Telomere-to-telomere pear (Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution.

Previously released pear genomes contain a plethora of gaps and unanchored genetic regions. Here, we report a telomere-to-telomere (T2T) gap-free genome for the red-skinned pear, 'Yunhong No. 1' (YH1; Pyrus pyrifolia), which is mainly cultivated in Yunnan Province (southwest China), the pear's primary region of origin. The YH1 genome is 501.20 Mb long with a contig N50 length of 29.26 Mb. All 17 chromosomes were assembled to the T2T level with 34 characterized telomeres. The 17 centromeres were predicted and mainly consist of centromeric-specific monomers (CEN198) and long terminal repeat (LTR) Gypsy elements (≥74.73%). By filling all unclosed gaps, the integrity of YH1 is markedly improved over previous P. pyrifolia genomes ('Cuiguan' and 'Nijisseiki'). A total of 1531 segmental duplication (SD) driven duplicated genes were identified and enriched in stress response pathways. Intrachromosomal SDs drove the expansion of disease resistance genes, suggesting the potential of SDs in adaptive pear evolution. A large proportion of duplicated gene pairs exhibit dosage effects or sub-/neo-functionalization, which may affect agronomic traits like stone cell content, sugar content, and fruit skin russet. Furthermore, as core regulators of anthocyanin biosynthesis, we found that MYB10 and MYB114 underwent various gene duplication events. Multiple copies of MYB10 and MYB114 displayed obvious dosage effects, indicating role differentiation in the formation of red-skinned pear fruit. In summary, the T2T gap-free pear genome provides invaluable resources for genome evolution and functional genomics.

Optimizing surgical management of iatrogenic bile duct injury: transhepatic percutaneous cholangial drainage combined with end-to-end biliary anastomosis.

Iatrogenic bile duct injury remains the most severe complication of gallbladder surgeries. To reduce post-operation complication, we introduce an improved approach for bile duct injury repairment, named transhepatic percutaneous cholangial drainage (TPCD) which combined with end-to-end biliary anastomosis. Clinical data obtained from 12 patients between February 2012 and May 2022 were retrospectively analyzed. Patient demographic, clinical, operative, and follow-up data were analyzed using descriptive statistics. All injuries were repaired successfully and no fatal cases occurred. The mean operative time and hospital stay duration were 367.5 ± 103.2 min and 11.3 ± 3.5 days, respectively. In two cases (16.7%), bile leakage occurred at the bile duct anastomosis site. Three patients (25.0%) developed low-grade fever and one patient (8.3%) developed a postoperative infection of the incision site. No postoperative bleeding or bile duct strictures occurred in any of the cases. The patients were followed up from 12 to 122 months (median, 70.5 months). No cholangitis or bile duct restenosis was observed after biliary drainage tube removal. There were no long-term bile duct-related complications seen in the follow-up time. It is safe and feasible for TPCD combined with end-to-end biliary anastomosis using in bile duct injury.

KNTC1 as a putative tumor oncogene in pancreatic cancer.

PURPOSE: Recent studies have demonstrated that kinetochore-associated protein 1 (KNTC1) plays a significant role in the carcinogenesis of numerous types of cancer. This study aimed to explore the role and possible mechanisms of KNTC1 in the development of pancreatic cancer. METHODS AND RESULTS: We analyzed differentially expressed genes by RNA sequencing in three paired pancreatic cancer and para-cancerous tissue samples and found that the expression of KNTC1 was significantly upregulated in pancreatic cancer. A Cancer and Tumor Gene Map pan-analysis showed that high expression of KNTC1 was related to poor prognosis in 9499 tumor samples. With immunohistochemical staining, we found that the high expression of KNTC1 in pancreatic cancer was related to pathological grade and clinical prognosis. Similarly, RT-PCR results indicated that the expression of KNTC1 was higher in three groups of pancreatic cancer cell lines (BxPC-3, PANC-1, and SW1990) than in normal pancreatic ductal cells. We introduced lentivirus-mediated shRNA targeting KNTC1 into PANC-1 and SW1990 cells and found that KNTC1 knockdown significantly decreased cell growth and increased cell apoptosis compared to the control group cells. Bioinformatic analysis of the cell expression profile revealed that differential genes were mainly enriched in the cell cycle, mitosis, and STAT3 signaling pathways, and co-immunoprecipitation confirmed an interaction between KNTC1 and cell division cycle associated 8. CONCLUSIONS: KNTC1 could be linked to the pathophysiology of pancreatic cancer and may be an early diagnostic marker of cervical precancerous lesions.

RNA-Seq Identification of Cd Responsive Transporters Provides Insights into the Association of Oxidation Resistance and Cd Accumulation in Cucumis sativus L.

Greenhouse vegetable production (GVP) has grown rapidly and has become a major force for cucumber production in China. In highly intensive GVP systems, excessive fertilization results in soil acidification, increasing Cd accumulation and oxidative stress damage in vegetables as well as increasing health risk of vegetable consumers. Therefore, enhancing antioxidant capacity and activating the expression level of Cd transporter genes seem to be feasible solutions to promote plant resistance to Cd stress and to reduce accumulated Cd concentration. Here, we used transcriptomics to identify five cucumber transporter genes (CsNRAMP1, CsNRAMP4, CsHMA1, CsZIP1, and CsZIP8) in response to cadmium stress, which were involved in Cd transport activity in yeast. Ionomics, gene expression, and REDOX reaction level association analyses have shown that the transcript of CsNRAMP4 was positively correlated with Cd accumulation and antioxidant capacity of cucumber roots. The expression level of CsHMA1 was negatively correlated with Cd-induced antioxidant capacity. The overexpression of CsHMA1 significantly relieved Cd stress-induced antioxidant activities. In addition, shoots with high CsHMA2 expression remarkably presented Cd bioaccumulation. Grafting experiments confirmed that CsHMA1 contributed to the high antioxidant capacity of cucumber, while CsHMA2 was responsible for the transport of Cd from the roots to the shoots. Our study elucidated a novel regulatory mechanism for Cd transport and oxidative damage removal in horticultural melons and provided a perspective to regulate Cd transport artificially by modulating Cd accumulation and resistance in plants.

Tumor Targeting Strategies of Smart Fluorescent Nanoparticles and Their Applications in Cancer Diagnosis and Treatment.

Advantages such as strong signal strength, resistance to photobleaching, tunable fluorescence emissions, high sensitivity, and biocompatibility are the driving forces for the application of fluorescent nanoparticles (FNPs) in cancer diagnosis and therapy. In addition, the large surface area and easy modification of FNPs provide a platform for the design of multifunctional nanoparticles (MFNPs) for tumor targeting, diagnosis, and treatment. In order to obtain better targeting and therapeutic effects, it is necessary to understand the properties and targeting mechanisms of FNPs, which are the foundation and play a key role in the targeting design of nanoparticles (NPs). Widely accepted and applied targeting mechanisms such as enhanced permeability and retention (EPR) effect, active targeting, and tumor microenvironment (TME) targeting are summarized here. Additionally, a freshly discovered targeting mechanism is introduced, termed cell membrane permeability targeting (CMPT), which improves the tumor-targeting rate from less than 5% of the EPR effect to more than 50%. A new design strategy is also summarized, which is promising for future clinical targeting NPs/nanomedicines design. The targeting mechanism and design strategy will inspire new insights and thoughts on targeting design and will speed up precision medicine and contribute to cancer therapy and early diagnosis.

Upconversion-Magnetic Carbon Sphere for Near Infrared Light-Triggered Bioimaging and Photothermal Therapy.

Nanoparticle-based theranostics combines tumor imaging and cancer therapy in one platform, but the synthesis of theranostic agents is impeded by chemical groups on the surface and the size and morphology of the components. Strategies to construct a multifunctional platform for bioimaging and photothermal therapy (PTT) are urgently needed. A new upconversion-magnetic agent (FeCUPs) based on hollow carbon spheres, which is both a photothermal agent and a dual carrier of luminescent and magnetic nanoparticles, provides an effective approach for tumor elimination. Methods: The morphology of FeCUPs was characterized for the construction and size adjustment of the theranostic agent using transmission electron microscopy, high-resolution transmission electron microscopy, energy dispersive spectroscopy and high angle annular dark field scanning transmission electron microscopy. The distribution of FeCUPs was tracked under in-situ upconversion luminescence (UCL) imaging and magnetic resonance imaging (MRI) in vivo. Photothermal therapy was carried out on tumor-bearing mice, after which the toxicity of PTT was evaluated by a blood biochemistry test and histological section analysis. Results: Stable and uniform loading of luminescent nanocomposites on three-dimensional carbon materials is reported for the first time. Based on the mechanism of synthesis, the size of the hybrid particles was adjusted from micrometers to nanometers. External magnetic field-enhanced photothermal therapy with multi-model imaging was accomplished using FeCUPs. Moreover, no cancer recurrence was found during 14 days of recovery without PTT. Conclusions: Hollow carbon spheres, photothermal agents loaded with upconversion nanoparticles inside and magnetic nanoparticles outside were prepared for photothermal therapy. The aggregation of FeCUPs in tumors by the local magnetic field was verified by MRI and UCL imaging, and PTT was enhanced.

A Highly Efficient Tumor-Targeting Nanoprobe with a Novel Cell Membrane Permeability Mechanism.

Efficient tumor targeting has been a great challenge in the clinic for a very long time. The traditional targeting methods based on enhanced permeability and retention (EPR) effects show only an ≈5% targeting rate. To solve this problem, a new graphene-based tumor cell nuclear targeting fluorescent nanoprobe (GTTN), with a new tumor-targeting mechanism, is developed. GTTN is a graphene-like single-crystalline structure amphiphilic fluorescent probe with a periphery that is functionalized by sulfonic and hydroxyl groups. This probe has the characteristic of specific tumor cell targeting, as it can directly cross the cell membrane and specifically target to the tumor cell nucleus by the changed permeability of the tumor cell membranes in the tumor tissue. This new targeting mechanism is named the cell membrane permeability targeting (CMPT) mechanism, which is very different from the EPR effect. These probes can recognize tumor tissue at a very early stage and track the invasion and metastasis of tumor cells at the single cell level. The tumor-targeting rate is improved from less than 5% to more than 50%. This achievement in efficient and accurate tumor cell targeting will speed up the arrival of a new era of tumor diagnosis and treatment.

Size, Shape, and Protein Corona Determine Cellular Uptake and Removal Mechanisms of Gold Nanoparticles.

Size, shape, and protein corona play a key role in cellular uptake and removal mechanisms of gold nanoparticles (Au NPs). The 15 nm nanoparticles (NP1), the 45 nm nanoparticles (NP2), and the rod-shaped nanoparticles (NR) enter into cells via a receptor-mediated endocytosis (RME) pathway. The star-shaped nanoparticles (NS) adopt not only clathrin-mediated, but also caveolin-mediated endocytosis pathways. However, the 80 nm nanoparitcles (NP3) mainly enter into the cells by macropinocytosis pathway due to the big size. Furthermore, the results indicate that the presence of protein corona can change the uptake mechanisms of Au NPs. The endocytosis pathway of NP1, NP2, and NS changes from RME to macropinocytosis pathway and NR changes from RME to clathrin and caveolin-independent pathway under the non-fetal bovine serun (FBS)-coated condition. Both FBS-coated and non-FBS-coated of five types of Au NPs are released out through the lysosomal exocytosis pathway. The size, shape, and protein corona have an effect on the exocytosis ratio and amount, but do not change the exocytosis mechanism. The systematic study of the endocytosis and exocytosis mechanism of Au NPs with different sizes and shapes will benefit the toxicology evaluation and nanomedicine application of Au NPs.

Toxic effects of zinc oxide nanoparticles combined with vitamin C and casein phosphopeptides on gastric epithelium cells and the intestinal absorption of mice.

Zinc oxide nanomaterials have become common food additives in recent years. Casein phosphopeptides (CPP) and vitamin C (VC) are used as functional food additives together with ZnO nanoparticles (ZnO NPs) in many commercial foods. Our previous studies showed that VC can increase the cytotoxicity induced by ZnO NPs both in vitro and in vivo, while CPP can have a cytoprotective effect against oxidative stress induced by ZnO NPs. However, the combined toxic effect of the three additives together in food is unknown. Herein, we have investigated the combined toxicity of ZnO NPs, CPP and VC by altering the sequence of their addition to clarify their toxic mechanisms in the composite systems. When the order of addition of the three materials changes, the cytotoxicity induced by the ZnO NPs changes due to the different concentrations of dissolved Zn ions in the different groups. We have also probed the intestinal absorption of Zn ions with an everted gut sac model. The amount of Zn2+ absorbed in the intestine in different composite systems also responds differently to the sequence of addition of the additives. VC is more powerful at controlling the synergistic toxic effect induced by ZnO NPs compared to the protective role of CPP in the combined systems.

Tumor Cell-Specific Nuclear Targeting of Functionalized Graphene Quantum Dots In Vivo.

Specific targeting of tumor tissues is essential for tumor imaging and therapeutics but remains challenging. Here, we report an unprecedented method using synthetic sulfonic-graphene quantum dots (sulfonic-GQDs) to exactly target the cancer cell nuclei in vivo without any bio- ligand modification, with no intervention in cells of normal tissues. The key factor for such selectivity is the high interstitial fluid pressure (IFP) in tumor tissues, which allows the penetration of sulfonic-GQDs into the plasma membrane of tumor cells. In vitro, the sulfonic-GQDs are repelled out of the cell membrane because of the repulsive force between negatively charged sulfonic-GQDs and the cell membranes which contributes to the low distribution in normal tissues in vivo. However, the plasma membrane-crossing process can be activated by incubating cells in ultrathin film culture medium because of the attachment of sulfonic-GQDs on cell memebranes. Molecular dynamics simulations demonstrated that, once transported across the plasma membrane, the negatively charged functional groups of these GQDs will leave the membrane with a self-cleaning function retaining a small enough size to achieve penetration through the nuclear membrane into the nucleus. Our study showed that IFP is a previously unrecognized mechanism for specific targeting of tumor cell nuclei and suggested that sulfonic-GQDs may be developed into novel tools for tumor-specific imaging and therapeutics.

Enhancement of the Immune Function by Titanium Dioxide Nanorods and Their Application in Cancer Immunotherapy.

With the rapid development of nanotherapy, concerns surrounding the possible use of nanomaterials-mediated immunomodulation are growing. Thus, evaluating the effects of novel materials for potential application in nanotherapy is essential. Herein, we studied the effects of TiO2-nanorods (NRs) on the immune function and their potential application in immunotherapy. TiO2-NRs exerted specific immunomodulatory effects on the main immune cells. Cytokines TNF-α and IL-2, which play a key role in antitumor processes, were upregulated more significantly than other cytokines (IL-4, IL-5, IFN-γ) in the main immune cells. The cells group treated with a high dose of TiO2-NRs (50 mg/L) for 12 h produced a higher TNF-α content of 530.4 pg/mL relative to that (238.2 pg/mL) treated with saline solution only. The TNF-α content increased to 2.2- and 4.9-fold for macrophages and lymphocytes, respectively. Also, we conclude that TiO2-NRs exposure may trigger T cell proliferation and bias toward Th1 immune response and cause a long-lasting activation of lymphocytes involved in adaptive immunity rather than an innate immunity in BALB/c mice. Furthermore, we explored the potential application of TiO2-NRs in immunotherapy. At a given dose of 1 mg/kg, the inhibition rate by TiO2-NRs (26.7%) was much higher than that by DOX (13.3%).

Techniques for Investigating Molecular Toxicology of Nanomaterials.

Nanotechnology has been a rapidly developing field in the past few decades, resulting in the more and more exposure of nanomaterials to human. The increased applications of nanomaterials for industrial, commercial and life purposes, such as fillers, catalysts, semiconductors, paints, cosmetic additives and drug carriers, have caused both obvious and potential impacts on human health and environment. Nanotoxicology is used to study the safety of nanomaterials and has grown at the historic moment. Molecular toxicology is a new subdiscipline to study the interactions and impacts of materials at the molecular level. To better understand the relationship between the molecular toxicology and nanomaterials, this review summarizes the typical techniques and methods in molecular toxicology which are applied when investigating the toxicology of nanomaterials and include six categories: namely; genetic mutation detection, gene expression analysis, DNA damage detection, chromosomal aberration analysis, proteomics, and metabolomics. Each category involves several experimental techniques and methods.

Cytotoxicity Evaluation of pH-Controlled Antitumor Drug Release System of Titanium Dioxide Nanotubes.

Application of nanotechnology and nanomaterials in cancer therapeutics has attracted much attention in recent years. Nano titanium dioxide is one of the most important inorganic functional materials. Cellular toxicity of pH-controlled antitumor drug release system of titanium dioxide nanotubes (TiO2-NTs) in pancreatic cancer cells (SW1990) was evaluated in this paper. The anticancer drug, doxorubicin (DOX) was easily loaded on TiO2-NTs through adsorption forces because of its high specific surface area and perfect surface activity. The drug release from the nanotubes was pH dependent. The toxicological effects were studied after co-incubation of SW1990 with TiO2-NTs-DOX, TiO2-NTs and DOX, respectively. The cellular effect of DOX released from the TiO2-NTs-DOX was same as when DOX was used alone, indicating that the synthesized TiO2-NTs are well qualified as drug carriers in antitumor drug controlled-release system.

Excess titanium dioxide nanoparticles on the cell surface induce cytotoxicity by hindering ion exchange and disrupting exocytosis processes.

To date, considerable effort has been devoted to determine the potential toxicity of nanoparticles to cells and organisms. However, determining the mechanism of cytotoxicity induced by different types of nanoparticles remains challenging. Herein, typically low toxicity nanomaterials were used as a model to investigate the mechanism of cytotoxicity induced by low toxicity nanomaterials. We studied the effect of nano-TiO2, nano-Al2O3 and nano-SiO2 deposition films on the ion concentration on a cell-free system simulating the cell membrane. The results showed that the ion concentration of K(+), Ca(2+), Na(+), Mg(2+) and SO4(2-) decreased significantly following filtration of the prepared deposition films. More specifically, at a high nano-TiO2 concentration (200 mg L(-1)) and a long nano-TiO2 deposition time (48 h), the concentration of Na(+) decreased from 2958.01 to 2775.72, 2749.86, 2757.36, and 2719.82 mg L(-1), respectively, for the four types of nano-TiO2 studied. Likewise, the concentration of SO4(2-) decreased from 38.83 to 35.00, 35.80, 35.40, and 35.27 mg L(-1), respectively. The other two kinds of typical low toxicity nanomaterials (nano-Al2O3 and nano-SiO2) have a similar impact on the ion concentration change trend. Adsorption of ions on nanoparticles and the hydrated shell around the ions strongly hindered the ions through the nanoparticle films. The endocytosed nanoparticles could be released from the cells without inducing cytotoxicity. Hindering the ion exchange and disrupting the exocytosis process are the main factors that induce cytotoxicity in the presence of excess nano-TiO2 on the cell surface. The current findings may offer a universal principle for understanding the mechanism of cytotoxicity induced by low toxicity nanomaterials.

A combined toxicity study of zinc oxide nanoparticles and vitamin C in food additives.

At present, safety evaluation standards for nanofood additives are made based on the toxic effects of a single additive. Since the size, surface properties and chemical nature influence the toxicity of nanomaterials, the toxicity may have dramatically changed when nanomaterials are used as food additives in a complex system. Herein, we investigated the combined toxicity of zinc oxide nanoparticles (ZnO NPs) and vitamin C (Vc, ascorbic acid). The results showed that Vc increased the cytotoxicity significantly compared with that of the ZnO only NPs. When the cells were exposed to ZnO NPs at a concentration less than 15 mg L(-1), or to Vc at a concentration less than 300 mg L(-1), there was no significant cytotoxicity, both in the case of gastric epithelial cell line (GES-1) and neural stem cells (NSCs). However, when 15 mg L(-1) of ZnO NPs and 300 mg L(-1) of Vc were introduced to cells together, the cell viability decreased sharply indicating significant cytotoxicity. Moreover, the significant increase in toxicity was also shown in the in vivo experiments. The dose of the ZnO NPs and Vc used in the in vivo study was calculated according to the state of food and nutrition enhancer standard. After repeated oral exposure to ZnO NPs plus Vc, the injury of the liver and kidneys in mice has been indicated by the change of these indices. These findings demonstrate that the synergistic toxicity presented in a complex system is essential for the toxicological evaluation and safety assessment of nanofood.

Gram-scale synthesis of single-crystalline graphene quantum dots with superior optical properties.

Graphene quantum dots (GQDs) have various alluring properties and potential applications, but their large-scale applications are limited by current synthetic methods that commonly produce GQDs in small amounts. Moreover, GQDs usually exhibit polycrystalline or highly defective structures and thus poor optical properties. Here we report the gram-scale synthesis of single-crystalline GQDs by a facile molecular fusion route under mild and green hydrothermal conditions. The synthesis involves the nitration of pyrene followed by hydrothermal treatment in alkaline aqueous solutions, where alkaline species play a crucial role in tuning their size, functionalization and optical properties. The single-crystalline GQDs are bestowed with excellent optical properties such as bright excitonic fluorescence, strong excitonic absorption bands extending to the visible region, large molar extinction coefficients and long-term photostability. These high-quality GQDs can find a large array of novel applications in bioimaging, biosensing, light emitting diodes, solar cells, hydrogen production, fuel cells and supercapacitors.

Cytotoxicity evaluation and subcellular location of titanium dioxide nanotubes.

TiO(2) nanotubes (TiO(2)-NTs) are currently attracting a high interest because the intrinsic properties of TiO(2) provide the basis for many outstanding functional features. Herein, we focus on the cytotoxicity and sublocation of TiO(2)-NTs in neural stem cells (NSCs). The cytotoxicity of TiO(2)-NTs is investigated using the methyl tetrazolium cytotoxicity and reactive oxygen species assay, the apoptosis assay by flow cytometry. Cell viability assay shows that TiO(2)-NTs inside cells are nontoxic at the low concentration. A time-dependent relationship is observed, while a dose-dependent relationship is seen only at the concentration higher than 150 µg/ml. The uptake happens shortly after incubation with cells. TiO(2)-NTs can easily pass through the cell membrane and enter into the cells. The uptake amount is increased with prolonging incubation time and reach to maximum at 48 h. Transmission electron microscopy and confocal is used to study subcellular location of TiO(2)-NTs. It is found that TiO(2)-NTs traversed cell membrane and localized in many vesicles (endosomes and lysosomes) and cytoplasm. TiO(2)-NTs in NSCs firstly disperse or metabolism by lysosomal enzymes and then exocytosis from NSCs.