Four MYB transcription factors regulate suberization and non-localized lignification at the root endodermis in rice.

In response to variable environments, rice (Oryza sativa) roots have developed lignified and suberized diffusion barriers at the endodermis to permit selective nutrient uptake for optimal growth. Here, we demonstrate that endodermal suberization and non-localized lignification are redundantly regulated by four MYB transcription factors: OsMYB39a, OsMYB41, OsMYB92a, and OsMYB92b. These transcription factors function downstream of the OsMYB36a/b/c, CASPARIAN STRIP INTEGRITY FACTOR (OsCIF)-SCHENGEN3 (OsSGN3), and stress-inducible signaling pathways in rice. Knockout of all four MYB genes resulted in the complete absence of endodermal suberin lamellae (SL) and almost no lignin deposition between the Casparian strip and the cortex-facing lignified band at cell corners under all conditions examined. In contrast, endodermis-specific overexpression of any of these MYB genes was sufficient to induce strong endodermal suberization and non-localized lignification near the root tip. Furthermore, OsMYB92a-overexpressing lines showed an altered ionomic profile and enhanced salinity tolerance. Transcriptome analysis identified 152 downstream genes regulated by OsMYB39a/41/92a/92b, including the key SL formation gene OsCYP86A1 and other genes involved in endodermal lignification and suberization under normal and stress conditions. Our results provide important insights into the molecular mechanisms underlying suberization and non-localized lignification at the root endodermis and their physiological significance in ion homeostasis and acclimation to environmental stress.

Small peptide signaling via OsCIF1/2 mediates Casparian strip formation at the root endodermal and nonendodermal cell layers in rice.

The Casparian strip (CS) is a ring-like lignin structure deposited between endodermal cells that forms an apoplastic barrier to control the selective uptake of nutrients in vascular plants. However, the molecular mechanism of CS formation in rice (Oryza sativa), which possesses one CS each in the endodermis and exodermis, is relatively unknown. Here, we functionally characterized CS INTEGRITY FACTOR1 (OsCIF1a, OsCIF1b), OsCIF2, and SCHENGEN3 (OsSGN3a, OsSGN3b) in rice. OsCIF1s and OsCIF2 were mainly expressed in the stele, while OsSGN3s localized around the CS at the endodermis. Knockout of all three OsCIFs or both OsSGN3s resulted in a discontinuous CS and a dramatic reduction in compensatory (less localized) lignification and suberization at the endodermis. By contrast, ectopic overexpression of OsCIF1 or OsCIF2 induced CS formation as well as overlignification and oversuberization at single or double cortical cell layers adjacent to the endodermis. Ectopic co-overexpression of OsCIF1 and SHORTROOT1 (OsSHR1) induced the formation of more CS-like structures at multiple cortical cell layers. Transcriptome analysis identified 112 downstream genes modulated by the OsCIF1/2-OsSGN3 signaling pathway, which is involved in CS formation and activation of the compensatory machinery in native endodermis and nonnative endodermis-like cell layers. Our results provide important insights into the molecular mechanism of CIF-mediated CS formation at the root endodermal and nonendodermal cell layers.

Multi-indicator comparative evaluation for deep learning-based protein sequence design methods.

MOTIVATION: Proteins found in nature represent only a fraction of the vast space of possible proteins. Protein design presents an opportunity to explore and expand this protein landscape. Within protein design, protein sequence design plays a crucial role, and numerous successful methods have been developed. Notably, deep learning-based protein sequence design methods have experienced significant advancements in recent years. However, a comprehensive and systematic comparison and evaluation of these methods have been lacking, with indicators provided by different methods often inconsistent or lacking effectiveness. RESULTS: To address this gap, we have designed a diverse set of indicators that cover several important aspects, including sequence recovery, diversity, root-mean-square deviation of protein structure, secondary structure, and the distribution of polar and nonpolar amino acids. In our evaluation, we have employed an improved weighted inferiority-superiority distance method to comprehensively assess the performance of eight widely used deep learning-based protein sequence design methods. Our evaluation not only provides rankings of these methods but also offers optimization suggestions by analyzing the strengths and weaknesses of each method. Furthermore, we have developed a method to select the best temperature parameter and proposed solutions for the common issue of designing sequences with consecutive repetitive amino acids, which is often encountered in protein design methods. These findings can greatly assist users in selecting suitable protein sequence design methods. Overall, our work contributes to the field of protein sequence design by providing a comprehensive evaluation system and optimization suggestions for different methods.

ACOX1 deficiency-induced lipid metabolic disorder facilitates chronic interstitial fibrosis development in renal allografts.

Chronic interstitial fibrosis presents a significant challenge to the long-term survival of transplanted kidneys. Our research has shown that reduced expression of acyl-coenzyme A oxidase 1 (ACOX1), which is the rate-limiting enzyme in the peroxisomal fatty acid ß-oxidation pathway, contributes to the development of fibrosis in renal allografts. ACOX1 deficiency leads to lipid accumulation and excessive oxidation of polyunsaturated fatty acids (PUFAs), which mediate epithelial-mesenchymal transition (EMT) and extracellular matrix (ECM) reorganization respectively, thus causing fibrosis in renal allografts. Furthermore, activation of Toll-like receptor 4 (TLR4)-nuclear factor kappa-B (NF-κB) signaling induced ACOX1 downregulation in a DNA methyltransferase 1 (DNMT1)-dependent manner. Overconsumption of PUFA resulted in endoplasmic reticulum (ER) stress, which played a vital role in facilitating ECM reorganization. Supplementation with PUFAs contributed to delayed fibrosis in a rat model of renal transplantation. The study provides a novel therapeutic approach that can delay chronic interstitial fibrosis in renal allografts by targeting the disorder of lipid metabolism.

Polyamines from myeloid-derived suppressor cells promote Th17 polarization and disease progression.

Myeloid-derived suppressor cells (MDSCs) are a group of immature myeloid cells that play an important role in diseases. MDSCs promote Th17 differentiation and aggravate systemic lupus erythematosus (SLE) progression by producing arginase-1 to metabolize arginine. However, the metabolic regulators remain unknown. Here, we report that MDSC derivative polyamines can promote Th17 differentiation via miR-542-5p in vitro. Th17 polarization was enhanced in response to polyamine treatment or upon miR-542-5p overexpression. The TGF-ß/SMAD3 pathway was shown to be involved in miR-542-5p-facilitated Th17 differentiation. Furthermore, miR-542-5p expression positively correlated with the levels of polyamine synthetases in peripheral blood mononuclear cells of patients with SLE as well as disease severity. In humanized SLE model mice, MDSC depletion decreased the levels of Th17 cells, accompanied by reduced expression of miR-542-5p and these polyamine synthetases. In addition, miR-542-5p expression positively correlated with the Th17 level and disease severity in both patients and humanized SLE mice. Together, our data reveal a novel molecular pathway by which MDSC-derived polyamine metabolism enhances Th17 differentiation and aggravates SLE.

HIT 2.0: an enhanced platform for Herbal Ingredients' Targets.

Literature-described targets of herbal ingredients have been explored to facilitate the mechanistic study of herbs, as well as the new drug discovery. Though several databases provided similar information, the majority of them are limited to literatures before 2010 and need to be updated urgently. HIT 2.0 was here constructed as the latest curated dataset focusing on Herbal Ingredients' Targets covering PubMed literatures 2000-2020. Currently, HIT 2.0 hosts 10 031 compound-target activity pairs with quality indicators between 2208 targets and 1237 ingredients from more than 1250 reputable herbs. The molecular targets cover those genes/proteins being directly/indirectly activated/inhibited, protein binders, and enzymes substrates or products. Also included are those genes regulated under the treatment of individual ingredient. Crosslinks were made to databases of TTD, DrugBank, KEGG, PDB, UniProt, Pfam, NCBI, TCM-ID and others. More importantly, HIT enables automatic Target-mining and My-target curation from daily released PubMed literatures. Thus, users can retrieve and download the latest abstracts containing potential targets for interested compounds, even for those not yet covered in HIT. Further, users can log into 'My-target' system, to curate personal target-profiling on line based on retrieved abstracts. HIT can be accessible at http://hit2.badd-cao.net.

Overexpression of an ART1-Interacting Gene OsNAC016 Improves Al Tolerance in Rice.

Rice (Oryza sativa) exhibits tremendous aluminum (Al)-tolerance. The C2H2-transcription factor (TF) ART1 critically regulates rice Al tolerance via modulation of specific gene expression. However, little is known about the posttranscriptional ART1 regulation. Here, we identified an ART1-interacted gene OsNAC016 via a yeast two-hybrid (Y2H) assay. OsNAC016 was primarily expressed in roots and weakly induced by Al. Immunostaining showed that OsNAC016 was a nuclear protein and localized in all root cells. Knockout of OsNAC016 did not alter Al sensitivity. Overexpression of OsNAC016 resulted in less Al aggregation within roots and enhanced Al tolerance in rice. Based on transcriptomic and qRT-PCR evaluations, certain cell-wall-related or ART-regulated gene expressions such as OsMYB30 and OsFRDL4 were altered in OsNAC016-overexpressing plants. These results indicated that OsNAC016 interacts with ART1 to cooperatively regulate some Al-tolerance genes and is a critical regulatory factor in rice Al tolerance.

The TERT copy number gain is sensitive to telomerase inhibitors in human melanoma.

Telomerase reverse transcriptase (TERT) copy number gain is frequently observed in Asian melanoma patients. Here, we explored the correlation between TERT copy number and the effect of telomerase inhibitors in melanoma. A total of 78 melanoma cases were enrolled in the study. The TERT copy number was examined by QuantiGene Plex DNA assay. The sensitivity to telomerase inhibitors was evaluated in cell lines and patient-derived xenograft (PDX) models with or without TERT copy number gain. Among the 78 patients, 33.3% showed TERT copy number gain, and the incidence of this gain in acral melanoma (61.5%) was higher than that in other melanoma subtypes (P=0.02). The telomerase inhibitors 6-thio-2'-deoxyguanosine (6-Thio-dG) and epigallocatechin-3-gallate (EGCG) inhibited cell viability and repressed tumor growth in PDX models with TERT copy number gain. TERT copy number gain is frequently observed in Chinese patients with melanoma. Targeting telomerase may benefit melanoma patients with TERT copy number gain.

Biochemical Toxicity and Potential Detoxification Mechanisms in Earthworms Eisenia fetida Exposed to Sulfamethazine and Copper.

The present study investigated the biochemical toxicity and potential detoxification mechanisms in earthworms Eisenia fetida exposed to sulfamethazine (SMZ) (7.5, 15 and 30 mg kg-1) either alone or in combination with Copper (Cu) (100 mg kg-1) in soil. The results showed that increasing concentrations of SMZ in soil activated superoxide dismutase, catalase and glutathione peroxidase isozymes, suggesting reactive oxygen species (ROS) burst in earthworms. Treatment with SMZ and Cu separately or in combination caused protein oxidation and damage, elevating the synthesis of ubiquitin, the 20S proteasome, cytochrome P450 (CYP450), and heat shock protein 70 (HSP70). Such treatments also induced the activities of proteases, endoproteinase (EP) and glutathione S-transferases (GSTs). The results suggested that the ubiquitin-20S proteasome, proteases, EP and HSP70 were involved in degradation or remediation of oxidatively damaged proteins. Elevated levels of CYP450 and GSTs also participated in the detoxification of the earthworms.

Kimura's disease with membranoproliferative glomerulonephritis: a case report with literature review.

BACKGROUND: Kimura's disease is a rare disease and its etiology is still unclear. Here we reported a case with lymphadenopathy complicated with secondary membranoproliferative glomerulonephritis. CASE PRESENTATION: A 46-year-old Chinese man presented with bilateral tumor-like nodules over his neck during the past 6 months and developed edema for 15 days. His blood pressure was 145/90 mmHg, multiple 1 × 1 cm masses were found over bilateral post-auricular and submandibular areas, along with trace edema of the lower extremities. Laboratory data showed an increased peripheral eosinophil count at 3.66 × 109/L (50% of total leukocytes), with a 24-hour urine total protein of 8 g and a serum albumin of 19 g/L, and serum IgE of 2930 IU/ml (<100 IU/ml). The patient underwent renal biopsy, which revealed membranoproliferative glomerulonephritis with eosinophilic infiltration of the interstitium. Lymph node biopsy showed eosinophilic lymphoid follicular granuloma. Bone marrow biopsy showed no abnormalities. A diagnosis of Kimura's disease was then established. We started him on prednisone 60 mg/day (1 mg/kg), and tapered the dose to 55 mg/day 2 months later, followed by a gradual reduction of 2.5 mg every 2 weeks. Valsartan was given for blood pressure control. His neck nodules shrank after 2 weeks of treatment and complete renal remission was achieved 3 months later. No relapse occurred after follow-up for 31 months. CONCLUSION: Kimura's disease can present with bilateral neck nodules and nephrotic syndrome (membranoproliferative glomerulonephritis), and prednisone can be a suitable choice of treatment.

Evaluation of vertebral artery anomaly in basilar invagination and prevention of vascular injury during surgical intervention: CTA features and analysis.

OBJECTIVE: To evaluate vertebral artery anomaly at the craniovertebral junction (CVJ) in patients with basilar invagination (BI) by computed tomographic angiography (CTA), and to discuss the prevention strategy of vascular injury. METHODS: The primary axial, multiple planar reconstruction and volume-rendering cervicocranial CTA images of 39 BI patients were analysed to evaluate vertebral artery anomaly at the CVJ: persistent first intersegmental artery (PFIA), fenestrated vertebral artery (FEN), and extracranial C1/2 origin of posterior inferior cerebellar artery (PICA), high-riding vertebral artery, side-to-side asymmetry and irregular midline carotid artery loop was determined by subjective vision. 100 patients who underwent CTA for reasons other than CVJ deformity were enrolled as normal controls to evaluate the prevalence of vertebral artery anomaly in a normal population. Chi-square test was utilized for comparing the prevalence of vertebral artery anomaly between these two groups. RESULTS: The incidence of PFIA was 25.6% (10/39), FEN was 7.7% (3/39), PICA was 5.1% (2/39), and the total incidence of extraosseous anomalous course of vertebral artery was 38.5% (15/39), significantly higher than that of control group, 7.0% (7/100) (P < 0.01). The incidence of high-riding vertebral artery and side-to-side asymmetry were 61.5% (24/39) and 30.8% (12/39), respectively. An irregular midline carotid artery loop was observed in five patients (12.8%). CONCLUSION: Vertebral artery anomaly, which can be clearly depicted by CTA, is more frequent in BI patients. Preoperative CTA should be performed for this patient population to prevent vascular injury. These slides can be retrieved under Electronic Supplementary Material.

Overexpression of the metastasis-associated gene MTA3 correlates with tumor progression and poor prognosis in hepatocellular carcinoma.

BACKGROUND AND AIM: Hepatocellular carcinoma (HCC) is one of the most common and aggressive cancers in the world. However, there remains a lack of effective diagnostic and treatment markers. We aimed to explore metastasis-associated protein 3 (MTA3) expression and function in HCC and its relationship with clinicopathological factors. METHODS: We investigated the expression pattern and clinicopathological significance of MTA3 in 90 patients with HCC via immunohistochemistry and explored MTA3 function via gene knockdown of MTA3. RESULTS: MTA3 was overexpressed in HCC cell nuclei and downregulated in HCC cell cytoplasm. The former finding correlated with metastasis (P = 0.010) and poor prognosis (P = 0.018). In addition, deleting MTA3 inhibited HCC cell growth, invasion, and metastasis in vitro, as shown in the colony formation, migration, and wound-healing assays. CONCLUSIONS: These results indicate that MTA3 is an oncogene of HCC, predicts poor prognosis of HCC, and may be a future marker of HCC treatment.

Schsphenines A and B, two new lignans from the fruit of Schisandra sphenanthera with cardioprotective Activities.

Schsphenines A (1) and B (2), two new lignans were isolated from the fruit of Schisandra sphenanthera, together with six known ones respectively identified as schisanhenol (3), methylgomisin O (4), wuweilignan E (5), neglschisandrin E (6), schisandrin A (7) and schisandrin B (8). The structures of isolated compounds were determined by UV, IR, HR-ESI-MS, NMR, ORD analysis and quantum chemical calculation. The in vitro cardioprotective activities of all compounds were studied on H2O2-injury H9C2 cells using the MTT method. Compound 1 exhibited a considerable protective effect with cell viability in 79.94 ± 2.36%. This research provided useful information for the utilisation of S. sphenanthera as the TCM.

The impact of JC viruria on renal transplant recovery and prognosis.

Postoperative JC viruria is common in kidney transplant recipients, however there remains a dearth of research on perioperative JCV infection in this population. The clinical significance of JCV monitoring in kidney transplant recipients remains unclear. Based on JCV urine monitoring during the perioperative phase, renal transplant recipients who underwent perioperative and postoperative monitoring at our center were categorized into two groups: the perioperative JC virus infection group and the control group consisting of recipients without detectable JCV DNA in plasma or urine during the two-year follow-up period. A comparative analysis of baseline data was initially performed, followed by a 1:1 propensity score matching of 80 cases from each group. Within the first month after transplantation, the JC viruria group exhibited a significant decrease in the incidence of delayed graft function compared to the control group (P = 0.031).Over the two-year postoperative period, the JC viruria group displayed a significantly lower rate of acute rejection (P = 0.027). Notably, the JC viruria group demonstrated higher estimated glomerular filtration rate levels compared to the control group, particularly within the first year post-transplantation. Moreover, recipient and transplant kidney survival rates did not significantly differ between the two groups (P = 0.642). Perioperative JC viruria in kidney transplant recipients may persist beyond the initial two postoperative years. The presence of JCV is associated with lower rates of DGF and acute rejection, indicating a favorable post-transplant recovery. These findings provide novel insights into the importance of postoperative JCV monitoring.

Immunotoxicity of microplastics and polychlorinated biphenyls alone or in combination to Crassostrea gigas.

Microplastics (MPs) and polychlorinated biphenyls (PCBs) are pervasive pollutants in the marine environment, exerting adverse effects on marine organisms. While it is suggested that their exposure may compromise the immune responses of marine organisms, the cumulative immunotoxic effects remain uncertain. Additionally, the intricate mechanisms underlying the immunotoxicity of PCBs and MPs in marine organisms are not yet fully comprehended. To illuminate their combined biological impacts, Crassostrea gigas were exposed to 50 µg/L MPs (30-µm porous) alone, as well as 10 or 100 ng/L PCBs individually or in combination with 50 µg/L of MPs for 28 days. Our data demonstrated that oysters treated with the pollutants examined led to decreased total haemocyte count, inhibited phagocytosis of haemocytes, enhanced the intracellular contents of reactive oxygen species, lipid peroxidation and DNA damage, reduced lysozyme concentration and activity, gave rise to superoxide dismutase. Catalaseand glutathione S-transferaseactivity. The expression of three immune-related genes (NF-κB, TNF-α, TLR-6) was drastically suppressed by the PCBs and MPs treatment, while the apoptosis pathway-related genes (BAX and Caspase-3) showed a significant increase. In addition, compared to oysters treated with a single type of pollutant, coexposure to MPs and PCBs exerted more severe adverse impacts on all the parameters investigated, indicating a significant synergistic effect. Therefore, the risk of MPs and PCBs chemicals on marine organisms should be paid more attention.

Role of mitochondria in pathogenesis and therapy of renal fibrosis.

Renal fibrosis, specifically tubulointerstitial fibrosis, represents the predominant pathological consequence observed in the context of progressive chronic kidney conditions. The pathogenesis of renal fibrosis encompasses a multifaceted interplay of mechanisms, including but not limited to interstitial fibroblast proliferation, activation, augmented production of extracellular matrix (ECM) components, and impaired ECM degradation. Notably, mitochondria, the intracellular organelles responsible for orchestrating biological oxidation processes in mammalian cells, assume a pivotal role within this intricate milieu. Mitochondrial dysfunction, when manifest, can incite a cascade of events, including inflammatory responses, perturbed mitochondrial autophagy, and associated processes, ultimately culminating in the genesis of renal fibrosis. This comprehensive review endeavors to furnish an exegesis of mitochondrial pathophysiology and biogenesis, elucidating the precise mechanisms through which mitochondrial aberrations contribute to the onset and progression of renal fibrosis. We explored how mitochondrial dysfunction, mitochondrial cytopathy and mitochondrial autophagy mediate ECM deposition and renal fibrosis from a multicellular perspective of mesangial cells, endothelial cells, podocytes, macrophages and fibroblasts. Furthermore, it succinctly encapsulates the most recent advancements in the realm of mitochondrial-targeted therapeutic strategies aimed at mitigating renal fibrosis.

IgM kappa proliferative glomerulonephritis with monoclonal immunoglobulin deposition complicated with nocardiosis dermatitis: a case report and review of literature.

Rationale: Monoclonal gammopathy of renal significance (MGRS) represents a group of disorders caused by monoclonal immunoglobulin (M protein) secreted by B cells or plasma cells. Proliferative glomerulonephritis with monoclonal immunoglobulin deposition (PGNMID) is a glomerular disease and a form of MGRS. Here, we presented a rare case of a patient with IgM kappa PGNMID complicated with nocardiosis dermatitis. Patient concerns and diagnoses: A 56-year-old man was admitted to the hospital because of cutaneous purpura and proteinuria. His initial pathological diagnosis indicated membranous proliferative glomerulonephritis, IgM(++), and subacute interstitial nephritis. Based on further examination, he was finally diagnosed to have IgM kappa PGNMID and subacute interstitial nephritis. After the initial diagnosis, the patient received hormonal therapy. During the treatment, nocardiosis dermatitis emerged as a complication, and the hormonal therapy was gradually reduced. The patient refused further treatment with rituximab, and his health is currently stable. Outcomes: IgM kappa PGNMID complicated with nocardiosis dermatitis is an extremely rare occurrence. Laboratory examination and pathological analysis are required to confirm the diagnosis of this disorder. Timely and accurate diagnosis is essential for the appropriate treatment of PGNMID.

Systematic treatment in gastric cancer patients with overt bleeding: A propensity score matching analysis.

BACKGROUND: Hemorrhage, which is not a rare complication in patients with gastric cancer (GC)/gastroesophageal junction cancer (GEJC), can lead to a poor prognosis. However, no study has examined the effectiveness and safety of chemotherapy as an initial therapy for GC/GEJC patients with overt bleeding (OB). AIM: To investigate the impact of OB on the survival and treatment-related adverse events (TRAEs) of GC/GEJC patients. METHODS: Patients with advanced or metastatic GC/GEJC who received systematic treatment at Peking University Third Hospital were enrolled in this study. Propensity score matching (PSM) analysis was performed. RESULTS: After 1:2 PSM analysis, 93 patients were assessed, including 32 patients with OB before treatment (OBBT) and 61 patients without OBBT. The disease control rate was 90.6% in the group with OBBT and 88.5% in the group without OBBT, and this difference was not statistically significant. There was no difference in the incidence of TRAEs between the group with OBBT and the group without OBBT. The median overall survival (mOS) was 15.2 months for patients with OBBT and 23.7 months for those without OBBT [hazard ratio (HR) = 1.101, 95% confidence interval (CI): 0.672-1.804, log rank P = 0.701]. The mOS was worse for patients with OB after treatment (OBAT) than for those without OBAT (11.4 months vs 23.7 months, HR = 1.787, 95%CI: 1.006-3.175, log rank P = 0.044). CONCLUSION: The mOS for GC/GEJC patients with OBBT was similar to that for those without OBBT, but the mOS for patients with OBAT was worse than that for those without OBAT.

Structure-based virtual screening discovers novel PKMYT1 inhibitors.

PKMYT1, a member of the WEE family, plays a crucial role in the cell cycle by specifically phosphorylating CDK1-CyclinB at Tyr15 and Thr14. Recent investigations have revealed that the amplification of CCNE1 and the inhibition of PKMYT1 kinase collectively result in synthetic lethality, further indicating that PKMYT1 is promising as an effective target for tumor therapy. Existing PKMYT1 inhibitors are mostly derivatives of RP-6306 or pan-inhibitors, limiting their further development. Herein, we conducted virtual screening of a natural product library, and in vitro enzyme experiments demonstrated that EGCG, GCG, and luteolin exhibited potent inhibitory activities with IC50 values of 0.137 µM, 0.159 µM, and 1.5 µM, respectively. Subsequently, analysis of the hit compounds and RP-6306, using different molecular simulation methods, revealed that stable hydrogen bonds with Asp251 and Glu157 in the DFG region were vital for binding to PKMYT1, more so than hydrogen bonds in the hinge and loop regions.