was linked to the mutant's improved antioxidant capacity, with elevated activities of antioxidant enzymes and higher expression levels of related genes. Our findings suggest that DDT1 plays a crucial role in regulating both plant height and drought stress responses. The potential for using gene editing of DDT1 to mitigate the dwarf phenotype while retaining improved drought resistance offers promising avenues for rice improvement.

Intraperitoneal laparoscopic single-site lymph node dissection in modified supine position during laparoscopic radical nephroureterectomy.

Technique modifications that aim to improve ergonomics of the surgical procedure without repositioning the upper tract urothelial carcinoma patients remain a challenge to urologists. We offer a novel technique to perform intraperitoneal laparoscopic single-site radical nephroureterectomy and pelvic lymph nodes dissection/retroperitoneal lymph nodes dissection in a supine position. Our novel technique is feasible and offers a significant improvement in operative efficiency, particularly in patients with locally advanced disease.

Learning Spatio-Temporal Pulse Representation With Global-Local Interaction and Supervision for Remote Prediction of Heart Rate.

Recent studies have demonstrated the benefit of extracting and fusing pulse signals from multi-scale region-of-interests (ROIs). However, these methods suffer from heavy computational load. This paper aims to effectively utilize multi-scale rPPG features with a more compact architecture. Inspired by recent research works exploring two-path architecture that leverages global and local information with bidirectional bridge in between. This paper designs a novel architecture Global-Local Interaction and Supervision Network (GLISNet), which uses a local path to learn representations in the original scale and a global path to learn representations in the other scale capturing multi-scale information. A light-weight rPPG signal generation block is attached to the output of each path that maps the pulse representation to the pulse output. A hybrid loss function is utilized enabling the local and global representations to learn directly from the training data. Extensive experiments are conducted on two publicly available datasets, and results demonstrate that GLISNet achieves superior performance in terms of signal-to-noise ratio (SNR), mean absolute error (MAE), and root mean squared error (RMSE). In terms of SNR, GLISNet has an increase of 4.41% compared with the second best algorithm PhysNet on PURE dataset. The MAE has a decrease of 13.16% compared with the second best algorithm DeeprPPG on UBFC-rPPG dataset. The RMSE has a decrease of 26.29% compared with the second best algorithm PhysNet on UBFC-rPPG dataset. Experiments on MIHR dataset demonstrates the robustness of GLISNet under low-light environment.

Study on the correlation between lifestyle and negative conversion time in patients diagnosed with coronavirus disease (COVID-19): a retrospective cohort study.

BACKGROUND: As of early December 2022, China eased the coronavirus disease (COVID-19) restriction, affecting over 80% of the country's population and posing a severe threat to public health. Previous studies mostly focused factors on the severity/mortality rate of hospitalized COVID-19 patients, but limited studies explored factors associated with virus-negative conversion, particularly lifestyles. Therefore, the aim of our study was to analyze the correlation between lifestyle factors and the negative conversion time in COVID-19 patients. METHODS: We recruited individuals aged 18 years or older who had a clear time record for both the diagnosis and negative conversion of COVID-19 and completed the electronic questionnaire with no missing data. Dietary data collected from the questionnaire was analyzed using exploratory factor analysis to establish dietary patterns. Age segmentation was performed using restricted cubic spline (RCS) plots. The association between lifestyle factors and the time to negative conversion in different age groups, was assessed using Kaplan-Meier plots and Cox regression analysis. RESULT: Out of 514 participants, all achieved viral negative conversion within a median time of 11 days. Based on nutrient intake, we identified four dietary patterns. The relationship between age and negative conversion rate, as depicted by RCS plots, exhibited an inverted "U" shape. We categorized age into three segments: <35 years, 35-45 years, and ≥ 45 years. For individuals under 35, our study indicated that a higher protein intake was linked to a faster recovery among COVID-19 patients, while medical staff or those receiving prescription treatments exhibited a slower recovery rate (P < 0.05). The 35 ~ 45 age group showed that adequate sleep and physical exercise were associated with a shorter time to negative conversion, whereas southern regions and a higher intake of carbohydrates were related with a longer conversion time (P < 0.05). Among individuals aged ≥ 45 years, the negative conversion time was primarily associated with physical exercise and being a medical staff member(P < 0.05). CONCLUSION: Our research suggests that adequate sleep, physical exercise and a higher protein intake can help alleviate COVID-19 symptoms, while a higher level of carbohydrates intake may hinder recovery from COVID-19.

PABPN1 promotes clear cell renal cell carcinoma progression by suppressing the alternative polyadenylation of SGPL1 and CREG1.

Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism in cancer development and progression. Poly(A) binding protein nuclear 1 (PABPN1) is a gene that encodes abundant nuclear protein, binds with high affinity to nascent poly(A) tails, and is crucial for 3'-UTR (3'-untranslated region) APA. Although PABPN1 has been recently reported as a dominant master APA regulator in clear cell renal cell carcinoma (ccRCC), the underlying functional mechanism remain unclear and the genes subject to PABPN1 regulation that contribute to ccRCC progression have not been identified. Here, we found that PABPN1 is upregulated in ccRCC, and its expression is highly associated with the clinical prognosis of ccRCC patients. PABPN1 promotes ccRCC cell proliferation, migration, invasion, and exerts an influence on sphingolipid metabolism and cell cycle. Moreover, PABPN1 depletion significantly suppressed cancer cell growth via induction of cell cycle arrest and apoptosis. In particular, we characterized PABPN1-regulated 3'-UTR APA of sphingosine-1-phosphate lyase 1 (SGPL1) and cellular repressor of E1A stimulated genes 1 (CREG1), which contribute to ccRCC progression. Collectively, our data revealed that PABPN1 promotes ccRCC progression at least in part, by suppressing SGPL1 and CREG1. Thus, PABPN1 may be a potential therapeutic target in ccRCC.

Comprehensive analysis of alternative polyadenylation regulators of CTLA4 and immune infiltration in clear cell renal cell carcinoma.

Background: Clear cell renal cell carcinoma (ccRCC) is the most common renal cancer. Alternative polyadenylation (APA) plays an important role in the progression and immunity of multiple tumors. Although immunotherapy has emerged as an important treatment option for metastatic renal cell carcinoma, whether APA affects the tumor immune microenvironment (TIME) in ccRCC remains unclear. Methods: Patients with ccRCC were classified into two groups by performing a consensus clustering analysis of APA factor expression profiles. The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases were used to assess the association between APA regulators and ccRCC prognosis. Through the use of the R package, GSVA, the correlation between SNRNP70 expression and tumor immune features were analyzed. Results: The TCGA data revealed that APA regulators were associated with Cytotoxic T-Lymphocyte Associated Protein 4 (CTLA4) expression. Cluster 1 exhibited a higher grade and histological tumor stage, as well as a worse prognosis compared to Cluster 2. A ssGSEA analysis demonstrated that Cluster 2 possessed an extensively higher level of immune infiltration. Moreover, high SNRNP70 expression was found to be positively correlated with CTLA4 expression and a poor prognosis in ccRCC. Thus, SNRNP70 might represent a novel immune-related prognostic biomarker in ccRCC. A pan-cancer analysis suggested that SNRNP70 may also play a role in other types of cancer by affecting the TIME. Conclusions: The data from this study indicate that APA regulators play a key role in immune infiltration in ccRCC. SNRNP70 is a promising prognostic biomarker and a potential target for ccRCC's immunotherapy.

Human menstrual blood-derived stem cells alleviate autoimmune hepatitis via JNK/MAPK signaling pathway in vivo and in vitro.

Autoimmune hepatitis (AIH) is a severe globally distributed liver disease that could occur at any age. Human menstrual blood-derived stem cells (MenSCs) have shown therapeutic effect in acute lung injury and liver failure. However, their role in the curative effect of AIH remains unclear. Here, a classic AIH mouse model was constructed through intravenous injection with concanavalin A (Con A). MenSCs were intravenously injected while Con A injection in the treatment groups. The results showed that the mortality by Con A injection was significantly decreased by MenSCs treatment and liver function tests and histological analysis were also ameliorated. The results of phosphoproteomic analysis and RNA-seq revealed that MenSCs improved AIH, mainly by apoptosis and c-Jun N-terminal kinase/mitogen-activated protein signaling pathways. Apoptosis analysis demonstrated that the protein expression of cleaved caspase 3 was increased by Con A injection and reduced by MenSCs transplantation, consistent with the TUNEL staining results. An AML12 co-culture system and JNK inhibitor (SP600125) were used to verify the JNK/MAPK and apoptosis signaling pathways. These findings suggested that MenSCs could be a promising strategy for AIH.

PABPN1 regulates mRNA alternative polyadenylation to inhibit bladder cancer progression.

BACKGROUND: About 10-20% of patients with bladder cancer (BC) progress to muscle-invasive diseases, of which the underlying key molecular events have yet to be addressed. RESULTS: Here, we identified poly(A) binding protein nuclear 1 (PABPN1), a general factor of alternative polyadenylation (APA), was downregulated in BC. Overexpression and knockdown of PABPN1 significantly decreased and increased BC aggressiveness, respectively. Mechanistically, we provide evidence that the preference of PABPN1-bound polyadenylation signals (PASs) depends on the relative location between canonical and non-canonical PASs. PABPN1 shapes inputs converging on Wnt signaling, cell cycle, and lipid biosynthesis. CONCLUSIONS: Together, these findings provide insights into how PABPN1-mediated APA regulation contributes to BC progression, and suggest that pharmacological targeting PABPN1 might have therapeutic potential in patients with BC.

Lengthening of 3' Untranslated Regions of mRNAs by Alternative Polyadenylation Is Associated With Tumor Progression and Poor Prognosis of Clear Cell Renal Cell Carcinoma.

Alternative polyadenylation (APA) is emerging as a major posttranscriptional mechanism for gene regulation in cancer. A prevailing hypothesis is that shortening of the 3' untranslated region (3'UTR) increases oncoprotein expression because of the loss of miRNA-binding sites (MBSs). We showed that the longer 3'UTR is associated with a more advanced tumor stage in patients with clear cell renal cell carcinoma (ccRCC). More surprisingly, 3'UTR shortening is correlated with better overall survival in patients with ccRCC. Furthermore, we identified a mechanism by which longer transcripts lead to increased oncogenic protein and decreased tumor-suppressive protein expression compared to the shorter transcripts. In our model, shortening of 3'UTRs by APA may increase the mRNA stability of the majority of the potential tumor-suppressor genes due to the loss of MBSs and AU-rich elements (AREs). Unlike potential tumor-suppressor genes, the potential oncogenes display much lower MBS and ARE density and globally much higher m6A density in distal 3'UTRs. As a result, 3'UTRs shortening decreases the mRNA stability of potential oncogenes and enhances the mRNA stability of potential tumor-suppressor genes. Our findings highlight the cancer-specific pattern of APA regulation and extend our understanding of the mechanism of APA-mediated 3'UTR length changes in cancer biology.

Comprehensive analysis of lower mitochondrial complex I expression is associated with cell metastasis of clear cell renal cell carcinoma.

Background: Clear cell renal cell carcinoma (ccRCC) is characterized by high metastasis potential. It is of great importance to explore the mechanisms underlying ccRCC metastasis and to enable development of potent therapeutics. The mitochondrial complex I (CI) had been considered to play an important role in the development of cancers, but less known in ccRCC. Methods: We utilized available public databases of ccRCC, including single-cell RNA sequencing (scRNA-seq) data GSE73121 and The Cancer Genome Atlas-kidney renal clear cell carcinoma (TCGA-KIRC). Principal component analysis (PCA) and t-Distributed Stochastic Neighbor Embedding (tSNE) analysis were evaluated the heterogeneity of metastatic renal cell carcinoma (mRCC) and primary renal cell carcinoma (pRCC). Protein-protein interaction (PPI) network identified critical gene. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) performed to explore the potential biologic pathways. Results: Our study revealed a significant gene expression heterogeneity between pRCC and mRCC. A PPI network based on differentially expressed genes (DEGs) identified electron transport chain (ETC), especially mitochondrial CI, as the key network hub. Further analysis revealed that the role of mitochondrial CI is associated with tumor metastasis and immune responds of ccRCC. Although CI had low frequency mutations in ccRCC, CI expression is associated with the high frequency mutated genes. A prognosis model included 7 CI genes, and these had a significant effect on overall survival (OS). The area under the curve at 1, 3, and 5 years was 0.717, 0.685, and 0.728, respectively. Transcription factor analysis predicted that PPARG possibly is a potential transcription activator of CI genes in ccRCC. Conclusions: Overall, we found that CI expression is associated with ccRCC progress. CI and PPARG may be potential biomarkers for metastatic ccRCC.

Interactome and Ubiquitinome Analyses Identify Functional Targets of Herpes Simplex Virus 1 Infected Cell Protein 0.

Herpes simplex virus 1 (HSV-1) can productively infect multiple cell types and establish latent infection in neurons. Infected cell protein 0 (ICP0) is an HSV-1 E3 ubiquitin ligase crucial for productive infection and reactivation from latency. However, our knowledge about its targets especially in neuronal cells is limited. We confirmed that, like in non-neuronal cells, ICP0-null virus exhibited major replication defects in primary mouse neurons and Neuro-2a cells. We identified many ICP0-interacting proteins in Neuro-2a cells, 293T cells, and human foreskin fibroblasts by mass spectrometry-based interactome analysis. Co-immunoprecipitation assays validated ICP0 interactions with acyl-coenzyme A thioesterase 8 (ACOT8), complement C1q binding protein (C1QBP), ovarian tumour domain-containing protein 4 (OTUD4), sorting nexin 9 (SNX9), and vimentin (VIM) in both Neuro-2a and 293T cells. Overexpression and knockdown experiments showed that SNX9 restricted replication of an ICP0-null but not wild-type virus in Neuro-2a cells. Ubiquitinome analysis by immunoprecipitating the trypsin-digested ubiquitin reminant followed by mass spectrometry identified numerous candidate ubiquitination substrates of ICP0 in infected Neuro-2a cells, among which OTUD4 and VIM were novel substrates confirmed to be ubiquitinated by transfected ICP0 in Neuro-2a cells despite no evidence of their degradation by ICP0. Expression of OTUD4 was induced independently of ICP0 during HSV-1 infection. Overexpressed OTUD4 enhanced type I interferon expression during infection with the ICP0-null but not wild-type virus. In summary, by combining two proteomic approaches followed by confirmatory and functional experiments, we identified and validated multiple novel targets of ICP0 and revealed potential restrictive activities of SNX9 and OTUD4 in neuronal cells.

Integrative Proteomic Analysis of Multiple Posttranslational Modifications in Inflammatory Response.

Posttranslational modifications (PTMs) of proteins, particularly acetylation, phosphorylation, and ubiquitination, play critical roles in the host innate immune response. PTMs' dynamic changes and the crosstalk among them are complicated. To build a comprehensive dynamic network of inflammation-related proteins, we integrated data from the whole-cell proteome (WCP), acetylome, phosphoproteome, and ubiquitinome of human and mouse macrophages. Our datasets of acetylation, phosphorylation, and ubiquitination sites helped identify PTM crosstalk within and across proteins involved in the inflammatory response. Stimulation of macrophages by lipopolysaccharide (LPS) resulted in both degradative and non-degradative ubiquitination. Moreover, this study contributes to the interpretation of the roles of known inflammatory molecules and the discovery of novel inflammatory proteins.

Integrative proteomics reveals the role of E3 ubiquitin ligase SYVN1 in hepatocellular carcinoma metastasis.

BACKGROUND: Tumor metastasis is a major factor for poor prognosis of hepatocellular carcinoma (HCC), but the relationship between ubiquitination and metastasis need to be studied more systematically. We analyzed the ubiquitinome of HCC in this study to have a more comprehensive insight into human HCC metastasis. METHODS: The protein ubiquitination levels in 15 HCC specimens with vascular invasion and 15 without vascular invasion were detected by ubiquitinome. Proteins with significantly different ubiquitination levels between HCCs with and without vascular invasion were used to predict E3 ubiquitin ligases associated with tumor metastasis. The topological network of protein substrates and corresponding E3 ubiquitin ligases was constructed to identify the key E3 ubiquitin ligase. Besides, the growth, migration and invasion ability of LM3 and HUH7 hepatoma cell lines with and without SYVN1 expression interference were measured by cell proliferation assay, subcutaneous tumor assay, umphal vein endothelium tube formation assay, transwell migration and invasion assays. Finally, the interacting proteins of SYVN1 were screened and verified by protein interaction omics, immunofluorescence, and immunoprecipitation. Ubiquitin levels of related protein substrates in LM3 and HUH7 cells were compared in negative control, SYVN1 knockdown, and SYVN1 overexpression groups. RESULTS: In this study, our whole-cell proteomic dataset and ubiquitinomic dataset contained approximately 5600 proteins and 12,000 ubiquitinated sites. We discovered increased ubiquitinated sites with shorter ubiquitin chains during the progression of HCC metastasis. In addition, proteomic and ubiquitinomic analyses revealed that high expression of E3 ubiquitin-protein ligase SYVN1 is related with tumor metastasis. Furthermore, we found that SYVN1 interacted with heat shock protein 90 (HSP90) and impacted the ubiquitination of eukaryotic elongation factor 2 kinase (EEF2K). CONCLUSIONS: The ubiquitination profiles of HCC with and without vascular invasion were significantly different. SYVN1 was the most important E3 ubiquitin-protein ligase responsible for this phenomenon, and it was related with tumor metastasis and growth. Therefore, SYVN1 might be a potential therapeutic target for HCC.

c-Myc affects hedgehog pathway via KCNQ1OT1/RAC1: A new mechanism for regulating HSC proliferation and epithelial-mesenchymal transition.

BACKGROUND: This study aimed to probe into the potential mechanism of KCNQ1OT1 in liver fibrosis. METHODS: The pathological changes in liver tissues were observed by Masson and hematoxylin-eosin (HE) staining. The proliferation or cell cycle of hepatic stellate cells (HSCs) was analyzed by MTT or flow cytometry. The expressions of epithelial markers E-cadherin, interstitial markers Snail and Vimentin, and hedgehog signaling pathway-related molecules Hhip, Shh, and Gli2 were detected by Western blot. The interaction or binding of c-Myc with the KCNQ1OT1 promoter was analyzed by dual-luciferase reporter gene or Chromatin immunoprecipitation (ChIP)-qPCR, and the interaction between KCNQ1OT1 and RAC1 was assessed by RNA immunoprecipitation and RNA pull-down. Moreover, the stability of RAC1 protein was detected by cycloheximide-chase and ubiquitination. RESULTS: c-Myc and KCNQ1OT1 were up-regulated in liver fibrosis tissues and cells. After the interference with c-Myc in primary-1-Day HSCs, the down-regulated KCNQ1OT1 restrained HSC proliferation and EMT by down-regulating RAC1 expression and restraining the hedgehog pathway. CONCLUSION: Our results indicated that the interference with c-Myc down-regulated RAC1 expression and restrained the hedgehog pathway by down-regulating KCNQ1OT1, thus restraining HSC proliferation and EMT in liver fibrosis.

Mass Spectrometry Analysis of SARS-CoV-2 Nucleocapsid Protein Reveals Camouflaging Glycans and Unique Post-Translational Modifications.

The devastating coronavirus disease 2019 (COVID-19) pandemic has prompted worldwide efforts to study structural biological traits of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its viral components. Compared to the Spike protein, which is the primary target for currently available vaccines or antibodies, knowledge about other virion structural components is incomplete. Using high-resolution mass spectrometry, we report a comprehensive post-translational modification (PTM) analysis of nucleocapsid phosphoprotein (NCP), the most abundant structural component of the SARS-CoV-2 virion. In addition to phosphoryl groups, we show that the SARS-CoV-2 NCP is decorated with a variety of PTMs, including N-glycans and ubiquitin. Based on newly identified PTMs, refined protein structural models of SARS-CoV-2 NCP were proposed and potential immune recognition epitopes of NCP were aligned with PTMs. These data can facilitate the design of novel vaccines or therapeutics targeting NCP, as valuable alternatives to the current vaccination and treatment paradigm that is under threat of the ever-mutating SARS-CoV-2 Spike protein.

Extended lymphadenectomy in hilar cholangiocarcinoma: What it will bring?

Lymph node dissection is always a hot issue in radical resection of hilar cholangiocarcinoma (HCCA). There are still controversies regarding whether some lymph nodes should be dissected, of which the para-aortic lymph nodes are the most controversial. This review synthesized findings in the literature using the PubMed database of articles in the English language published between 1990 and 2019 on the effectiveness of extended lymphadenectomy including para-aortic lymph nodes dissection in radical resection of HCCA. Hepatobiliary surgeons have basically achieved a consensus that enough lymph nodes should be obtained to accurately stage HCCA. Only a very small number of studies have focused on the effectiveness of extended lymphadenectomy including para-aortic nodes dissection on HCCA. They reported that extended lymphadenectomy can bring some survival benefits for patients with potential para-aortic lymph node metastasis and more lymph nodes can be obtained to make the patient's tumor staging more accurate without increasing the related complications. Extended lymphadenectomy should not be adopted for HCCA patients with intraoperatively confirmed distant lymph node metastases. For these patients, radical resection combined with postoperative adjuvant chemotherapy seems to be a better choice. A prospective, multicenter, randomized, controlled clinical study of regional lymphotomy and extended lymphadenectomy in HCCA should be conducted to guide clinical practice. A standardized extended lymphadenectomy may help to more accurately stage HCCA. Future studies are required to further assess whether extended lymphadenectomy can improve long-term survival in negative celiac, superior mesenteric, and para-aortic lymph node diseases.

Artificial liver support system therapy in acute-on-chronic hepatitis B liver failure: Classification and regression tree analysis.

Artificial liver support systems (ALSS) are widely used to treat patients with hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF). The aims of the present study were to investigate the subgroups of patients with HBV-ACLF who may benefit from ALSS therapy, and the relevant patient-specific factors. 489 ALSS-treated HBV-ACLF patients were enrolled, and served as derivation and validation cohorts for classification and regression tree (CART) analysis. CART analysis identified three factors prognostic of survival: hepatic encephalopathy (HE), prothrombin time (PT), and total bilirubin (TBil) level; and two distinct risk groups: low (28-day mortality 10.2-39.5%) and high risk (63.8-91.1%). The CART model showed that patients lacking HE and with a PT ≤ 27.8 s and a TBil level ≤455 µmol/L experienced less 28-day mortality after ALSS therapy. For HBV-ACLF patients with HE and a PT > 27.8 s, mortality remained high after such therapy. Patients lacking HE with a PT ≤ 27.8 s and TBil level ≤ 455 µmol/L may benefit markedly from ALSS therapy. For HBV-ACLF patients at high risk, unnecessary ALSS therapy should be avoided. The CART model is a novel user-friendly tool for screening HBV-ACLF patient eligibility for ALSS therapy, and will aid clinicians via ACLF risk stratification and therapeutic guidance.