Construction of an artificial phosphoketolase pathway that efficiently catabolizes multiple carbon sources to acetyl-CoA.

The canonical glycolysis pathway is responsible for converting glucose into 2 molecules of acetyl-coenzyme A (acetyl-CoA) through a cascade of 11 biochemical reactions. Here, we have designed and constructed an artificial phosphoketolase (APK) pathway, which consists of only 3 types of biochemical reactions. The core enzyme in this pathway is phosphoketolase, while phosphatase and isomerase act as auxiliary enzymes. The APK pathway has the potential to achieve a 100% carbon yield to acetyl-CoA from any monosaccharide by integrating a one-carbon condensation reaction. We tested the APK pathway in vitro, demonstrating that it could efficiently catabolize typical C1-C6 carbohydrates to acetyl-CoA with yields ranging from 83% to 95%. Furthermore, we engineered Escherichia coli stain capable of growth utilizing APK pathway when glycerol act as a carbon source. This novel catabolic pathway holds promising route for future biomanufacturing and offering a stoichiometric production platform using multiple carbon sources.

A Negative Regulatory Feedback Loop within the JAK-STAT Pathway Mediated by the Protein Tyrosine Phosphatase DUSP14 in Shrimp.

The JAK-STAT pathway is a central communication node for various biological processes. Its activation is characterized by phosphorylation and nuclear translocation of the transcription factor STAT. The regulatory balance of JAK-STAT signaling is important for maintenance of immune homeostasis. Protein tyrosine phosphatases (PTPs) induce dephosphorylation of tyrosine residues in intracellular proteins and generally function as negative regulators in cell signaling. However, the roles of PTPs in JAK-STAT signaling, especially in invertebrates, remain largely unknown. Pacific white shrimp Penaeus vannamei is currently an important model for studying invertebrate immunity. This study identified a novel member of the dual-specificity phosphatase (DUSP) subclass of the PTP superfamily in P. vannamei, named PvDUSP14. By interacting with and dephosphorylating STAT, PvDUSP14 inhibits the excessive activation of the JAK-STAT pathway, and silencing of PvDUSP14 significantly enhances humoral and cellular immunity in shrimp. The promoter of PvDUSP14 contains a STAT-binding motif and can be directly activated by STAT, suggesting that PvDUSP14 is a regulatory target gene of the JAK-STAT pathway and mediates a negative feedback regulatory loop. This feedback loop plays a role in maintaining homeostasis of JAK-STAT signaling and is involved in antibacterial and antiviral immune responses in shrimp. Therefore, the current study revealed a novel inhibitory mechanism of JAK-STAT signaling, which is of significance for studying the regulatory mechanisms of immune homeostasis in invertebrates.

Molecular mechanism of the interaction between Megalocytivirus-induced virus-mock basement membrane (VMBM) and lymphatic endothelial cells.

IMPORTANCE: Viruses are able to mimic the physiological or pathological mechanism of the host to favor their infection and replication. Virus-mock basement membrane (VMBM) is a Megalocytivirus-induced extracellular structure formed on the surface of infected cells and structurally and functionally mimics the basement membrane of the host. VMBM provides specific support for lymphatic endothelial cells (LECs) rather than blood endothelial cells to adhere to the surface of infected cells, which constitutes a unique phenomenon of Megalocytivirus infection. Here, the structure of VMBM and the interactions between VMBM components and LECs have been analyzed at the molecular level. The regulatory effect of VMBM components on the proliferation and migration of LECs has also been explored. This study helps to understand the mechanism of LEC-specific attachment to VMBM and to address the issue of where the LECs come from in the context of Megalocytivirus infection.

SPL16 and SPL23 mediate photoperiodic control of seasonal growth in Populus trees.

Perennial trees in boreal and temperate regions undergo growth cessation and bud set under short photoperiods, which are regulated by phytochrome B (phyB) photoreceptors and PHYTOCHROME INTERACTING FACTOR 8 (PIF8) proteins. However, the direct signaling components downstream of the phyB-PIF8 module remain unclear. We found that short photoperiods suppressed the expression of miR156, while upregulated the expression of miR156-targeted SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE 16 (SPL16) and SPL23 in leaves and shoot apices of Populus trees. Accordingly, either overexpression of MIR156a/c or mutagenesis of SPL16/23 resulted in the attenuation of growth cessation and bud set under short days (SD), whereas overexpression of SPL16 and SPL23 conferred early growth cessation. We further showed that SPL16 and SPL23 directly suppressed FLOWERING LOCUS T2 (FT2) expression while promoted BRANCHED1 (BRC1.1 and BRC1.2) expression. Moreover, we revealed that PIF8.1/8.2, positive regulators of growth cessation, directly bound to promoters of MIR156a and MIR156c and inhibited their expression to modulate downstream pathways. Our results reveal a connection between the phyB-PIF8 module-mediated photoperiod perception and the miR156-SPL16/23-FT2/BRC1 regulatory cascades in SD-induced growth cessation. Our study provides insights into the rewiring of a conserved miR156-SPL module in the regulation of seasonal growth in Populus trees.

Phytochrome-interacting factors play shared and distinct roles in regulating shade avoidance responses in Populus trees.

Plants adjust their growth and development in response to changing light caused by canopy shade. The molecular mechanisms underlying shade avoidance responses have been widely studied in Arabidopsis and annual crop species, yet the shade avoidance signalling in woody perennial trees remains poorly understood. Here, we first showed that PtophyB1/2 photoreceptors serve conserved roles in attenuating the shade avoidance syndrome (SAS) in poplars. Next, we conducted a systematic identification and characterization of eight PtoPIF genes in Populus tomentosa. Knocking out different PtoPIFs led to attenuated shade responses to varying extents, whereas overexpression of PtoPIFs, particularly PtoPIF3.1 and PtoPIF3.2, led to constitutive SAS phenotypes under normal light and enhanced SAS responses under simulated shade. Notably, our results revealed that distinct from Arabidopsis PIF4 and PIF5, which are major regulators of SAS, the Populus homologues PtoPIF4.1 and PtoPIF4.2 seem to play a minor role in controlling shade responses. Moreover, we showed that PtoPIF3.1/3.2 could directly activate the expression of the auxin biosynthetic gene PtoYUC8 in response to shade, suggesting a conserved PIF-YUC-auxin pathway in modulating SAS in tree. Overall, our study provides insights into shared and divergent functions of PtoPIF members in regulating various aspects of the SAS in Populus.

Head-to-head comparison of prostate-specific membrane antigen PET and multiparametric MRI in the diagnosis of pretreatment patients with prostate cancer: a meta-analysis.

OBJECTIVES: To compare prostate-specific membrane antigen (PSMA) PET with multiparametric MRI (mpMRI) in the diagnosis of pretreatment prostate cancer (PCa). METHODS: Pubmed, Embase, Medline, Web of Science, and Cochrane Library were searched for eligible studies published before June 22, 2022. We assessed risk of bias and applicability by using QUADAS-2 tool. Data synthesis was performed with Stata 17.0 software, using the "midas" and "meqrlogit" packages. RESULTS: We included 29 articles focusing on primary cancer detection, 18 articles about primary staging, and two articles containing them both. For PSMA PET versus mpMRI in primary PCa detection, sensitivities and specificities in the per-patient analysis were 0.90 and 0.84 (p<0.0001), and 0.66 and 0.60 (p <0.0001), and in the per-lesion analysis they were 0.79 and 0.78 (p <0.0001), and 0.84 and 0.82 (p <0.0001). For the per-patient analysis of PSMA PET versus mpMRI in primary staging, sensitivities and specificities in extracapsular extension detection were 0.59 and 0.66 (p =0.005), and 0.79 and 0.76 (p =0.0074), and in seminal vesicle infiltration (SVI) detection they were 0.51 and 0.60 (p =0.0008), and 0.93 and 0.96 (p =0.0092). For PSMA PET versus mpMRI in lymph node metastasis (LNM) detection, sensitivities and specificities in the per-patient analysis were 0.68 and 0.46 (p <0.0001), and 0.91 and 0.90 (p =0.81), and in the per-lesion analysis they were 0.67 and 0.36 (p <0.0001), and 0.99 and 0.99 (p =0.18). CONCLUSION: PSMA PET has higher diagnostic value than mpMRI in the detection of primary PCa. Regarding the primary staging, mpMRI has potential advantages in SVI detection, while PSMA PET has relative advantages in LNM detection. CLINICAL RELEVANCE STATEMENT: The integration of prostate-specific membrane antigen (PSMA) PET into the diagnostic pathway may be helpful for improving the accuracy of prostate cancer detection. However, further studies are needed to address the cost implications and evaluate its utility in specific patient populations or clinical scenarios. Moreover, we recommend the combination of PSMA PET and mpMRI for cancer staging. KEY POINTS: • Prostate-specific membrane antigen PET has higher sensitivity and specificity for primary tumor detection in prostate cancer compared to multiparametric MRI. • Prostate-specific membrane antigen PET also has significantly better sensitivity and specificity for lymph node metastases of prostate cancer compared to multiparametric MRI. • Multiparametric MRI has better accuracy for extracapsular extension and seminal vesicle infiltration compared to ate-specific membrane antigen PET.

A novel chitinase Chi6 with immunosuppressive activity promotes white spot syndrome virus (WSSV) infection in Penaeus vannamei.

Chitinases, a group of glycosylase hydrolases that can hydrolyze chitin, are involved in immune regulation in animals. White spot syndrome virus (WSSV) causes huge losses to crustacean aquaculture every year. We identified a novel chitinase Chi6 from Pacific white shrimp Penaeus vannamei, which contains a catalytic domain but no chitin-binding domain. The Chi6 expression was regulated by multiple immune signaling pathways and increased after immune stimulations. Silencing of Chi6 by RNAi in vivo did not affect Vibrio parahaemolyticus infection, but significantly increased the survival rate of WSSV-infected shrimp. The expression of multiple WSSV immediate early and structural genes was also decreased upon Chi6 silencing. The recombinant Chi6 protein showed no effect on bacterial growth but could attenuate shrimp hemocyte phagocytosis. The mRNA levels of several key elements and downstream genes of the MAPK and Dorsal pathways in Chi6-silenced shrimp were significantly up-regulated, suggesting an inhibitory effect of Chi6 on humoral immune response. Moreover, Chi6 enhanced the regulatory effect of Dorsal on the expression of WSSV ie1 gene. Therefore, Chi6 promotes WSSV infection through immunosuppression and regulation of WSSV gene expression. Targeting Chi6 could be a potential strategy for controlling WSSV disease in shrimp farming.

[Selection and validation of reference genes for quantitative real-time PCR analysis in Paeonia veitchii].

Paeonia veitchii and P. lactiflora are both original plants of the famous Chinese medicinal drug Paeoniae Radix Rubra in the Chinese Pharmacopoeia. They have important medicinal value and great potential in the flower market. The selection of stable and reliable reference genes is a necessary prerequisite for molecular research on P. veitchii. In this study, two reference genes, Actin and GAPDH, were selected as candidate genes from the transcriptome data of P. veitchii. The expression levels of the two candidate genes in different tissues(phloem, xylem, stem, leaf, petiole, and ovary) and different growth stages(bud stage, flowering stage, and dormant stage) of P. veitchii were detected using real-time fluorescence quantitative technology(qRT-PCR). Then, the stability of the expression of the two reference genes was comprehensively analyzed using geNorm, NormFinder, BestKeeper, ΔCT, and RefFinder. The results showed that the expression patterns of Actin and GAPDH were stable in different tissues and growth stages of P. veitchii. Furthermore, the expression levels of eight genes(Pv-TPS01, Pv-TPS02, Pv-CYP01, Pv-CYP02, Pv-CYP03, Pv-BAHD01, Pv-UGT01, and Pv-UGT02) in different tissues were further detected based on the transcriptome data of P. veitchii. The results showed that when Actin and GAPDH were used as reference genes, the expression trends of the eight genes in different tissues of P. veitchii were consistent, validating the reliability of Actin and GAPDH as reference genes for P. veitchii. In conclusion, this study finds that Actin and GAPDH can be used as reference genes for studying gene expression levels in different tissues and growth stages of P. veitchii.

Tree Shrew Cells Transduced with Human CD4 and CCR5 Support Early Steps of HIV-1 Replication, but Viral Infectivity Is Restricted by APOBEC3.

The host range of human immunodeficiency virus type 1 (HIV-1) is narrow. Therefore, using ordinary animal models to study HIV-1 replication, pathogenesis, and therapy is impractical. The lack of applicable animal models for HIV-1 research spurred our investigation on whether tree shrews (Tupaia belangeri chinensis), which are susceptible to many types of human viruses, can act as an animal model for HIV-1. Here, we report that tree shrew primary cells are refractory to wild-type HIV-1 but support the early replication steps of HIV-1 pseudotyped with the vesicular stomatitis virus glycoprotein envelope (VSV-G), which can bypass entry receptors. The exogenous expression of human CD4 renders the tree shrew cell line infectible to X4-tropic HIV-1IIIB, suggesting that tree shrew CXCR4 is a functional HIV-1 coreceptor. However, tree shrew cells did not produce infectious HIV-1 progeny virions, even with the human CD4 receptor. Subsequently, we identified tree shrew (ts) apolipoprotein B editing catalytic polypeptide 3 (tsAPOBEC3) proteins as active inhibitors of HIV-1 particle infectivity, with virus infectivity reduced 10- to 1,000-fold. Unlike human APOBEC3G, the tsA3Z2c-Z1b protein was not degraded by the HIV-1 viral infectivity factor (Vif) but markedly restricted HIV-1 replication through mutagenicity and reverse transcription inhibition. The pooled knockout of tsA3Z2c-Z1b partially restored the infectivity of the HIV-1 progeny. This work suggests that tsAPOBEC3 proteins serve as an additional barrier to the development of HIV-1 tree shrew models, even when virus entry is overcome by exogenous expression of human CD4. IMPORTANCE The development of animal models is critical for studying human diseases and their pathogenesis and for evaluating drug and vaccine efficacy. For improved AIDS research, the ideal animal model of HIV-1 infection should be a small laboratory mammal that closely mimics virus replication in humans. Tree shrews exhibit considerable potential as animal models for the study of human diseases and therapeutic responses. Here, we report that human CD4-expressing tree shrew cells support the early steps of HIV-1 replication and that tree shrew CXCR4 is a functional coreceptor of HIV-1. However, tree shrew cells harbor additional restrictions that lead to the production of HIV-1 virions with low infectivity. Thus, the tsAPOBEC3 proteins are partial barriers to developing tree shrews as an HIV-1 model. Our results provide insight into the genetic basis of HIV inhibition in tree shrews and build a foundation for the establishment of gene-edited tree shrew HIV-1-infected models.

A MicroRNA-1-Mediated Inhibition of the NF-κB Pathway by the JAK-STAT Pathway in the Invertebrate Litopenaeus vannamei.

The JAK-STAT and NF-κB pathways are conserved cellular signaling cascades orchestrating a variety of biological processes. The regulatory interactions between these two pathways have been well studied in vertebrates but less concerned in invertebrates, hindering further understanding of immune signaling evolution. The Pacific white shrimp Litopenaeus vannamei is now an important model for studying invertebrate immunity and cellular signaling mechanisms. In this study, the microRNA-1 (miR-1) molecule from L. vannamei was identified, and its mature and precursor sequences were analyzed. The miR-1 promoter contained a STAT binding site and its transcriptional activity could be regulated by the JAK-STAT pathway. The target gene of miR-1 was identified as MyD88, the upstream component of the Dorsal (the NF-κB homolog) pathway. By suppressing the expression of MyD88, miR-1 attenuated activation of the Dorsal pathway. With miR-1 as the mediator, STAT also exerted a negative regulatory effect on the Dorsal pathway. Moreover, miR-1 was involved in regulation of the expression of a set of immune effector genes and the phagocytic activity of hemocytes and had an inhibitory or excitatory effect on antibacterial or antiviral responses, respectively. Taken together, the current study revealed a microRNA-mediated inhibition of the NF-κB pathway by the JAK-STAT pathway in an invertebrate, which could contribute to immune homeostasis and shaping immune responses.

An Alu Element Insertion in Intron 1 Results in Aberrant Alternative Splicing of APOBEC3G Pre-mRNA in Northern Pig-Tailed Macaques (Macaca leonina) That May Reduce APOBEC3G-Mediated Hypermutation Pressure on HIV-1.

APOBEC3 family members, particularly APOBEC3F and APOBEC3G, inhibit the replication and spread of various retroviruses by inducing hypermutation in newly synthesized viral DNA. Viral hypermutation by APOBEC3 is associated with viral evolution, viral transmission, and disease progression. In recent years, increasing attention has been paid to targeting APOBEC3G for AIDS therapy. Thus, a controllable model system using species such as macaques, which provide a relatively ideal in vivo system, is needed for the study of APOBEC3-related issues. To appropriately utilize this animal model for biomedical research, important differences between human and macaque APOBEC3s must be considered. In this study, we found that the ratio of APOBEC3G-mediated/APOBEC3-mediated HIV-1 hypermutation footprints was much lower in peripheral blood mononuclear cells (PBMCs) from northern pig-tailed macaques than in PBMCs from humans. Next, we identified a novel and conserved APOBEC3G pre-mRNA alternative splicing pattern in macaques, which differed from that in humans and resulted from an Alu element insertion into macaque APOBEC3G gene intron 1. This alternative splicing pattern generating an aberrant APOBEC3G mRNA isoform may significantly dilute full-length APOBEC3G and reduce APOBEC3G-mediated hypermutation pressure on HIV-1 in northern pig-tailed macaques, which was supported by the elimination of other possibilities accounting for this hypermutation difference between the two hosts.IMPORTANCE APOBEC3 family members, particularly APOBEC3F and APOBEC3G, are important cellular antiviral factors. Recently, more attention has been paid to targeting APOBEC3G for AIDS therapy. To appropriately utilize macaque animal models for the study of APOBEC3-related issues, it is important that the differences between human and macaque APOBEC3s are clarified. In this study, we identified a novel and conserved APOBEC3G pre-mRNA alternative splicing pattern in macaques, which differed from that in humans and which may reduce the APOBEC3G-mediated hypermutation pressure on HIV-1 in northern pig-tailed macaques (NPMs). Our work provides important information for the proper application of macaque animal models for APOBEC3-related issues in AIDS research and a better understanding of the biological functions of APOBEC3 proteins.

Hepatitis B Virus Virions Produced Under Nucleos(t)ide Analogue Treatment Are Mainly Not Infectious Because of Irreversible DNA Chain Termination.

Nucleos(t)ide analogues (NAs) have been widely used for the treatment of chronic hepatitis B (CHB). Because viral DNA polymerase lacks proofreading function (3' exonuclease activity), theoretically, the incorporated NAs would irreversibly terminate viral DNA synthesis. This study explored the natures of nascent hepatitis B virus (HBV) DNA and infectivity of progeny virions produced under NA treatment. HBV infectivity was determined by infection of HepG2-NTCP cells and primary human hepatocytes (PHHs). Biochemical properties of HBV DNA in the progeny virions were investigated by qPCR, northern blotting, or Southern blotting hybridization, sucrose gradient centrifugation, and in vitro endogenous DNA polymerase assay. Progeny HBV virions produced under NA treatment were mainly not infectious to HepG2-NTCP cells or PHHs. Biochemical analysis revealed that under NA treatment, HBV DNA in nucleaocapsids or virions were predominantly short minus-strand DNA with irreversible termination. This finding was supported by the observation of first disappearance of relaxed circular DNA and then the proportional decline of HBV-DNA levels corresponding to the regions of PreC/C, S, and X genes in serial sera of patients receiving NA treatment. Conclusion: HBV virions produced under NA treatment are predominantly replication deficient because the viral genomes are truncated and elongation of DNA chains is irreversibly terminated. Clinically, our results suggest that the viral loads of CHB patients under NA therapy vary with the different regions of genome being detected by qPCR assays. Our findings also imply that NA prevention of perinatal and sexual HBV transmission as well as infection of transplanted livers works not only by reducing viral loads, but also by producing noninfectious virions.

In Situ Measurement of Thallium in Natural Waters by a Technique Based on Diffusive Gradients in Thin Films Containing a δ-MnO2 Gel Layer.

Thallium (Tl) has been identified as a priority contaminant because of its severe toxic effects. Exact measurement of Tl is a challenge because it is difficult to avoid altering the element's chemical speciation during sampling, transport, and storage. In situ measurement may be a good choice. Based on the in situ technique of diffusive gradients in thin films (DGT), new DGT devices equipped with novel laboratory-synthesized manganese oxide (δ-MnO2) binding gels were developed and systematically validated for the measurement of Tl, including Tl(I) and Tl(III) species, in water. Comparison between Chelex binding gel and δ-MnO2 gel on the uptake kinetics of Tl demonstrated that δ-MnO2 binding gels could adsorb Tl rapidly and effectively. Removal of Tl from the δ-MnO2 gels was achieved by use of 1 mol·L-1 oxalic acid, yielding elution efficiencies of 1.0 for Tl(I) and 0.86 for TI(III). Theoretical responses from DGT devices loaded with δ-MnO2 gel (δ-MnO2-DGT) were obtained irrespective of pH (4-9) and ionic strength (0.1-200 mmol·L-1 NaNO3). δ-MnO2-DGT showed good potential for long-term monitoring of Tl due to its high adsorption capacity of 27.1 µg·cm-2 and the stable performance of δ-MnO2 binding gel kept in solution, containing only 10 mmol·L-1 NaNO3, for at least 117 days. Field deployment trials confirmed that δ-MnO2-DGT can accurately measure the time-averaged concentrations of Tl in fluvial watercourses. In summary, the newly developed δ-MnO2-DGT technique shows potential for environmental monitoring and biogeochemical investigation of Tl in waters.

A novel C-type lectin with microbiostatic and immune regulatory functions from Litopenaeus vannamei.

C-type lectins (CTLs) are a group of lectins with at least one carbohydrate recognition domain (CRD), the binding of which to carbohydrates requires the presence of calcium ions. CTLs generally function as pattern recognition receptors (PRRs), essentially participating in innate immunity. In the current study, a novel CTL termed LvCTL5 was identified from Pacific white shrimp Litopenaeus vannamei, which shared sequence identities with other crustacean CTLs. LvCTL5 was highly expressed in hepatopancreas and could be activated by infection with bacteria, virus and fungi. The recombinant LvCTL5 protein purified from E. coli showed microbiostatic and agglutination activities against bacteria and fungi in vitro. Silencing of LvCTL5 in vivo could significantly affect expression of a series of immune effector genes and down-regulate the phagocytic activity of hemocytes. Compared with controls, the LvCTL5-silenced shrimp were highly susceptible to Vibrio parahaemolyticus and white spot syndrome virus (WSSV) infections. These suggest that LvCTL5 has microbiostatic and immune regulatory activities and is implicated in antiviral and antibacterial responses.

A JAK-STAT pathway target gene encoding a single WAP domain (SWD)-containing protein from Litopenaeus vannamei.

In shrimp, the JAK-STAT pathway is essentially implicated in both antiviral and antibacterial responses. However, few regulatory target genes of the JAK-STAT pathway in shrimp have been reported so far. In this study, a novel single WAP domain-containing peptide (LvSWD4) was identified from Pacific white shrimp Litopenaeus vannamei. The promoter of LvSWD4 was predicted to harbor multiple STAT-binding DNA motifs. Over-expression of the JAK-STAT pathway components STAT, JAK and Domeless in vitro significantly enhanced the transcriptional activity of the LvSWD4 promoter, and in vivo silencing of STAT and the the JAK-STAT pathway upstream regulator IRF down-regulated the expression of LvSWD4, suggesting that LvSWD4 could be a target gene of the JAK-STAT pathway. The expression of LvSWD4 was significantly increased after infection with Gram-negative and positive bacteria, fungi and virus, and silencing of LvSWD4 increased the susceptibility of shrimp to V. parahaemolyticus and WSSV infections. In vitro experiments also demonstrated that the recombinant LvSWD4 protein had significant inhibitory activities against Gram negative bacteria V. parahaemolyticus and E. coli and Gram positive bacteria S. aureus and B. subtilis. Furthermore, silencing of LvSWD4 in vivo significantly affected expression of various immune functional genes and attenuated the phagocytic activity of hemocytes. These suggested that as a target gene of STAT, LvSWD4 was essentially implicated in shrimp immunity, which could constitute part of the mechanism underlying the immune function of the shrimp JAK-STAT pathway.

Integrated immunogenomic analysis of single-cell and bulk profiling reveals novel tumor antigens and subtype-specific therapeutic agents in lung adenocarcinoma.

Background: In recent years, mRNA-based vaccines with promising safety and functional characteristics have gained significant momentum in cancer immunotherapy. However, stable immunological molecular subtypes of lung adenocarcinoma (LUAD) and novel tumor antigens for LUAD mRNA vaccine development remain elusive. Therefore, a novel approach is urgently needed to identify suitable LUAD subtypes and potential tumor antigens. Methods: The Cancer Genome Atlas (TCGA), the Genotype Tissue Expression (GTEx), and Gene Expression Omnibus (GEO) databases were utilized to retrieve gene expression data. The LUAD Immunological Multi-Omics Classification (LIMOC) system was developed using seven machine learning (ML) algorithms by performing integrative immunogenomic analysis of single-cell and bulk tissue transcriptome profiling. Subsequently, a panel of approaches was applied to identify novel tumor antigens. Results: First, the LIMOC system was construct to identify three subtypes: LIMOC1, LIMOC2, and LIMOC3. Second, we identified CHIT1, LILRA4, and MEP1A as novel tumor antigens in LUAD; these genes were up-regulated, amplified, and mutated, and showed a positive association with APC infiltration, making them promising candidates for designing mRNA vaccines. Notably, the LIMOC2 subtype had the worst prognosis and could benefit most from mRNA immunization. Furthermore, we performed a comprehensive in silico screening of approximately 2000 compounds and identified Sorafenib and Azacitidine as potential subtype-specific therapeutic agents. Conclusions: Overall, our study established a robust LIMOC system and identified CHIT1, LILRA4, and MEP1A as promising tumor antigen candidates for development of anti-LUAD mRNA vaccines, particularly for the LIMOC2 subtype.

MLF-IOSC: Multi-Level Fusion Network With Independent Operation Search Cell for Low-Dose CT Denoising.

Computed tomography (CT) is widely used in clinical medicine, and low-dose CT (LDCT) has become popular to reduce potential patient harm during CT acquisition. However, LDCT aggravates the problem of noise and artifacts in CT images, increasing diagnosis difficulty. Through deep learning, denoising CT images by artificial neural network has aroused great interest for medical imaging and has been hugely successful. We propose a framework to achieve excellent LDCT noise reduction using independent operation search cells, inspired by neural architecture search, and introduce the Laplacian to further improve image quality. Employing patch-based training, the proposed method can effectively eliminate CT image noise while retaining the original structures and details, hence significantly improving diagnosis efficiency and promoting LDCT clinical applications.

Insight into adsorption process and mechanisms of Cr(III) using carboxymethyl cellulose-g-poly(acrylic acid-co-acrylamide)/attapulgite composite hydrogel.

Cr(III) as one of the most concerned potentially toxic elements, is discharged from relevant industries and Cr(VI) reduction. Hydrogel-based adsorption could be one of the promising approaches for Cr(III) removal. Featured with environmental friendliness and low cost, carboxymethyl cellulose (CMC) was employed for the hydrogel synthesis, and attapulgite (APT) could be used to strengthen its stability. However, the adsorption performance and mechanisms need to be examined. In the present study, carboxymethyl cellulose-g-poly(acrylic acid-co-acrylamide)/ attapulgite (CMC-g-p(AA-co-AM)/APT) was synthesised via in situ copolymerisation. Its efficacy for removing Cr(III) from an aqueous solution was investigated using batch adsorption experiments. Results showed that the introduction of APT enhanced the thermal stability but decreased the swelling performance of the hydrogel. The prepared hydrogel could strongly adsorb Cr(III) at a wide pH range of 3.0-7.0. Cr(III) can be efficiently removed by the composite hydrogel within 1-2 h. At low concentration, CMC-g-p(AA-co-AM)/APT could slightly adsorbed more Cr(III) than CMC-g-p(AA-co-AM). The maximum absorption of CMC-g-p(AA-co-AM) and CMC-g-p(AA-co-AM)/APT were 74.8 and 47.7 mg/g at 298 K, respectively. The negative value of ΔHo and ΔGo indicated the adsorption of Cr(III) onto the two studied hydrogels is an exothermic and spontaneous process. Ion exchange and complexation, as implied by EDS, FT-IR and XPS, combining with electrostatic attraction are the possible adsorption mechanisms for Cr(III) onto the prepared hydrogels. All the results above suggests that the composite hydrogel CMC-g-p(AA-co-AM)/APT can be a promising candidate for the removal of Cr(III) from waste water.

Comparative genomics reveals the hybrid origin of a macaque group.

Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque species and show that the fascicularis group originated from an ancient hybridization between the sinica and silenus groups ~3.45 to 3.56 million years ago. The X chromosomes and low-recombination regions exhibited equal contributions from each parental lineage, suggesting that they were less affected by subsequent backcrossing and hence could have played an important role in maintaining hybrid integrity. We identified many reproduction-associated genes that could have contributed to the development of the mixed sexual phenotypes characteristic of the fascicularis group. The phylogeny within the silenus group was also resolved, and functional experimentation confirmed that all extant Western silenus species are susceptible to HIV-1 infection. Our study provides novel insights into macaque evolution and reveals a hybrid speciation event that has occurred only very rarely in primates.

The Non-Receptor Protein Tyrosine Phosphatase PTPN6 Mediates a Positive Regulatory Approach From the Interferon Regulatory Factor to the JAK/STAT Pathway in Litopenaeus vannamei.

SH2-domain-containing protein tyrosine phosphatases (PTPs), belonging to the class I PTP superfamily, are responsible for the dephosphorylation on the phosphorylated tyrosine residues in some proteins that are involved in multiple biological processes in eukaryotes. The Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathway transduce signaling responding to interferons and initiate cellular antiviral responses. The activity of the JAK/STAT pathway is generally orchestrated by the de-/phosphorylation of the tyrosine and serine residues of JAKs and STATs, in which the dephosphorylation processes are mainly controlled by PTPs. In the present study, an SH2-domian-contianing PTP, temporally named as LvPTPN6, was identified in Litopenaeus vannamei. LvPTPN6 shares high similarity with PTPN6s from other organisms and was phylogenetically categorized into the clade of arthropods that differs from those of fishes and mammals. LvPTPN6 was constitutively expressed in all detected tissues, located mainly in the cytoplasm, and differentially induced in hemocyte and gill after the challenge of stimulants, indicating its complicated regulatory roles in shrimp immune responses. Intriguingly, the expression of LvPTPN6 was regulated by interferon regulatory factor (IRF), which could directly bind to the LvPTPN6 promoter. Surprisingly, unlike other PTPN6s, LvPTPN6 could promote the dimerization of STAT and facilitate its nuclear localization, which further elevated the expression of STAT-targeting immune effector genes and enhanced the antiviral immunity of shrimp. Therefore, this study suggests a PTPN6-mediated regulatory approach from IRF to the JAK/STAT signaling pathway in shrimp, which provides new insights into the regulatory roles of PTPs in the JAK/STAT signaling pathway and contributes to the further understanding of the mechanisms of antiviral immunity in invertebrates.