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The aim of this study was to study the effects of human umbilical cord mesenchymal stem cells (HUC-MSCs) on glutathione (GSH) metabolism in human ovarian cancer cells induced by phosphoramide mustard (PM). The experiment was divided into five groups, namely, the blank group (ovarian cancer cells), the control group (ovarian cancer cells + HUC-MSCs), the model group (ovarian cancer cells + PM), the treatment group (ovarian cancer cells + PM + HUC-MSCs), and the inhibitor group (ovarian cancer cells + PM + HUC-MSCs + extracellular signal-regulated protein kinase inhibitor PD98059). The apoptosis rate of ovarian cancer cells was detected by flow cytometry. Intracellular levels of oxidized glutathione (GSSG), GSH, γ-glutamyl cysteine synthetase (γ-GCS), and intracellular reactive oxygen species (ROS) were detected by enzyme-linked immunosorbent assay. Protein imprinting and real-time fluorescence quantitative PCR were used to detect extracellular regulated protein kinase (ERK), p-ERK heme oxygenase-1 (HO-1), and nuclear factor E2-related factor 2 (Nrf2) protein levels. First, the apoptosis rate in the model group was increased compared with that of the blank group. The levels of γ-GCS, p-ERK, HO-1, and Nrf-2 decreased, while the levels of malondialdehyde, GSSG, and ROS increased. Second, compared with the model group, the apoptosis rate in the treatment group decreased. GSH, γ-GCS, p-ERK, HO-1, and Nrf2 levels increased. Malondialdehyde, GSSG, and ROS levels decreased. Third, after the administration of ERK inhibitor, the apoptosis rate of cells increased. GSH, p-ERK, and HO-1 levels decreased. GSSG and ROS levels increased (P < 0.05), and γ-GCS level had a downward trend compared with the treatment group. To conclude, HUC-MSCs may regulate the ERK–Nrf2–HO-1 pathway to increase γ-GCS expression and GSH production, reduce ROS level and apoptosis of ovarian cancer cells, and improve antioxidant capacity.

[Objective] The study aims to explore the antibacterial activity and allelopathy of flavonoids from leaves of Eleutherococcus brachypus, and to provide the basis for the development of plant-derived antimicrobial agents and the application of their allelopathy in plant protection and agricultural production. [Methods] Leaf flavonoids was extracted by an ultrasonic-assisted method from E. brachypus leaves, then the antibacterial sphere, the minimum inhibitory concentration (MIC), the apoptosis rate, MDA content, ROS content, and the activity of antioxidant enzymes of epidermal cells from onion scaly leaves, as well as the inhibitory rate of the onion root and shoot growth were determined with different concentrations of leaf flavonoid extracts (100%, 50%, and 25%). [Results] (1) The yield of leaf flavonoids from E. brachypus was 42.3 mg/g. (2) At same concentration, the diameter of the inhibition zone was S. aureus > B. subtilis > Salmonella, respectively, and expanded with the increase in the extract concentrations with the same strain. The minimum inhibitory concentration of the three strains was also S. aureus < B. subtilis < Salmonella, respectively. (3) Each concentration of leaf flavonoids from E. brachypus induced apoptosis in the upper epidermal cells of Allium cepa. Meanwhile, as the concentration of flavonoid extracts increased, the apoptosis rate, MDA content, and H2O2 content were increased. POD activity and CAT activity were increased first and then decreased during the same time of treatment, which were higher in treatment groups than the control. (4) The growth of root and shoot of the onion scale leaves were inhibited under the treatment of flavonoids extracts, which was negatively correlated with the treatment dose. [Conclusion] The antibacterial effects of the leaf flavonoid extracts of E. brachypus on Gram-positive bacteria are better than that of Gram-negative bacteria, and the antibacterial effects are positively correlated with the concentration of flavonoid extracts. Moreover, all these changes suggest that the allelopathic mechanism of flavonoid extracts from E. brachypus may be due to the overproduction of ROS and the inhibition of antioxidant enzyme activity, which cause oxidative damage to membrane lipids and cell death.

The aim of this study is to assess the impact of serum magnesium (Mg) levels on prognostic outcomes in patients with non-small cell lung cancer (NSCLC) undergoing treatment with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKI). A cohort comprising 91 patients with NSCLC with epidermal growth factor receptor mutations received EGFR-TKI therapy. Assessments of liver and kidney function and electrolyte levels were conducted before treatment initiation and after completing two cycles of EGFR-TKI therapy. Data on variables such as age, gender, presence of distant metastasis, smoking history, other therapeutic interventions, and the specific TKI used were collected for analysis. Cox regression analysis revealed that patients with higher Mg levels prior to EGFR-TKI therapy had significantly longer progression-free survival (PFS) and overall survival (OS). Elevated Mg levels remained predictive of PFS and OS after two cycles of EGFR-TKI therapy. Multiple regression analysis confirmed these findings. Additionally, it was observed that smokers might represent a unique population, demonstrating a correlation between OS and Mg levels. Our findings indicate that serum Mg level is a prognostic factor in patients with NSCLC undergoing EGFR-TKI therapy. This may provide new insights into the underlying mechanisms of EGFR-TKI therapy related to electrolyte balance.

NAC transcription factors (TFs) are one of the largest plant-specific gene families and play important roles in plant growth, development, and the biotic and abiotic stress response. Although the sequencing of Jojoba (Simmondsia chinensis) has been completed, the genome-wide identification and analysis of its NAC TFs has not been reported. In this study, a total of 57 genes were identified in Jojoba, which were divided into eight groups based on phylogenetic analysis. The genes clustered in the same groups have a similar gene structure and motif distribution. Based on the analysis of cis-elements in NAC TFs, nine cis-acting elements were identified in the promoter region that involved in light response, hormonal response, and stress response. Synteny analysis showed a greater collinearity between Jojoba and V. vinifera than Arabidopsis thaliana. The 24 genes in the Jojoba NAC TFs are derived from fragment replication, which may be the main source of NAC amplification. Gene expression analysis identified seven genes that were highly expressed in seeds. The differential expression analysis of NAC TFs in cotyledon and embryonic axis tissues showed that the expression of 10 genes was up-regulated and 1 gene was down-regulated. This study provides more information on the classification, gene structure, conserved motif, and evolution of NAC TFs in Jojoba, facilitating further exploration of their specific functional analysis in Jojoba seed development.

Summary: Immune checkpoint blockade therapies are still ineffective for most patients with colorectal cancer (CRC). Immunogenic cell death (ICD) enables the release of key immunostimulatory signals to drive efficient anti-tumor immunity, which could be used to potentiate the effects of immune checkpoint inhibitors. Here, we showed that inhibition of valosin-containing protein (VCP) elicits ICD in CRC. Meanwhile, VCP inhibitor upregulates PD-L1 expression and compromises anti-tumor immunity in vivo. Mechanistically, VCP transcriptionally regulates PD-L1 expression in a JAK1-dependent manner. Combining VCP inhibitor with anti-PD1 remodels tumor immune microenvironment and reduces tumor growth in mouse models of CRC. Addition of oncolytic virus further augments the therapeutic activity of the combination regimen. Our study shows the molecular mechanism for regulating PD-L1 expression by VCP and suggests that inhibition of VCP has the potential to increase the efficacy of immunotherapy in CRC.

Highlights 1. High-throughput screening of ATG4B inhibitors based on FDA-approved drug library 2. Ebselen can covalently bind to ATG4B at Cys74 3. Ebselen can promote ATG4B oligomerization at Cys292 and Cys361 4. Ebselen suppresses the growth of colorectal cancer cells and xenograft tumors via ATG4B inhibition

Non-alcoholic fatty liver disease (NAFLD) is a type of metabolic stress liver injury closely related to insulin resistance (IR) and genetic susceptibility without alcohol consumption, which encompasses a spectrum of liver disorders ranging from simple hepatic lipid accumulation, known as steatosis, to the more severe form of steatohepatitis (NASH). NASH can progress to cirrhosis and hepatocellular carcinoma (HCC), posing significant health risks. As a multisystem disease, NAFLD is closely associated with systemic insulin resistance, central obesity, and metabolic disorders, which contribute to its pathogenesis and the development of extrahepatic complications, such as cardiovascular disease (CVD), type 2 diabetes mellitus, chronic kidney disease, and certain extrahepatic cancers. Recent evidence highlights the indispensable roles of intestinal barrier dysfunction and gut microbiota in the onset and progression of NAFLD/NASH. This review provides a comprehensive insight into the role of intestinal barrier dysfunction and gut microbiota in NAFLD, including intestinal barrier function and assessment, inflammatory factors, TLR4 signaling, and the gut–liver axis. Finally, we conclude with a discussion on the potential therapeutic strategies targeting gut permeability and gut microbiota in individuals with NAFLD/NASH, such as interventions with medications/probiotics, fecal transplantation (FMT), and modifications in lifestyle, including exercise and diet.

MicroRNAs (miRNAs) are small, noncoding RNAs that play a crucial role in the complex and dynamic network that regulates the apoptosis of porcine ovarian granulosa cells (POGCs). Resveratrol (RSV) is a nonflavonoid polyphenol compound that is involved in follicular development and ovulation. In previous study, we established a model of RSV treatment of POGCs, confirming the regulatory effect of RSV in POGCs. To investigate the miRNA-level effects of RSV on POGCs to reveal differentially expressed miRNAs, a control group (n = 3, 0 μM RSV group), a low RSV group (n = 3, 50 μM RSV group), and a high RSV group (n = 3, 100 μM RSV group) were created for small RNA-seq. In total, 113 differentially expressed miRNAs (DE-miRNAs) were identified, and a RT-qPCR analysis showed a correlation with the sequencing data. Functional annotation analysis revealed that DE-miRNAs in the LOW vs. CON group may be involved in cell development, proliferation, and apoptosis. In the HIGH vs. CON group, RSV functions were associated with metabolic processes and responses to stimuli, while the pathways were related to PI3K24, Akt, Wnt, and apoptosis. In addition, we constructed miRNA-mRNA networks related to Apoptosis and Metabolism. Then, ssc-miR-34a and ssc-miR-143-5p were selected as key miRNAs. In conclusion, this study provided an improved understanding of effects of RSV on POGCs apoptosis through the miRNA modulations. The results suggest that RSV may promote POGCs apoptosis by stimulating the miRNA expressions and provided a better understanding of the role of miRNAs combined with RSV in ovarian granulosa cell development in pigs.

Abstract Intricate assembly of multiple molecular chromophores assisted by protein scaffolds is essential in tuning the optical absorption and energy transfer in the light‐harvesting complexes of the photosynthetic systems in nature. However, it remains a challenge to achieve such structural complexity and functionality in synthetic polymer‐chromophore systems. Here, we report a series of polyester‐tethered pyrrolopyrrole cyanine derivatives and their colloidal nanoparticles dispersed in water, which show tunable J‐ or H‐aggregation excitonic coupling and near‐infrared fluorescence by precise control of the polymer chain lengths, composition, and temperature. Moreover, the optimal fluorescence or photothermal effect of the J‐aggregate nanoparticles enables broad applications in fluorescence or photoacoustic bioimaging and phototherapy.

F1012-2, a novel sesquiterpene lactone isolated from the Chinese herbal medicine Eupatorium lindleyanum DC, exhibits an antitumor effect. In this study, we investigated the anticancer activities of F1012-2 on ten human breast cancer lines and demonstrated significantly lower IC50 values for triple-negative breast cancer (TNBC) than for non-TNBC cell lines. The transcription factors p53 and nuclear factor-κB (NF-κB) are important regulators of tumorigenesis. F1012-2 not only depleted mutant p53, but also activated wild-type p53. F1012-2 reduced the expression of phosphorylated p65 and p105 NF-κB family members and coregulated p53, NF-κB members and their dependent targets. To further clarify the key role of p53, lentivirus small hairpin RNA (shRNA) infection was used to knockdown p53 in MDA-MB-231 cells. F1012-2 significantly reduced the inhibitory effect on cell proliferation and apoptosis, while the levels of p53, NF-κB family members and their dependent genes were not significantly different. F1012-2 exhibited a significant antitumor effect and reduced the expression of p53 in MDA-MB-231 xenografts. Taken together, our results show that F1012-2 exhibited an inhibitory effect on TNBC and affected the regulation of p53/NF-κB signaling pathways.

Purpose: This study aims to develop a prediction model to categorize the risk of early death among breast cancer patients with bone metastases using machine learning models.Methods: This study examined 16,189 bone metastatic breast cancer patients between 2010 and 2019 from a large oncological database in the United States. The patients were divided into two groups at random in a 90:10 ratio. The majority of patients (n = 14,582, 90%) were served as the training group to train and optimize prediction models, whereas patients in the validation group (n = 1,607, 10%) were utilized to validate the prediction models. Four models were introduced in the study: the logistic regression model, gradient boosting tree model, decision tree model, and random forest model.Results: Early death accounted for 17.4% of all included patients. Multivariate analysis demonstrated that older age; a separated, divorced, or widowed marital status; nonmetropolitan counties; brain metastasis; liver metastasis; lung metastasis; and histologic type of unspecified neoplasms were significantly associated with more early death, whereas a lower grade, a positive estrogen receptor (ER) status, cancer-directed surgery, radiation, and chemotherapy were significantly the protective factors. For the purpose of developing prediction models, the 12 variables were used. Among all the four models, the gradient boosting tree had the greatest AUC [0.829, 95% confident interval (CI): 0.802–0.856], and the random forest (0.828, 95% CI: 0.801–0.855) and logistic regression (0.819, 95% CI: 0.791–0.847) models came in second and third, respectively. The discrimination slopes for the three models were 0.258, 0.223, and 0.240, respectively, and the corresponding accuracy rates were 0.801, 0.770, and 0.762, respectively. The Brier score of gradient boosting tree was the lowest (0.109), followed by the random forest (0.111) and logistic regression (0.112) models. Risk stratification showed that patients in the high-risk group (46.31%) had a greater six-fold chance of early death than those in the low-risk group (7.50%).Conclusion: The gradient boosting tree model demonstrates promising performance with favorable discrimination and calibration in the study, and this model can stratify the risk probability of early death among bone metastatic breast cancer patients.

Autophagy is an evolutionarily conserved self-protecting mechanism implicated in cellular homeostasis. ATG4B plays a vital role in autophagy process via undertaking priming and delipidation of LC3. Chemical inhibitors and regulative modifications such as oxidation of ATG4B have been demonstrated to modulate autophagy function. Whether and how ATG4B could be regulated by metal ions is largely unknown. Copper is an essential trace metal served as static co-factors in redox reactions in physiology process. Excessive accumulation of copper in ATP7B mutant cells leads to pathology progression such as insoluble Mallory body (MB) in Wilson disease (WD). The clearance of MB via autophagy pathway was thought as a promising strategy for WD. Here, we discovered that copper ion instead of other ions could inhibit the activity of ATG4B followed by autophagy suppression. In addition, copper could induce ATG4B oligomers depending on cysteine oxidation which could be abolished in reduced condition. Copper also promotes the formation of insoluble ATG4B aggregates, as well as p62-and ubiquitin-positive aggregates, which is consistent with the components of MB caused by copper overload in WD cell model. Importantly, overexpression of ATG4B could partially reduce the formation of MB and rescue impaired autophagy. Taken together, our results uncovered for the first time a new damage mechanism mediated by copper and implied new insights of the crosstalk between the toxicity of copper and autophagy in the pathogenesis of WD.

Erythrocytes are often used for the development of cell membrane camouflaged nanoparticles (NPs) due to their wide range of sources. However, whether the difference between autologous and allogeneic sources for the erythrocyte membranes have an influence on the performance of camouflaged NPs, which is still inconclusive. To this end, we developed two aggregation-induced emission (AIE) photosensitizers camouflaged with erythrocyte membranes (E-M), named E-Mauto@P and E-Mallo@P, which were prepared using autologous- and allogeneic-derived erythrocytes, respectively. In vivo, E-M@P-mediated photodynamic therapy (PDT) effectively inhibited tumor growth, and this therapeutic effect did not differ between E-Mauto@P and E-Mallo@P. Importantly, there were no differences between E-Mauto@P and E-Mallo@P treated mice in terms of general condition, organ function or immune system. Both E-Mauto@P and E-Mallo@P have been shown not to cross the placental barrier and do not affect the development of the embryo, which could be a good platform for the treatment of pregnancy-related disorders. These findings provided more detailed evidences for erythrocyte membrane camouflaged NPs as a promising therapeutic platform, since there is no difference in efficacy or biosafety of either autologous or allogeneic erythrocyte-derived NPs.

Pulmonary arterial hypertension (PAH) is a chronic, lethal pulmonary disease characterized by pulmonary vascular remodeling. It leads to malignant results, such as rupture of pulmonary arterial dissection, dyspnea, right heart failure, and even death. Previous studies have confirmed that one of the main pathological changes of this disease is abnormal mitochondrial dynamics, which include mitochondrial fission, fusion, and autophagy that keep a dynamic balance under certain physiological state. Dynamin-related protein 1 (Drp1), the key molecule in mitochondrial fission, mediates mitochondrial fission while also affecting mitochondrial fusion and autophagy through numerous pathways. There are various abnormalities of Drp1 in PAH pathophysiology, including Drp1 overexpression and activation as well as an upregulation of its outer mitochondrial membrane ligands. These aberrant alterations will eventually induce the development of PAH. With the process of recent studies, the structure and function of Drp1 have been gradually revealed. Meanwhile, inhibitors targeting this pathway have also been discovered. This review aims to shed more light on the mechanism of Drp1 and its inhibitors in the abnormal mitochondrial dynamics of PAH. Furthermore, it seeks to provide more novel insights to clinical therapy.

Myocardial reperfusion is an effective therapy for acute myocardial infarction (AMI). However, ischemia/reperfusion (I/R) injury following myocardial reperfusion is a significant limitation for AMI treatment. Five prime to Xist (FTX) was recognized as a biomarker of multiple diseases, including heart disease. However, the molecular mechanism of FTX in I/R injury is unclear.

No studies have systematically compared time-resolved and multi-tissue innate immune responses for European eels (Anguilla anguilla) with Aeromonas hydrophila infection by a high throughput method. Here, we challenged European eels with A. hydrophila (infected) or PBS (control). A low fatality rate (16.1%) was observed for the infected group at 2 ​d post-infection (dpi). Then we examined transcriptional profiles of intestines, livers and spleens from 12 European eels with/without infection by A. hydrophila at 6, 18 and 36 ​h post-infection (hpi). The results showed that the most differentially expressed genes (DEGs) were found in the spleen at 6 hpi (7569 DEGs), followed by the intestine at 6 hpi (3129 DEGs) and the liver at 18 hpi (2722 DEGs). Only 540, 41 and 130 DEGs were found in the spleen, liver, and intestine at 36 hpi, respectively. The comparison of DEG numbers and enriched KEGG pathways suggested a consistent time-course immune response in these tissues. A similar enrichment of pattern recognition receptors-related pathways including Toll-like receptors, NOD-like receptors and RIG-I-like receptors was found in the liver and spleen, but not in the intestine. Among immune-related DEGs, 62 paralogue pairs were found, and the expression trends of most paralogues were consistent. Some paralogues of immune-related DEGs had unique domains. Furthermore, large clusters representing similar tissue were shown for the intestine and spleen. A different co-expression network involved in cytokine signal transduction and interaction existed between the liver and spleen. This study has provided time-resolved and multi-tissue transcriptome characteristics of A. anguilla in response to A. hydrophila infection.

Environmental DNA (eDNA) originates from cellular material shed by organisms into aquatic or terrestrial environments and can be sampled and monitored using metabarcoding technology, which is revolutionizing fish biodiversity monitoring. Several reviews concerning fish eDNA have focused on standard sampling methods and its applications, though a systematic review focused on marker genes, databases, and bioinformatic pipelines has not yet been published. Here, we present a comprehensive literature review of studies applying metabarcoding technology to fish eDNA for the purpose of fish biodiversity monitoring. We systematically provide the available universal primers used to amplify barcoding sequences from fish eDNA, and then discuss reference barcoding databases, relevant bioinformatic analyses, as well as developed pipelines. The performances of universal primers and their relevant reference databases are summarized. Combined use of multiple primer pairs targeted for more than one gene marker (e.g., 12S, 16S, Cytb, COI), and use of both local and public databases are recommended as approaches to improve the sensitivity and reliability of fish eDNA analyses. We also compare the effectiveness of eDNA metabarcoding to traditional approaches for monitoring fish biodiversity and highlight challenges and future perspectives associated with this new tool. Ultimately, we advocate for greater incorporation of eDNA analysis into fish biodiversity assessments to assist environmental managers.

The complex and diverse structural forms make it impossible to define universal shape coefficients for large-span roof structures, which usually need to be obtained by wind tunnel tests. However, the number of test measurement points is limited, which leads to obvious limitations in the study of wind loads on large-span roof structures. Taking a large-span folded-plate roof as an example, based on the wind tunnel pressure test results of the rigid model, the proper orthogonal decomposition (POD) method is used to reconstruct the wind pressure field of the roof using the first several eigenmodes. The wind pressure of several typical characteristic points is predicted based on four different interpolations methods, and the accuracy and feasibility of POD method in reconstruction and prediction of wind pressure field of large-span roof are analyzed and studied from multiple perspectives. The results show that the order of the selected structural eigenmodes has an impact on the reconstruction accuracy of the wind pressure field. The more orders are selected, the closer the wind pressure field reconstruction is to the true value. The reconstruction effect of the wind pressure field based on the POD method is related to the spatial position of the predicted point, and the reconstruction effect of the wind field based on the fluctuating wind pressure is obviously better than the that based on the mean wind pressure. When the POD method is used to predict the wind pressure of an unknown point, different interpolation methods can achieve ideal results. Among them, the bilinear interpolation method has the highest prediction accuracy, and the adjacent point interpolation method and Griddata V4 interpolation method only have certain errors in the low frequency region.

Aberrant Notch signaling profoundly affects cancer progression. Especially the Notch3 receptor was found to be dysregulated in cancer, where its expression is correlated with worse clinicopathological features and poor prognosis. The activation of Notch3 signaling is closely related to the activation of cancer stem cells (CSCs), a small subpopulation in cancer that is responsible for cancer progression. In addition, Notch3 signaling also contributes to tumor chemoresistance against several drugs, including doxorubicin, platinum, taxane, epidermal growth factor receptor (EGFR)–tyrosine kinase inhibitors (TKIs) and gemcitabine, through complex mechanisms. In this review, we mainly focus on discussing the molecular mechanisms by which Notch3 modulates cancer stemness and chemoresistance, as well as other cancer behaviors including metastasis and angiogenesis. What’s more, we propose potential treatment strategies to block Notch3 signaling, such as non-coding RNAs, antibodies and antibody-drug conjugates, providing a comprehensive reference for research on precise targeted cancer therapy.

Faced with the challenges posed by infectious diseases and cancer, nucleic acid vaccines present excellent prospects in clinical applications. Compared with traditional vaccines, nucleic acid vaccines have the characteristics of high efficiency and low cost. Therefore, nucleic acid vaccines have potential advantages in disease prevention and treatment. However, the low immunogenicity and instability of nucleic acid vaccines have limited their development. Therefore, a large number of studies have been conducted to improve their immunogenicity and stability by improving delivery methods, thereby supporting progress and development for clinical applications. This article mainly reviews the advantages, disadvantages, mechanisms, delivery methods, and clinical applications of nucleic acid vaccines.

One of the main functions of physiological color change is thermoregulation. This change occurs much more rapidly than morphological color change, but the underlying mechanism remains poorly understood. Here, we studied the thermal dependence and molecular basis of physiological color change in lizards using Takydromus septentrionalis (Lacertidae) as the model system. Body color was thermally sensitive, becoming increasingly light as body temperatures deviated from the level (∼30°C) preferred by this species. We identified 3389 differentially expressed genes (DEGs) between lizards at 24°C and 30°C, and 1,097 DEGs between lizards at 36°C and 30°C. Temperature affected the cAMP signal pathway, motor proteins, cytoskeleton, and the expression of genes related to melanocyte-stimulating hormone (MSH) and melanocyte-concentrating hormone (MCH). Our data suggest that the role of physiological color change in thermoregulation is achieved in T. septentrionalis by altering the arrangement of pigments and thus the amount of solar radiation absorbed and reflected. G protein-coupling system inhibits adenylate cyclase activity to transform ATP into cAMP and thereby causes rapid pigment aggregation. MCH deactivates the G proteins and thereby initiates pigment dispersion. This mechanism differs from that reported for teleost fish where MCH activates the G proteins and thereby causes pigment aggregation. This article has an associated First Person interview with the first author of the paper.

The bearing capacity of an open caisson under lateral loads is a key factor affecting the normal operation of an open caisson. It will inevitably have a disturbing effect on the surrounding soil layers during the sinking process of the caisson; that is, a disturbance ring will develop around the caisson. Based on the Jurong Yangtze River water supply project, the lateral bearing characteristics of the open caisson are analyzed by the numerical method with due consideration to soil disturbance, and the reinforcement scheme is optimized. The numerical results show that when the thickness of the disturbance ring is less than 0.5 m the disturbance ring has little effect on the lateral bearing capacity of the open caisson. An arc-shaped cement–soil reinforcement at the loading area can effectively improve the lateral bearing performance of the caisson. The optimized reinforcement thickness is 2 times that of the disturbance ring, and the reinforcement angle is approximately 60°.

Summary: Glioblastoma multiforme (GBM) is among the most aggressive of human cancers. Although differentiation therapy has been proposed as a potential approach to treat GBM, the mechanisms of induced differentiation remain poorly defined. Here, we established an induced differentiation model of GBM using cAMP activators that specifically directed GBM differentiation into astroglia. Transcriptomic and proteomic analyses revealed that oxidative phosphorylation and mitochondrial biogenesis are involved in induced differentiation of GBM. Dibutyryl cyclic AMP (dbcAMP) reverses the Warburg effect, as evidenced by increased oxygen consumption and reduced lactate production. Mitochondrial biogenesis induced by activation of the CREB-PGC1α pathway triggers metabolic shift and differentiation. Blocking mitochondrial biogenesis using mdivi1 or by silencing PGC1α abrogates differentiation; conversely, overexpression of PGC1α elicits differentiation. In GBM xenograft models and patient-derived GBM samples, cAMP activators also induce tumor growth inhibition and differentiation. Our data show that mitochondrial biogenesis and metabolic switch to oxidative phosphorylation drive the differentiation of tumor cells. : Xing et al. show that the metabolic shift from glycolysis to oxidative phosphorylation drives differentiation of GBM cells into astrocytes by cAMP activation. Mechanistically, the cAMP-CREB-PGC1α signal mediates mitochondrial biogenesis, which leads to metabolic reprogramming, induced differentiation, and tumor growth inhibition. Keywords: glioblastoma, induced differentiation, Warburg effect, metabolic reprogramming, oxidative phosphorylation, glycolysis, mitochondrial biogenesis, cyclic adenosine monophosphate, cAMP, PPARγ coactivator-1α, PGC1α

We present a patient with a unique neurological phenotype with a progressive neurodegenerative. An 18-year diagnostic odyssey for the patient ended when exome sequencing identified a homozygous PEX16 mutation suggesting an atypical peroxisomal biogenesis disorder (PBD). Interestingly, the patient's peroxisomal biochemical abnormalities were subtle, such that plasma very-long-chain fatty acids initially failed to provide a diagnosis. This case suggests that next-generation sequencing may be diagnostic in some atypical peroxisomal biogenesis disorders.

Comparative chromosome banding analysis and/or fluorescence in situ hybridization (FISH) studies are established approaches to compare human and ape chromosomes. FISH banding is a relatively new and not routinely applied method very well suited to provide to a better understanding of the evolutionary history of primate and human phylogeny. Here multicolor banding (MCB)-applying probes derived from Homo sapiens were used to analyze the chromosomes of Thai crab-eating macaque (Macaca fascicularis). The results agree with those of previous studies in other macaques, e.g. Macaca sylvanus or Macaca nemestrina. This result highlights that morphological differences within the Cercopithecoidea must be found rather in subchromosomal changes or even in epigenetics than in gross structural alterations.

Open reading frame (ORF) 45 of Kaposi's sarcoma-associated herpesvirus (KSHV) is a tegument protein. A genetic analysis with a null mutant suggested a possible role for this protein in the events leading to viral egress. In this study, ORF45 was found to interact with KIF3A, a kinesin-2 motor protein that transports cargoes along microtubules to cell periphery in a yeast two-hybrid screen. The association was confirmed by both co-immunoprecipitation and immunoflorescence approaches in primary effusion lymphoma cells following virus reactivation. ORF45 principally mediated the docking of entire viral capsid-tegument complexes onto the cargo-binding domain of KIF3A. Microtubules served as the major highways for transportation of these complexes as evidenced by drastically reduced viral titers upon treatment of cells with a microtubule depolymerizer, nocodazole. Confocal microscopic images further revealed close association of viral particles with microtubules. Inhibition of KIF3A-ORF45 interaction either by the use of a headless dominant negative (DN) mutant of KIF3A or through shRNA-mediated silencing of endogenous KIF3A expression noticeably decreased KSHV egress reflecting as appreciable reductions in the release of extracellular virions. Both these approaches, however, failed to impact HSV-1 egress, demonstrating the specificity of KIF3A in KSHV transportation. This study thus reports on transportation of KSHV viral complexes on microtubules by KIF3A, a kinesin motor thus far not implicated in virus transportation. All these findings shed light on the understudied but significant events in the KSHV life cycle, delineating a crucial role of a KSHV tegument protein in cellular transport of viral particles.

Abstract Background Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not reproducible in similar experiments. Meanwhile, new statistical methods for identifying DEGs continue to appear in the scientific literature. The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists. Results Using the data sets generated by the MicroArray Quality Control (MAQC) project, we investigated the impact on the reproducibility of DEG lists of a few widely used gene selection procedures. We present comprehensive results from inter-site comparisons using the same microarray platform, cross-platform comparisons using multiple microarray platforms, and comparisons between microarray results and those from TaqMan – the widely regarded "standard" gene expression platform. Our results demonstrate that (1) previously reported discordance between DEG lists could simply result from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion with a non-stringent P-value cutoff filtering, the DEG lists become much more reproducible, especially when fewer genes are selected as differentially expressed, as is the case in most microarray studies; and (3) the instability of short DEG lists solely based on P-value ranking is an expected mathematical consequence of the high variability of the t-values; the more stringent the P-value threshold, the less reproducible the DEG list is. These observations are also consistent with results from extensive simulation calculations. Conclusion We recommend the use of FC-ranking plus a non-stringent P cutoff as a straightforward and baseline practice in order to generate more reproducible DEG lists. Specifically, the P-value cutoff should not be stringent (too small) and FC should be as large as possible. Our results provide practical guidance to choose the appropriate FC and P-value cutoffs when selecting a given number of DEGs. The FC criterion enhances reproducibility, whereas the P criterion balances sensitivity and specificity.

The proto-oncoprotein Raf is pivotal for mitogen-activated protein kinase (MAPK) signaling, and its aberrant activation has been implicated in multiple human cancers. However, the precise molecular mechanism of Raf activation, especially for B-Raf, remains unresolved. By genetic and biochemical studies, we demonstrate that phosphorylation of tyrosine 510 is essential for activation of Drosophila Raf (Draf), which is an ortholog of mammalian B-Raf. Y510 of Draf is phosphorylated by the c-src homolog Src64B. Acidic substitution of Y510 promotes and phenylalanine substitution impairs Draf activation without affecting its enzymatic activity, suggesting that Y510 plays a purely regulatory role. We further show that Y510 regulates Draf activation by affecting the autoinhibitory interaction between the N- and C-terminal fragments of the protein. Finally, we show that Src64B is required for Draf activation in several developmental processes. Together, these results suggest a novel mechanism of Raf activation via Src-mediated tyrosine phosphorylation. Since Y510 is a conserved residue in the kinase domain of all Raf proteins, this mechanism is likely evolutionarily conserved.

[Objective] The rapid advancements in information technology and transportation have greatly augmented the influence of flow elements on shaping spatial patterns. The integration of flow elements with geospatial morphological elements is gaining significance in optimizing territorial spatial planning. This study aimed to explore the approaches and methodologies for assessing the suitability of territorial space development by integrating forms and flows, which may provide essential support for the optimizing of territorial spatial patterns. [Methods] In this study, we employed mobile signaling data, geospatial data, and other diverse information sources to develop an evaluation indicator system known as “form-flow integration”. This system was designed to assess the suitability of territorial space development. Spatial overlay, k-means clustering, and hierarchical analysis methods were used to perform an integrated evaluation of the suitability of territorial space development in the Nanjing Metropolitan Area. [Results] (1) The territorial space development suitability in the Nanjing Metropolitan Area shows distinct characteristics of concentrated agglomeration around a single center and spatial differentiation. Suitable regions are primarily concentrated in the urbanized areas of Nanjing-Ma’anshan-Chuzhou and Nanjing-Zhenjiang-Yangzhou, as well as the Jinshan District and Liyang City of Changzhou. On the contrary, the regions that are not suitable are predominantly situated in Chuzhou, Ma’anshan, and Xuancheng. (2) The evaluation findings pertaining to the geospatial morphological elements indicate that Nanjing City functions as the central hub of the metropolitan area, while multiple city center areas serve as diverse high development suitability hubs. This exemplifies a spatial distribution characteristic known as “one core and multiple poles”. Geospatial morphological elements play a pivotal role in the development of territorial space. (3) The evaluation results of flow elements partially depict the genuine dynamic characteristics of the territorial spatial structure, thereby unveiling a spatial pattern characterized by a “core-periphery” nature. There are substantial variations in the development suitability of Nanjing, Chuzhou, and Xuancheng Cities. The existence of a significant “siphon effect” in Nanjing City, along with persistent administrative obstacles across different regions, is apparent. [Conclusion] This study contributes to the advancement of evaluating the suitability of territorial space development by integrating “form” and “flow” elements. The evaluation method for development suitability is optimized, with regional functionality as the central focus. Additionally, this study proves the applicability of the new method at the scale of metropolitan area, which provides theoretical reference for the optimization of territorial spatial pattern in metropolitan area.

Abstract Background In the last decade, a large amount of microarray gene expression data has been accumulated in public repositories. Integrating and analyzing high-throughput gene expression data have become key activities for exploring gene functions, gene networks and biological pathways. Effectively utilizing these invaluable microarray data remains challenging due to a lack of powerful tools to integrate large-scale gene-expression information across diverse experiments and to search and visualize a large number of gene-expression data points. Results Gene Expression Browser is a microarray data integration, management and processing system with web-based search and visualization functions. An innovative method has been developed to define a treatment over a control for every microarray experiment to standardize and make microarray data from different experiments homogeneous. In the browser, data are pre-processed offline and the resulting data points are visualized online with a 2-layer dynamic web display. Users can view all treatments over control that affect the expression of a selected gene via Gene View, and view all genes that change in a selected treatment over control via treatment over control View. Users can also check the changes of expression profiles of a set of either the treatments over control or genes via Slide View. In addition, the relationships between genes and treatments over control are computed according to gene expression ratio and are shown as co-responsive genes and co-regulation treatments over control. Conclusion Gene Expression Browser is composed of a set of software tools, including a data extraction tool, a microarray data-management system, a data-annotation tool, a microarray data-processing pipeline, and a data search & visualization tool. The browser is deployed as a free public web service (http://www.ExpressionBrowser.com) that integrates 301 ATH1 gene microarray experiments from public data repositories (viz. the Gene Expression Omnibus repository at the National Center for Biotechnology Information and Nottingham Arabidopsis Stock Center). The set of Gene Expression Browser software tools can be easily applied to the large-scale expression data generated by other platforms and in other species.

Abstract Background An important goal of comparative genomics is the identification of functional elements through conservation analysis. Phylo-HMM was recently introduced to detect conserved elements based on multiple genome alignments, but the method has not been rigorously evaluated. Results We report here a simulation study to investigate the power of phylo-HMM. We show that the power of the phylo-HMM approach depends on many factors, the most important being the number of species-specific genomes used and evolutionary distances between pairs of species. This finding is consistent with results reported by other groups for simpler comparative genomics models. In addition, the conservation ratio of conserved elements and the expected length of the conserved elements are also major factors. In contrast, the influence of the topology and the nucleotide substitution model are relatively minor factors. Conclusion Our results provide for general guidelines on how to select the number of genomes and their evolutionary distance in comparative genomics studies, as well as the level of power we can expect under different parameter settings.