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As an important research topic in recent years, semantic segmentation has been widely applied to image understanding problems in various fields. With the successful application of deep learning methods in machine vision, the superior performance has been transferred to agricultural image processing by combining them with traditional methods. Semantic segmentation methods have revolutionized the development of agricultural automation and are commonly used for crop cover and type analysis, pest and disease identification, etc. We first give a review of the recent advances in traditional and deep learning methods for semantic segmentation of agricultural images according to different segmentation principles. Then we introduce the traditional methods that can effectively utilize the original image information and the powerful performance of deep learning-based methods. Finally, we outline their applications in agricultural image segmentation. In our literature, we identify the challenges in agricultural image segmentation and summarize the innovative developments that address these challenges. The robustness of the existing segmentation methods for processing complex images still needs to be improved urgently, and their generalization abilities are also insufficient. In particular, the limited number of labeled samples is a roadblock to new developed deep learning methods for their training and evaluation. To this, segmentation methods that augment the dataset or incorporate multimodal information enable deep learning methods to further improve the segmentation capabilities. This review provides a reference for the application of image semantic segmentation in the field of agricultural informatization.

Background: Several scholarly publications have thoroughly examined the significant role of autophagy in the pathogenesis, progression, and treatment of retinal diseases. This research utilized bibliometric analysis to identify the primary areas of focus and emerging trends within the discipline and offer a comprehensive summary. Methods: The research articles and reviews regarding autophagy and retinal diseases from 2009-01-01 to 2022-12-31 were from the Web of Science Core Collection (WOSCC). The software VOSviewer and CiteSpace were applied to analyze and visualize maps of countries, organizations, authors, journals, keyword networks, and citations in the field of autophagy in retinal diseases. Results: 854 qualified records (721 articles and 133 reviews) were retrieved in this research. The annual publication output of literature shows a growing trend. China is the most productive country, and the author with the most publications is Kai Kaarniranta. Journal Autophagy published the most articles in this field. Keywords analysis can effectively reflect the research hot spots and indicate that diabetic retinopathy and glaucoma have drawn more attention recently. Researchers have shifted the research emphasis on “AMPK”, “angiogenesis”, “mutation”, and “inflammation”. Conclusions: With the bibliometric analysis approach, we presented the number of publications, countries, regions, authors, institutions, keywords, and citations, which further helps researchers understand the hot spots and trends in the field of autophagy in retinal diseases and explore the issues in the rapidly developing area.

Summary: Increasing pollution of heavy metals poses great risks to animals globally. Their survival likely relies on an ability to detect and avoid harmful heavy metal ions (HMIs). Currently, little is known about the neural mechanisms of HMI detection. Here, we show that Drosophila and related species of Drosophilidae actively avoid toxic HMIs at micromolar concentrations. The high sensitivity to HMIs is biologically relevant. Particularly, their sensitivity to cadmium is as high as that to the most bitter substance, denatonium. Detection of HMIs in food requires Gr66a+ gustatory neurons but is independent of bitter-taste receptors. In these neurons, the ionotropic receptors IR76b, IR25a, and IR7a are required for the perception of heavy metals. Furthermore, IR47a mediates the activation of a distinct group of non-Gr66a+ gustatory neurons elicited by HMIs. Together, our findings reveal a surprising taste quality represented by noxious metal ions.

Background: Adverse eating behaviors and a high rate of obesity have been identified among children diagnosed with attention deficit hyperactivity disorder (ADHD). In this study, we investigate the relationships between eating behaviors and body fat mass among children with ADHD. Methods: All participants were recruited from the Children's Health Care Department of the Children's Hospital of Nanjing Medical University from June 2019 to June 2020. ADHD was diagnosed according to the diagnostic criteria of the 5th edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) by psychiatrists. Core ADHD symptoms defined by the DSM-5 were inattention and hyperactivity/impulsivity. The anthropomorphic indices defined by the World Health Organization (WHO) were utilized in this study (body mass index [BMI], underweight, normal body mass, overweight, obesity, short stature). Body fat mass, fat mass percentage (FM%), skeletal muscle mass, skeletal muscle mass percentage (SMM%) were tested via body composition meter, and eating behaviors were assessed by parents using the Chinese version of the Children's Eating Behavior Questionnaire (CEBQ). The CEBQ was comprised of subscales related to food avoidant behaviors (satiety responsiveness, slowness in eating, fussiness, and emotional undereating) and food approach behaviors (food responsiveness, enjoyment of Food, desire to drink, and emotional overeating). The associations among ADHD, obesity and adverse eating behavior were tested through correlation analysis, and a mediating effect model was established to explore the effect of eating behaviors. Results: A total of 548 participants aged 4–12 years were recruited. Among them, 396 were diagnosed with ADHD, with the remaining 152 enrolled in a control group. Compared with the control group, the ADHD group had higher incidences of overweight (22.5% vs. 14.5%) and obesity (13.4% vs. 8.6%) (p

Summary: The courtship ritual is a dynamic interplay between males and females. Courtship successfully leading to copulation is determined by the intention of both parties which is conveyed by complex action sequences. In Drosophila, the neural mechanisms controlling the female’s willingness to mate, or sexual receptivity, have only recently become the focus of investigations. Here, we report that pre-mating sexual receptivity in females requires activity within a subset of serotonergic projection neurons (SPNs), which positively regulate courtship success. Of interest, a male-derived sex peptide, SP, which was transferred to females during copulation acted to inhibit the activity of SPN and suppressed receptivity. Downstream of 5-HT, subsets of 5-HT7 receptor neurons played critical roles in SP-induced suppression of sexual receptivity. Together, our study reveals a complex serotonin signaling system in the central brain of Drosophila which manages the female’s desire to mate.

SiO2/Cu equipment-friendly infrared interfering agent was built from tetraethoxysilane and flake copper powder through in-situ synthesis reaction. SEM images indicated the encapsulation structure of the samples. FT-IR, XPS and XRD spectra revealed the presence of SiO2 that was coated into the surface and edge of Cu. The shielding performance and the electrical property could be controlled by adjusting the content of SiO2. The infrared transmittance of SiO2/Cu was 23.29% at 1 ∼ 3 μm, 22.92% at 3 ∼ 5 μm and 21.70% at 8 ∼ 14 μm. The mass extinction coefficient was 1.47 m2·g−1 at 1 ∼ 3 μm, 1.48 m2·g−1 at 3 ∼ 5 μm and 1.54 m2·g−1 at 8 ∼ 14 μm, and the resistivity was 1.20 × 1010 Ω·cm at 10 MPa. There was no significant difference found between the shielding performance of Cu and SiO2/Cu. Deposition of SiO2 in this structure supplies high resistivity and excellent shielding performance, and provides highly efficient infrared interfering agent without damaging the basic structure of Cu. This work demonstrates that in-situ synthesis method is a facile and efficient strategy to obtaining optimal shielding performance of SiO2/Cu equipment-friendly infrared interfering agent and met the expectations and synthesis methods from our original material design.

Trans-resveratrol (RES), a well-known polyphenol exerts various health-promoting benefits, including glucose homeostasis maintenance. Here, we have investigated the impact of insulin resistance (IR) on RES disposition. Rats were fed with 10%-fructose-water for 8 weeks for developing IR. The systemic exposure to RES significantly decreased (IR vs normal, AUC0-24h, 1.73, 3.79, 9.27 vs 2.50, 6.12, 12.6 μM∙h, 20, 50, 100 mg/kg, p

miR675 is highly expressed in several human tumor tissues and positively regulates cell progression. Herein, we demonstrate that miR675 promotes malignant transformation of human mesenchymal stem cells. Mechanistically, we reveal that miR675 enhances the expression of the polyubiquitin-binding protein p62. Intriguingly, P62 competes with SETD2 to bind histone H3 and then significantly reduces SETD2-binding capacity to substrate histone H3, triggering drastically the reduction of three methylation on histone H3 36th lysine (H3K36me3). Thereby, the H3K36me3-hMSH6-SKP2 triplex complex is significantly decreased. Notably, the ternary complex’s occupancy capacity on chromosome is absolutely reduced, preventing it from DNA damage repair. By virtue of the reductive degradation ability of SKP2 for aging histone H3.3 bound to mismatch DNA, the aging histone H3.3 repair is delayed. Therefore, the mismatch DNA escapes from repair, triggering the abnormal expression of several cell cycle-related genes and causing the malignant transformation of mesenchymal stem cells. These observations strongly suggest understanding the novel functions of miR675 will help in the development of novel therapeutic approaches in a broad range of cancer types. Keywords: miR675, human mesenchymal stem cell, malignant transformation, P62

Soymilk fermentation with kombucha was perfomed at 28 °C and 37 °C, and changes in the number of microorganisms, bioactivity and chemical compositions were analyzed during fermentation. Yeast, acetic acid bacteria (AAB), and lactic acid bacteria (LAB) showed substantial growth in the soymilk, and fermentation at 37 °C and 28 °C promoted the growth of LAB and AAB, respectively. The flatulence factors of raffinose and stachyose were entirely and mostly consumed during fermentation, respectively. Nearly all the glucoside isoflavones were transformed into aglycone isoflavones by β-glucosidase hydrolysis. Total phenolic, ferulic, chlorogenic and ascorbic acid (VC) contents significantly increased after fermentation. The antioxidant and inhibition activities to α-glucosidase and α-amylase of kombucha-fermented soymilk significantly increased, and were higher at 37 °C than at 28 °C. In conclusion, fermentation with kombucha can enhance the health-promoting properties of soymilk.

MicroRNAs are known to be involved in carcinogenesis. Recently, microRNA-372 (miR372) has been proven to play a substantial role in several human cancers, but its functions in liver cancer remain unclear. Herein, our results demonstrate that miR372 accelerates growth of liver cancer cells in vitro and in vivo. Mechanistically, miR372 enhances expression of Y-box-binding protein 1 (YB-1) by targeting for phosphatase and tensin homolog (PTEN) directly and consequently promotes phosphorylation of YB-1 via HULC looping dependent on ERK1/2 and PTEN. In particular, HULC knockdown or PTEN overexpression abrogated this miR372 action. Moreover, miR372 inhibits the degradation of β-catenin dependent on phosphorylation of YB-1 and then enhances the expression and activity of pyruvate kinase M2 isoform (PKM2) by β-catenin-LEF/TCF4 pathway. Furthermore, the loading of LEF/TCF4 on PKM2 promoter region was significantly increased in miR372 overexpressing Hep3B, and thus, glycolytic proton efflux rate (glycoPER) was significantly increased in rLV-miR372 group compared to the rLV group. Moreover, β-catenin knockdown abrogates this function of miR372. Ultimately, miR372 promotes the expression of erbB-2 through PKM2-pH3T11-acetylation on histone H3 lysine 9 (H3K9Ac) pathway. Of significance, both YB-1 knockdown and erbB-2 knockdown abrogate oncogenic action of miR372. Our observations suggest that miR372 promotes liver cancer cell cycle progress by activating cyclin-dependent kinase 2 (CDK2)-cyclin E-P21/Cip1 complex through miR372-YB-1-β-catenin-LEF/TCF4-PKM2-erbB-2 axis. This study elucidates a novel mechanism for miR372 in liver cancer cells and suggests that miR372 can be used as a novel therapeutic target of liver cancer.

Inflammatory and autophagy-related gene P62 is highly expressed in most human tumor tissues. Herein, we demonstrate that P62 promotes human mesenchymal stem cells’ malignant transformation via the cascade of P62-tumor necrosis factor alpha (TNF-α)-CUDR-CTCF-insulin growth factor II (IGFII)-H-Ras signaling. Mechanistically, we reveal P62 enhances IGFII transcriptional activity through forming IGFII promoter-enhancer chromatin loop and increasing METTL3 occupancy on IGFII 3′ UTR and enhances H-Ras overexpression by harboring inflammation-related factors, e.g., TNFR1, CLYD, EGR1, NFκB, TLR4, and PPARγ. Furthermore, the P62 cooperates with TNF-α to promote malignant transformation of mesenchymal stem cells. These findings, for the first time, provide insight into the positive role that P62 plays in malignant transformation of mesenchymal stem cells and reveal a novel link between P62 and the inflammation factors in mesenchymal stem cells.

Motivated by the possible large annihilation contributions implied by recent CDF and LHCb measurements on nonleptonic annihilation B-meson decays, and the refined experimental measurements on hadronic B-meson decays, we study the strength of annihilation contributions within QCD factorization (QCDF) in this paper. With the available measurements of two-body Bu,d,s→ππ,πK,KK decays, a comprehensive fit on the phenomenological parameters XAi,f (or ρAi,f and ϕAi,f) which are used to parameterize the endpoint singularity in annihilation amplitudes is performed with the statistical χ2 approach. It is found that (1) flavor symmetry breaking effects are hardly to be distinguished between XA,si and XA,di due to the large experimental errors and theoretical uncertainties, where XA,si and XA,di are related to the nonfactorization annihilation contributions in Bs and Bu,d decay, respectively. So XA,si≃XA,di is a good approximation by now. (2) In principle, parameter XAf which is related to the factorization annihilation contributions and independent of the initial state can be regarded as the same variable for Bu,d,s decays. (3) Numerically, two solutions are found, one is (ρAi,ϕAi[°])=(2.98−0.86+1.12,−105−24+34) and (ρAf,ϕAf[°])=(1.18−0.23+0.20,−40−8+11), the other is (ρAi,ϕAi[°])=(2.97−0.90+1.19,−105−24+32) and (ρAf,ϕAf[°])=(2.80−0.21+0.25,165−3+4). Obviously, nonfactorization annihilation parameter XAi is generally unequal to factorization annihilation parameter XAf, which differs from the traditional treatment. With the fitted parameters, all results for observables of Bu,d,s→ππ,πK,KK decays are in good agreement with experimental data.

The Kelch-like ECH-associated protein 1 (KEAP1) – Nuclear factor erythroid 2 -related factor 2 (NRF2) pathway is the major transcriptional stress response system in cells against oxidative and electrophilic stress. NRF2 is frequently constitutively active in many cancers, rendering the cells resistant to chemo- and radiotherapy. Loss-of-function (LOF) mutations in the repressor protein KEAP1 are common in non-small cell lung cancer, particularly adenocarcinoma. While the mutations can occur throughout the gene, they are enriched in certain areas, indicating that these may have unique functional importance. In this study, we show that in the GSEA analysis of TCGA lung adenocarcinoma RNA-seq data, the KEAP1 mutations in R320 and R470 were associated with enhanced Tumor Necrosis Factor alpha (TNFα) – Nuclear Factor kappa subunit B (NFκB) signaling as well as MYC and MTORC1 pathways. To address the functional role of these hotspot mutations, affinity purification and mass spectrometry (AP-MS) analysis of wild type (wt) KEAP1 and its mutation forms, R320Q and R470C were employed to interrogate differences in the protein interactome. We identified TNF receptor associated factor 2 (TRAF2) as a putative protein interaction partner. Both mutant KEAP1 forms showed increased interaction with TRAF2 and other anti-apoptotic proteins, suggesting that apoptosis signalling could be affected by the protein interactions. A549 lung adenocarcinoma cells overexpressing mutant KEAP1 showed high TRAF2-mediated NFκB activity and increased protection against apoptosis, XIAP being one of the key proteins involved in anti-apoptotic signalling. To conclude, KEAP1 R320Q and R470C and its interaction with TRAF2 leads to activation of NFκB pathway, thereby protecting against apoptosis.

Microbial fuel cell (MFC) could uses microorganisms to convert the solid wastes into electrical energy. Lead contaminated soil was remediated in MFC through internal electric field reduction, where Pb(II) was reduced to Pb produced on the cathode. When the composite remediation agents of MgO, Ca(H2PO4)2and montmorillonite were added to the soil, Pb can be solidified and adsorbed in the soil, which reduces the toxicity of lead leaching in the soil and makes Pb exist stably in the soil. After synergistic bioremediation, the Pb concentration was decreased by 374.62 mg/kg, whereas Pb in the acetic acid extractable state was mainly transformed into that in reducible state oxidizable state and residue state. Pb removal efficiency of contaminated soil at pH of 5 was the highest of 22.28% after remediation. The Pb removal efficiency at 10 g/kg Pb was 21.02%. The proportion of acetic acid extracted was decreased by 24.26%∼32.36%, 20.54%∼28.69%, and 34.09∼42.78% at the initial lead concentration of 2.5 g/kg, 5 g/kg and 10 g/kg, respectively. The proportion of extractable acetic acid in 10 g/kg Pb contaminated soil was decreased most, converting to oxidizable state (increased by 18.50%∼22.79%) and residue state (increased by 10.57%∼21.10%). This study provides alternative technology for the remediation of Pb contaminated soil in high concentration.

Drug-induced hyperglycemia/diabetes is a global issue. Some drugs induce hyperglycemia by activating the pregnane X receptor (PXR), but the mechanism is unclear. Here, we report that PXR activation induces hyperglycemia by impairing hepatic glucose metabolism due to inhibition of the hepatocyte nuclear factor 4-alpha (HNF4α)‒glucose transporter 2 (GLUT2) pathway. The PXR agonists atorvastatin and rifampicin significantly downregulated GLUT2 and HNF4α expression, and impaired glucose uptake and utilization in HepG2 cells. Overexpression of PXR downregulated GLUT2 and HNF4α expression, while silencing PXR upregulated HNF4α and GLUT2 expression. Silencing HNF4α decreased GLUT2 expression, while overexpressing HNF4α increased GLUT2 expression and glucose uptake. Silencing PXR or overexpressing HNF4α reversed the atorvastatin-induced decrease in GLUT2 expression and glucose uptake. In human primary hepatocytes, atorvastatin downregulated GLUT2 and HNF4α mRNA expression, which could be attenuated by silencing PXR. Silencing HNF4α downregulated GLUT2 mRNA expression. These findings were reproduced with mouse primary hepatocytes. Hnf4α plasmid increased Slc2a2 promoter activity. Hnf4α silencing or pregnenolone-16α-carbonitrile (PCN) suppressed the Slc2a2 promoter activity by decreasing HNF4α recruitment to the Slc2a2 promoter. Liver-specific Hnf4α deletion and PCN impaired glucose tolerance and hepatic glucose uptake, and decreased the expression of hepatic HNF4α and GLUT2. In conclusion, PXR activation impaired hepatic glucose metabolism partly by inhibiting the HNF4α‒GLUT2 pathway. These results highlight the molecular mechanisms by which PXR activators induce hyperglycemia/diabetes.

Summary: The paired-like homeobox transcription factor LEUTX is expressed in human preimplantation embryos between the 4- and 8-cell stages, and then silenced in somatic tissues. To characterize the function of LEUTX, we performed a multiomic characterization of LEUTX using two proteomics methods and three genome-wide sequencing approaches. Our results show that LEUTX stably interacts with the EP300 and CBP histone acetyltransferases through its 9 amino acid transactivation domain (9aaTAD), as mutation of this domain abolishes the interactions. LEUTX targets genomic cis-regulatory sequences that overlap with repetitive elements, and through these elements it is suggested to regulate the expression of its downstream genes. We find LEUTX to be a transcriptional activator, upregulating several genes linked to preimplantation development as well as 8-cell-like markers, such as DPPA3 and ZNF280A. Our results support a role for LEUTX in preimplantation development as an enhancer binding protein and as a potent transcriptional activator.

Due to its advantages of non-contact measurement and high sensitivity, light-induced thermoelastic spectroscopy (LITES) is one of the most promising methods for corrosive gas detection. In this manuscript, a highly sensitive hydrogen fluoride (HF) sensor based on LITES technique is reported for the first time. With simple structure and strong robustness, a shallow neural network (SNN) fitting algorithm is introduced into the field of spectroscopy data processing to achieve denoising. This algorithm provides an end-to-end approach that takes in the raw input data without any pre-processing and extracts features automatically. A continuous wave (CW) distributed feedback diode (DFB) laser with an emission wavelength of 1.27 µm was used as the excitation source. A Herriott multi-pass cell (MPC) with an optical length of 10.1 m was selected to enhance the laser absorption. A quartz tuning fork (QTF) with resonance frequency of 32,767.52 Hz was adopted as the thermoelastic detector. An Allan variance analysis was performed to demonstrate the system stability. When the integration time was 110 s, the minimum detection limit (MDL) was found to be 71 ppb. After the SNN fitting algorithm was used, the signal-to-noise ratio (SNR) of the HF-LITES sensor was improved by a factor of 2.0, which verified the effectiveness of this fitting algorithm for spectroscopy data processing.

In this paper, we report on the performance of quartz tuning fork (QTF) based laser spectroscopy sensing employing multiple QTFs. To avoid that resonance frequency mismatching of the QTFs degrades the sensor performance, two types of resonance frequency matching method are here proposed. A system based on the coupling of two sensing modules, one based on quartz-enhanced photoacoustic spectroscopy (QEPAS) and one on light-induced thermoelastic spectroscopy (LITES) technique, was realized to validate the proposed methods. Each module employed a different QTF (QTF1 and QTF2, respectively). Operating temperature or pressure of QTF2 were regulated to match the resonance frequency of QTF1, which operated at 25.0 °C and atmospheric pressure. Without regulation, the difference between QTF1 and QTF2 resonance frequencies was 2.42 Hz and the superposition coefficient η was only 54.7%. When the temperature regulation was carried out, at a QTF2 operating temperature of 67.5 °C, an optimal η value of 95.0% was obtained. For the pressure regulation approach, if operating QTF2 at pressure of 500 Torr, η reached a value of 97.2%. The obtained results show that the proposed two methods are effective in resonance frequency matching of QTFs for gas sensing systems.

Fibrous sheath interacting protein 1 (Fsip1) is a cytoskeletal structural protein of the sperm flagellar proteome. A few studies have reported that it plays a vital role in the tumorigenesis and cancer progression. However, little is known about the role of Fsip1 in spermatogenesis and mammalian sperm flagellogenesis. Fsip1 protein showed the highest expression in round spermatids, and was translocated from nucleus to the anterior region of the elongating spermatid head. To investigate its role we constructed homozygous Fsip1 null (Fsip1−/−) mice. We found that the homozygous Fsip1−/− mutant mice were infertile, with a low sperm count and impaired motility. Interestingly, a subtle phenotype characterized by abnormal head shape, and flagella deformities was observed in the sperm of Fsip1−/− mutant mice similar to the partial globozoospermia phenotype. Electron microscopy analysis of Fsip1−/− sperm revealed abnormal accumulation of mitochondria, disrupted axoneme and retained cytoplasm. Testicular sections showed increased cytoplasmic vacuoles in the elongated spermatid of Fsip1–/–mice, which indicated an intraflagellar transport (IFT) defect. Using proteomic approaches, we characterized the cellular components and the mechanism underlying this subtle phenotype. Our result indicated that Fsip1–/–downregulates the formation of acrosomal membrane and vesicles proteins, intraflagellar transport particles B, and sperm flagellum components. Our results suggest that Fsip1 is essential for normal spermiogenesis, and plays an essential role in the acrosome biogenesis and flagellogenesis by attenuating intraflagellar transport proteins.

Background: C4d is a specific biomarker for the diagnosis of antibody-mediated rejection (AMR) after cardiac transplantation. Although strongly recommended, routine C4d surveillance is hindered by the invasive nature of endomyocardial biopsy. Targeted ultrasound (US) has high sensitivity, and C4d is abundantly expressed within the graft of patients experiencing AMR, which makes it possible to visualize C4d deposition in vivo using targeted US. Methods: We designed a serial dilution of C4d-targeted microbubbles (MBC4d) using a streptavidin-biotin conjugation system. A rat model of AMR with C4d deposition was established by pre-sensitization with skin transplantation before cardiac transplantation. MBC4d were injected into recipients and then qualitatively and quantitatively analyzed using the destruction-replenishment method with a clinical US imaging system and analyzed by software. Findings: We successfully obtained qualitative images of C4d deposition in a wide cardiac allograft section, which, for the first time, reflected real-time C4d distribution. Moreover, normal intensity difference was used for quantitative analysis and exhibited an almost nearly linear correlation with the grade of C4d deposition according to the pathologic evidence. In addition, MBC4d injection did not affect the survival and aggravate injury, which demonstrates its safety. Interpretation: This study demonstrates a noninvasive, quantitative and safe evaluation method for C4d. As contrast-enhanced US has been widely used in clinical settings, this technology is expected to be applied quickly to clinical practice. Fund: National Natural Science Foundation of China and Guangdong Province, Leading Scientific Talents of Guangdong special support program, the Science and Technology Project of Guangdong Province and Guangzhou City. Keywords: Noninvasive, Antibody-mediated rejection, C4d, Cardiac transplantation, Targeted microbubbles

Diosgenin, mainly produced by Dioscorea species, is a traditional precursor of most hormonal drugs in the pharmaceutical industry. The mechanisms that underlie the origin and evolution of diosgenin biosynthesis in plants remain unclear. After sequencing the whole genome of Dioscorea zingiberensis, we revealed the evolutionary trajectory of the diosgenin biosynthetic pathway in Dioscorea and demonstrated the de novo biosynthesis of diosgenin in a yeast cell factory. First, we found that P450 gene duplication and neo-functionalization, driven by positive selection, played important roles in the origin of the diosgenin biosynthetic pathway. Subsequently, we found that the enrichment of diosgenin in the yam lineage was regulated by CpG islands, which evolved to regulate gene expression in the diosgenin pathway and balance the carbon flux between the biosynthesis of diosgenin and starch. Finally, by integrating genes from plants, animals, and yeast, we heterologously synthesized diosgenin to 10 mg/l in genetically-engineered yeast. Our study not only reveals the origin and evolutionary mechanisms of the diosgenin biosynthetic pathway in Dioscorea, but also introduces an alternative approach for the production of diosgenin through synthetic biology.

Minichromosome maintenance complex component 6 (MCM6) is involved in tumorigenesis of hepatocellular carcinoma (HCC). Because its effect on different populations remains unclear, this study investigated the impact of MCM6 on HCC in Southern Chinese Zhuang population. In addition to assessing the global mRNA levels of MCM6 based on The Cancer Genome Atlas database (TCGA) and The Gene Expression Omnibus database (GEO), associations between MCM6 mRNA levels and clinicopathological features were analyzed. High MCM6 levels were associated with high alpha-fetoprotein (AFP) (>20 ng/mL in serum) (P < 0.0001) and advanced clinical stage (III + IV) (P < 0.001). Higher MCM6 was associated with poorer outcomes (P < 0.01) in these databases. Furthermore, the mRNA and protein expression of MCM6 in the Guangxi Zhuang population was detected by quantitative polymerase chain reaction (qPCR), western blot, and immunohistochemistry (IHC). The results showed that MCM6 levels were up-regulated in the Zhuang population with HCC. Higher MCM6 protein levels were correlated with larger tumor size (>5 cm) (P = 0.038) and advanced clinical stage (III + IV) (p = 0.023). Bioinformatic enrichment analysis of MCM6 and its interacting proteins (CDT1,WEE1,TRIM28 and MKI67) suggested that in addition to being involved in the cell cycle process, these complexes could also be involved in protein binding, pre-replication complex assemble, and nucleus metabolism. Based on the protein-protein interaction (PPI) network with module screen, the interactions between MCM6 and its potential interacting proteins were further studied through protein docking with hot spot analysis. Additionally, the results of the algorithms combining the ROC of MCM6 and its interacting proteins showed that combination biomarker analysis has better HCC diagnosis ability than the single MCM6 test. The combination of MCM6 and TRIM28 was more suitable for the Guangxi Zhuang population. Overall, our study suggests that MCM6 plays an important role in the growth of HCC. MCM6 could be an optimal biomarker for diagnosing HCC and a potential molecular target for HCC therapy in the Zhuang population.

Summary: The RET proto-oncogene encodes receptor tyrosine kinase, expressed primarily in tissues of neural crest origin. De-regulation of RET signaling is implicated in several human cancers. Recent phosphatome interactome analysis identified PTPRA interacting with the neurotrophic factor (GDNF)-dependent RET-Ras-MAPK signaling-axis. Here, by identifying comprehensive interactomes of PTPRA and RET, we reveal their close physical and functional association. The PTPRA directly interacts with RET, and using the phosphoproteomic approach, we identify RET as a direct dephosphorylation substrate of PTPRA both in vivo and in vitro. The protein phosphatase domain-1 is indispensable for the PTPRA inhibitory role on RET activity and downstream Ras-MAPK signaling, whereas domain-2 has only minor effect. Furthermore, PTPRA also regulates the RET oncogenic mutant variant MEN2A activity and invasion capacity, whereas the MEN2B is insensitive to PTPRA. In sum, we discern PTPRA as a novel regulator of RET signaling in both health and cancer. : Biological Sciences; Molecular Biology; Cancer Subject Areas: Biological Sciences, Molecular Biology, Cancer

Mitochondria are central organelles to cellular metabolism. Their function relies largely on nuclear-encoded proteins that must be imported from the cytosol, and thus the protein import pathways are important for the maintenance of mitochondrial proteostasis. Mitochondrial HSP70 (mtHsp70) is a key component in facilitating the translocation of proteins through the inner membrane into the mitochondrial matrix. Its protein folding cycle is regulated by the nucleotide-exchange factor GrpE, which triggers the release of folded proteins by ATP rebinding. Vertebrates have two mitochondrial GrpE paralogs, GRPEL1 and 2, but without clearly defined roles. Using BioID proximity labeling to identify potential binding partners of the GRPELs in the mitochondrial matrix, we obtained results supporting a model where both GRPELs regulate mtHsp70 as homodimers. We show that GRPEL2 is not essential in human cultured cells, and its absence does not prevent mitochondrial protein import. Instead we find that GRPEL2 is redox regulated in oxidative stress. In the presence of hydrogen peroxide, GRPEL2 forms dimers through intermolecular disulfide bonds in which Cys87 is the thiol switch. We propose that the dimerization of GRPEL2 may activate the folding machinery responsible for protein import into mitochondrial matrix or enhance the chaperone activity of mtHSP70, thus protecting mitochondrial proteostasis in oxidative stress. Keywords: GRPEL2, Oxidative stress, mtHSP70, Redox regulation, Mitochondrial protein import, Protein folding

Summary: Developing a sensitive, low-cost, and easy-to-use point-of-care testing system for genotyping is important for informing treatment decisions and predicting the risk of underlying diseases. Conventional methods normally require complex operational procedures as well as expensive and sophisticated instruments. Here, we report a general approach that enables us to detect the genotype of multiple sample types directly without DNA purification. Moreover, the PCR results can be further quantitatively analyzed based on a magnetic lateral flow assay (MLFA) system, which avoids multiple steps needed for conventional nucleic acid biosensors. As a demonstration, we show that three genotypes of aldehyde dehydrogenase 2 (ALDH2) can be identified using a small volume of sample with an accuracy of 100% and a sensitivity of 1.0 × 102 cells/μL, which are better than those of the gold standard methods. We believe that the direct PCR-MLFA system represents a significant advance toward the development of portable, sensitive biomedical platforms. : Clinical Genetics; Analytical Chemistry; Fluidics; Biochemical Analysis Subject Areas: Clinical Genetics, Analytical Chemistry, Fluidics, Biochemical Analysis

The actin cytoskeleton and cytoplasmic intermediate filaments contribute to cell migration and morphogenesis, but the interplay between these two central cytoskeletal elements has remained elusive. Here, we find that specific actin stress fiber structures, transverse arcs, interact with vimentin intermediate filaments and promote their retrograde flow. Consequently, myosin-II-containing arcs are important for perinuclear localization of the vimentin network in cells. The vimentin network reciprocally restricts retrograde movement of arcs and hence controls the width of flat lamellum at the leading edge of the cell. Depletion of plectin recapitulates the vimentin organization phenotype of arc-deficient cells without affecting the integrity of vimentin filaments or stress fibers, demonstrating that this cytoskeletal cross-linker is required for productive interactions between vimentin and arcs. Collectively, our results reveal that plectin-mediated interplay between contractile actomyosin arcs and vimentin intermediate filaments controls the localization and dynamics of these two cytoskeletal systems and is consequently important for cell morphogenesis.