PacBio single-molecule long-read sequencing provides new insights into the complexity of full-length transcripts in oriental river prawn, macrobrachium nipponense.

BACKGROUND: Oriental river prawn (Macrobrachium nipponense) is one of the most dominant species in shrimp farming in China, which is a rich source of protein and contributes to a significant impact on the quality of human life. Thus, more complete and accurate annotation of gene models are important for the breeding research of oriental river prawn. RESULTS: A full-length transcriptome of oriental river prawn muscle was obtained using the PacBio Sequel platform. Then, 37.99 Gb of subreads were sequenced, including 584,498 circular consensus sequences, among which 512,216 were full length non-chimeric sequences. After Illumina-based correction of long PacBio reads, 6,599 error-corrected isoforms were identified. Transcriptome structural analysis revealed 2,263 and 2,555 alternative splicing (AS) events and alternative polyadenylation (APA) sites, respectively. In total, 620 novel genes (NGs), 197 putative transcription factors (TFs), and 291 novel long non-coding RNAs (lncRNAs) were identified. CONCLUSIONS: In summary, this study offers novel insights into the transcriptome complexity and diversity of this prawn species, and provides valuable information for understanding the genomic structure and improving the draft genome annotation of oriental river prawn.

[Effects of silencing the SEMG1 protein on the cycle and apoptosis of GC-1 spg cells].

OBJECTIVE: To investigate the effects of silencing the semenogelin 1 (SEMG1) protein on the cycle and apoptosis of the spermatogonia germ cell line (GC-1 spg). METHODS: SEMG1-specific siRNA was transfected into GC-1 spg cells by lipofectamine 2000 (the siRNA-SEMG1 group), the relative expression levels of the SEMG1 protein in the GC-1 spg cells of the siRNA-SEMG1, blank control and negative control groups were detected by Western blot, and the apoptosis and cycle of the cells in different groups were determined by flow cytometry. RESULTS: The expression of the SEMG1 protein in the GC-1 spg cells was dramatically decreased in the siRNA-SEMG1 group compared with those in the blank and negative control groups (1.80±0.05 vs 2.51±0.13 and 2.50±0.12， P < 0.01), but the apoptosis rate was remarkably higher in the former than in the latter two groups (ï¼»6.77 ± 0.15ï¼½% vs ï¼»0.70 ± 0.06ï¼½% and ï¼»0.8 ± 0.06ï¼½%, P < 0.01). No statistically significant difference was observed in the cell cycles among the three groups (P > 0.05). In addition, Western blot showed that the expression of the caspase-3 protein was significantly higher and that of the BCL2 protein markedly lower in the siRNA-SEMG1 than in the blank and negative control groups (P < 0.05). CONCLUSIONS: SEMG1-specific siRNA can effectively silence the expression of the SEMG1 protein in GC-1 spg cells and promote their apoptosis.

A nomogram based on preoperative inflammatory markers predicting the overall survival of pancreatic ductal adenocarcinoma.

BACKGROUND AND AIMS: Developing a preoperative prediction model for estimating the risk of pancreatic ductal adenocarcinoma (PDAC) patients before pancreaticoduodenectomy is a difficult task. The purpose of current study was to develop a prognostic nomogram based on inflammatory markers for PDAC patients. METHODS: Cox regression analysis was performed to calculate the overall survival (OS) and assess the prognostic factors based on 265 PDAC patients undergone surgery. The nomogram was built to estimate the probability of 1-year, 3-year, and 5-year OS. The predictive accuracy of nomogram was determined by concordance index, calibration curve, and time dependent receiver operating characteristics. RESULTS: In multivariable Cox analysis, vascular invasion, Tumor Grade, TNM stage, neutrophil-to-lymphocyte ratio, platelet-to-lymphocyte ratio, and albumin/globulin ratio were significantly associated with OS, which were all assembled into nomogram. The calibration curves for probability of survival showed optimal agreement between nomogram prediction and actual observation. The concordance index for 1-year, 3-year and 5-year OS prediction were 0.860 (95% confidence intervals (CI): 0.837-0.885), 0.837 (95%CI: 0.819-0.856), and 0.809 (95%CI: 0.787-0.829), respectively. The area under time dependent receiver operating characteristics curve of 1-year, 3-year, and 5-year OS prediction were 0.938 (95%CI: 0.886-0.989), 0.844 (95%CI: 0.782-0.906), and 0.884 (95%CI: 0.792-0.976), suggesting high discriminative ability of nomogram. It allowed significant distinction survival outcomes by grouping the patients evenly into three subgroups after sorting by total points. CONCLUSIONS: Based on clinicopathology characteristics and inflammatory markers, we developed a nomogram providing an individualized risk estimate for PDAC patients.

Single-nuclei RNA-seq reveals skin cell responses to Aeromonas hydrophila infection in Chinese longsnout catfish Leiocassis longirostris.

As the primary natural barrier that protects against adverse environmental conditions, the skin plays a crucial role in the innate immune response of fish, particularly in relation to bacterial infections. However, due to the diverse functionality and intricate anatomical and cellular composition of the skin, deciphering the immune response of the host is a challenging task. In this study, single nuclei RNA-sequencing (snRNA-seq) was performed on skin biopsies obtained from Chinese longsnout catfish (Leiocassis longirostris), comparing Aeromonas hydrophila-infected subjects to healthy control subjects. A total of 19,581 single nuclei cells were sequenced using 10x Genomics (10,400 in the control group and 9,181 in the treated group). Based on expressed unique transcriptional profiles, 33 cell clusters were identified and classified into 12 cell types including keratinocyte (KC), fibroblast (FB), endothelial cells (EC), secretory cells (SC), immune cells, smooth muscle cells (SMC), and other cells such as pericyte (PC), brush cell (BC), red blood cell (RBC), neuroendocrine cell (NDC), neuron cells (NC), and melanocyte (MC). Among these, three clusters of KCs, namely, KC1, KC2, and KC5 exhibited significant expansion after A. hydrophila infection. Analysis of pathway enrichment revealed that KC1 was primarily involved in environmental signal transduction, KC2 was primarily involved in endocrine function, and KC5 was primarily involved in metabolism. Finally, our findings suggest that neutrophils may play a crucial role in combating A. hydrophila infections. In summary, this study not only provides the first detailed comprehensive map of all cell types present in the skin of teleost fish but also sheds light on the immune response mechanism of the skin following A. hydrophila infection in Chinese longsnout catfish.

Glycine Decarboxylase (GLDC) Plays a Crucial Role in Regulating Energy Metabolism, Invasion, Metastasis and Immune Escape for Prostate Cancer.

Glycine decarboxylase (GLDC) is one of the core enzymes for glycine metabolism, and its biological roles in prostate cancer (PCa) are unclear. First, we found that GLDC plays a central role in glycolysis in 540 TCGA PCa patients. Subsequently, a metabolomic microarray showed that GLDC enhanced aerobic glycolysis in PCa cells, and GLDC and its enzyme activity enhanced glucose uptake, lactate production and lactate dehydrogenase (LDH) activity in PCa cells. Next, we found that GLDC was highly expressed in PCa, was directly regulated by hypoxia-inducible factor (HIF1-α) and regulated downstream LDHA expression. In addition, GLDC and its enzyme activity showed a strong ability to promote the migration and invasion of PCa both in vivo and in vitro. Furthermore, we found that the GLDC-high group had a higher TP53 mutation frequency, lower CD8+ T-cell infiltration, higher immune checkpoint expression, and higher immune exclusion scores than the GLDC-low group. Finally, the GLDC-based prognostic risk model by applying LASSO Cox regression also showed good predictive power for the clinical characteristics and survival in PCa patients. This evidence indicates that GLDC plays crucial roles in glycolytic metabolism, invasion and metastasis, and immune escape in PCa, and it is a potential therapeutic target for prostate cancer.

Genetic diversity of two color morphs of Northern snakehead (Channa argus) unveiled by the mitochondrial DNA D-loop region.

To analyze the genetic background of 'white' type Northern snakehead (Channa argus), and provide atheoretical basis for breeding of C. argus, the investigation of genetic diversity and population structure were investigated based on the complete sequences of mitochondrial DNA D-loop region for three cultured 'white' type C. argus populations, and four 'bicolor' type C. argus populations were used to compare with them; 28 mutation loci and 30 haplotypes were found in the D-loop sequence of all individuals with a total length of 907 bp. The highest haplotype diversity (Hd ) and nucleotide diversity (Pi ) in the 'white' type C. argus populations were 0.505 and 0.00057, respectively, which lower than those in the 'bicolor' type C. argus populations (Hd = 0.911, Pi = 0.00326). Population differentiation values (F ST) show that the four 'bicolor' type C. argus populations had obvious genetic differentiation (Fst: 0.21902-0.49428. p < 0.01), but not in the three 'white' type C. argus populations (Fst: -0.00571 to 0.07261. p > 0.05). The phylogenetic tree and Median Joining (MJ) network showed that the genetic distance among 'white' type C. argus populations is very close. Therefore, much attention should be paid to protecting population genetic diversity and avoiding inbreeding in the breeding of 'white' type C. argus.

Plasma cell subtypes analyzed using artificial intelligence algorithm for predicting biochemical recurrence, immune escape potential, and immunotherapy response of prostate cancer.

Background: Plasma cells as an important component of immune microenvironment plays a crucial role in immune escape and are closely related to immune therapy response. However, its role for prostate cancer is rarely understood. In this study, we intend to investigate the value of a new plasma cell molecular subtype for predicting the biochemical recurrence, immune escape and immunotherapy response in prostate cancer. Methods: Gene expression and clinicopathological data were collected from 481 prostate cancer patients in the Cancer Genome Atlas. Then, the immune characteristics of the patients were analyzed based on plasma cell infiltration fractions. The unsupervised clustering based machine learning algorithm was used to identify the molecular subtypes of the plasma cell. And the characteristic genes of plasma cell subtypes were screened out by three types of machine learning models to establish an artificial neural network for predicting plasma cell subtypes. Finally, the prediction artificial neural network of plasma cell infiltration subtypes was validated in an independent cohort of 449 prostate cancer patients from the Gene Expression Omnibus. Results: The plasma cell fraction in prostate cancer was significantly decreased in tumors with high T stage, high Gleason score and lymph node metastasis. In addition, low plasma cell fraction patients had a higher risk of biochemical recurrence. Based on the differential genes of plasma cells, plasma cell infiltration status of PCa patients were divided into two independent molecular subtypes(subtype 1 and subtype 2). Subtype 1 tends to be immunosuppressive plasma cells infiltrating to the PCa region, with a higher likelihood of biochemical recurrence, more active immune microenvironment, and stronger immune escape potential, leading to a poor response to immunotherapy. Subsequently, 10 characteristic genes of plasma cell subtype were screened out by three machine learning algorithms. Finally, an artificial neural network was constructed by those 10 genes to predict the plasma cell subtype of new patients. This artificial neural network was validated in an independent validation set, and the similar results were gained. Conclusions: Plasma cell infiltration subtypes could provide a potent prognostic predictor for prostate cancer and be an option for potential responders to prostate cancer immunotherapy.

Clinical cure and liver fibrosis reversal after postoperative antiviral combination therapy in hepatitis B-associated non-cirrhotic hepatocellular carcinoma: A case report.

BACKGROUND: The incidence of hepatocellular carcinoma (HCC) is high in China, and approximately 15%-20% of HCC cases occur in the absence of cirrhosis. Compared with patients with cirrhotic HCC, those with non-cirrhotic HCC have longer postoperative tumor-free survival. However, the overall survival time is not significantly increased, and the risk of postoperative recurrence remains. Strategies to improve the postoperative survival rate in these patients are currently required. CASE SUMMARY: A 47-year-old man with a family history of HCC was found to have hepatitis B virus (HBV) infection 25 years ago. In 2000, he was administered lamivudine for 2 years, and entecavir (ETV 0.5 mg) was administered in 2006. In October 2016, magnetic resonance imaging revealed a tumor in the liver (5.3 cm × 5 cm × 5 cm); no intraoperative hepatic and portal vein and bile duct tumor thrombi were found; and postoperative pathological examination confirmed a grade II HCC with no nodular cirrhosis (G1S3). ETV was continued, and no significant changes were observed on imaging. After receiving pegylated interferon alfa-2b (PEG IFNα-2b) (180 µg) + ETV in February 2019, the HBsAg titer decreased significantly within 12 wk. After receiving hepatitis B vaccine (60 µg) in 12 wk, HBsAg serological conversion was realized at 48 wk. During the treatment, no obvious adverse reactions were observed, except for early alanine aminotransferase flares. The reexamination results of liver pathology were G2S1, and reversal of liver fibrosis was achieved. CONCLUSION: The therapeutic regimen of ETV+ PEG IFNα-2b + hepatitis B vaccine for patients with HBV-associated non-cirrhotic HCC following hepatectomy can achieve an HBV clinical cure and prolong the recurrence-free survival.

In situ observation of the crystal structure transition of Pt-Sn intermetallic nanoparticles during deactivation and regeneration.

The mechanism of the deactivation and regeneration of PtSn intermetallic compound nanoparticle (iNP) catalysts was studied by in situ TEM investigation. Our study reveals the reversible dynamic structural transition of the iNPs during deactivation and regeneration, which provides a direct correlation between the atomic structure and the catalytic activity of the iNPs.

BMI1 activates P-glycoprotein via transcription repression of miR-3682-3p and enhances chemoresistance of bladder cancer cell.

Chemoresistance is the most significant reason for the failure of cancer treatment following radical cystectomy. The response rate to the first-line chemotherapy of cisplatin and gemcitabine does not exceed 50%. In our previous research, elevated BMI1 (B-cell specific Moloney murine leukemia virus integration region 1) expression in bladder cancer conferred poor survival and was associated with chemoresistance. Herein, via analysis of The Cancer Genome Atlas database and validation of clinical samples, BMI1 was elevated in patients with bladder cancer resistant to cisplatin and gemcitabine, which conferred tumor relapse and progression. Consistently, BMI1 was markedly increased in the established cisplatin- and gemcitabine-resistant T24 cells (T24/DDP&GEM). Functionally, BMI1 overexpression dramatically promoted drug efflux, enhanced viability and decreased apoptosis of bladder cancer cells upon treatment with cisplatin or gemcitabine, whereas BMI1 downregulation reversed this effect. Mechanically, upon interaction with p53, BMI1 was recruited on the promoter of miR-3682-3p gene concomitant with an increase in the mono-ubiquitination of histone H2A lysine 119, leading to transcription repression of miR-3682-3p gene followed by derepression of ABCB1 (ATP binding cassette subfamily B member 1) gene. Moreover, suppression of P-glycoprotein by miR-3682-3p mimics or its inhibitor XR-9576, could significantly reverse chemoresistance of T24/DDP&GEM cells. These results provided a novel insight into a portion of the mechanism underlying BMI1-mediated chemoresistance in bladder cancer.

Comprehensive signature analysis of drug metabolism differences in the White, Black and Asian prostate cancer patients.

The drug response sensitivity and related prognosis of prostate cancer varied from races, while the original mechanism remains rarely understood. In this study, the comprehensive signature including transcriptomics, epigenome and single nucleotide polymorphisms (SNPs) of 485 PCa cases- including 415 Whites, 58 Blacks and 12 Asians from the TCGA database were analyzed to investigate the drug metabolism differences between races. We found that Blacks and Whites had a more prominent drug metabolism, cytotoxic therapy resistance, and endocrine therapy resistance than Asians, while Whites were more prominent in drug metabolism, cytotoxic therapy resistance and endocrine therapy resistance than Blacks. Subsequently, the targeted regulation analysis indicated that the racial differences in cytotoxic therapy resistance, endocrine therapy resistance, might originate from drug metabolisms, and 19 drug metabolism-related core genes were confirmed in the multi-omics network for subsequent analysis. Furthermore, we verified that CYP1A1, CYP3A4, CYP2B6, UGT2B17, UGT2B7, UGT1A8, UGT2B11, GAS5, SNHG6, XIST significantly affected antineoplastic drugs sensitivities in PCa cell lines, and these genes also showed good predictive efficiency of drug response and treatment outcomes for PCa in this cohort of patients. These findings revealed a comprehensive signature of drug metabolism differences for the Whites, Blacks and Asians, and it may provide some evidence for making individualized treatment strategies.

microRNA-1236 promotes chondrocyte apoptosis in osteoarthritis via direct suppression of PIK3R3.

AIMS: Chondrocyte degeneration is the main cause of osteoarthritis (OA) and increased evidence suggests that miRNAs could have vital roles in the pathology of various cartilage illnesses. miR-1236 has been found to contribute to inflammation in diseases such as pneumonia. However, the exact role of miR-1236 in OA is poorly understood. MATERIALS AND METHODS: H&E staining and saffron fixation experiments were employed to determine OA tissues. qRT-PCR and immunohistochemistry were used to detect the expression levels of miR-1236 and PIK3R3. Western blot was performed to detect the expression levels of proteins. Luciferase reporter assays were utilized to investigate the interaction between miR-1236 and PIK3R3. Cell counting assays and AO/EB were used to quantify cell growth and apoptosis. KEY FINDINGS: miR-1236 was up-regulated in OA knee cartilage compared to normal cartilage. Up-regulated expression of miR-1236 suppressed cell proliferation as well as induced apoptosis in chondrocytes. Bioinformatics identified PIK3R3 as a target of miR-1236. Co-transfection with miR-1236 and PIK3R3 could reverse cell apoptosis induced by the miR-1236 mimic. SIGNIFICANCE: These data enhance our understanding on the role of miR-1236 in OA and identifies miR-1236 as a potential biomarker or possible treatment target within OA.

In Situ Growth of 3D/2D (CsPbBr3/CsPb2Br5) Perovskite Heterojunctions toward Optoelectronic Devices.

Two-dimensional (2D) CsPb2Br5 exhibits intriguing functions in enhancing the performance of optoelectronic devices in terms of environmental stability and luminescence properties when composited with other perovskites in different dimensionalities. We built a type I three-dimensional (3D) CsPbBr3/2D CsPb2Br5 heterojunction through phase transition where CsPbBr3 quantum dots in situ grew into 2D CsPb2Br5. A thorough growth mechanism study in combination with excited state dynamic investigations via femtosecond spectroscopy and first-principles calculations revealed that the type I hierarchy enhanced the stability of the heterojunction and spurred its luminous quantum yield by prolonging the lifetime of photogenerated carriers. Mixing the heterojunction with other phosphors yielded white-light-emitting diodes with a color rendering index of 94%. The work thus not only offered one new avenue for building heterojunctions by using the "soft crystal" nature of perovskites but also disentangled the enhanced luminescence mechanism of the heterojunction that can be harnessed for promising applications in the luminescence and display fields.

In situ growth of luminescent perovskite fibers in natural hollow templates.

Natural hollow fibers were used as templates to in situ produce thin Cs4PbX6 nanosheets on the inner walls, forming luminescent fibers that integrated the advantages of the large length of fibers and the emission tunability of perovskites, and exhibited great robustness as well for multiple applications like warning signs, anti-counterfeiting and fashion.

An ultrasensitive polydopamine bi-functionalized SERS immunoassay for exosome-based diagnosis and classification of pancreatic cancer.

Early diagnosis and metastasis monitoring for pancreatic cancer are extremely difficult due to a lack of sensitive liquid biopsy methods and reliable biomarkers. Herein, we developed easy-to-prepare and effective polydopamine-modified immunocapture substrates and an ultrathin polydopamine-encapsulated antibody-reporter-Ag(shell)-Au(core) multilayer (PEARL) Surface-Enhanced Raman Scattering (SERS) nano-tag with a quantitative signal of the Raman reporter at 1072 cm-1, which achieved ultrasensitive and specific detection of pancreatic cancer-derived exosomes with a detection limit of only one exosome in 2 µL of sample solution (approximately 9 × 10-19 mol L-1). Furthermore, by analyzing a 2 µL clinical serum sample, the migration inhibitory factor (MIF) antibody-based SERS immunoassay could not only discriminate pancreatic cancer patients (n = 71) from healthy individuals (n = 32), but also distinguish metastasized tumors from metastasis-free tumors, and Tumor Node Metastasis (TNM) P1-2 stages from the P3 stage (the discriminatory sensitivity was 95.7%). Thus, this novel immunoassay provides a powerful tool for the early diagnosis, classification and metastasis monitoring of pancreatic cancer patients.

Synthesis and biological evaluation of novel tanshinone IIA derivatives for treating pain.

Due to ineffectiveness and side effects of existing analgesics, chronic pain has become one of the most complex and difficult problems in the clinic. Monoacylglycerol lipase (MAGL) is an essential hydrolase in the endocannabinoid system and has been identified as a potential target for the treatment of pain. In the present study, we designed and synthesized twelve tanshinone IIA analogs and screened their activity against MAGL. Selected compounds were tested for analgesic activity in vivo, with the acetic acid writhing test model. Among the test compounds, compound III-3 (IC50 120 nmol·L-1) showed significant activity against MAGL and ameliorated the clinical progression in the mouse pain model. Additionally, compound III-3, substitution with N-methyl-2-morpholinoacetamide, demonstrated improved solubility relative to tanshinone IIA.

2D bismuthene fabricated via acid-intercalated exfoliation showing strong nonlinear near-infrared responses for mode-locking lasers.

The rediscovery of black phosphorus (BP) has expanded the 2D family into Group 15 (Nitrogen Group) elements, among which bismuthene is the latest member with extraordinary opto-electronic, catalytic and biocompatible properties and potential as a 2D topological insulator. However, bulk Bi is not easily mechanically exfoliated as its counterpart of BP. Thus, to date, the reports on 2D Bi fabrication are rare, and investigations on its nonlinear optical properties are even less. Herein, we rationally designed a new strategy combining acid-interaction and liquid exfoliation to successfully transform metal bulk Bi into few-layer semiconductor, which resulted in unseen opto-electronic properties, such as tunable nonlinear responses all the way to the near-infrared (NIR) region. This band is critical for telecommunication and military purposes, but currently, functioning materials are extremely scarce. The origin of this strong saturable absorption was thoroughly explored through time-resolved spectroscopy spanning from the fs to µs timescale, which indicated ultrafast fs to ps carrier dynamics in the early stage and long exciton bleaching recovery up to µs. As a proof-of-concept application, the as-prepared 2D Bi was employed as a saturable absorber to mode-lock a Tm-doped fiber laser and successfully realized a 2 µm NIR-wavelength output. This study not only offers an effective and scalable method to fabricate the new 2D family member bismuthene with extraordinary stability, but also explores its strong and broad nonlinear responses extending into the NIR region and fundamental photoinduced dynamics, which demonstrate the full potential of 2D Bi for application in opto-electronic devices and nonlinear optics.

[Studies on fluorescent properties of multi-walled carbon nanotubes before and after concentrated nitric acid treatment].

Fluorescent properties of multi-walled carbon nanotubes (MWNTs) before and after concentrated nitric acid treatment were studied. The results show that both multi-walled carbon nanotubes (MWNTs) and treated multi-walled carbon nanotubes (t-MWNTs) could emit fluorescence; compared with MWNTs, fluorescence from t-MWNTs is stronger and fluorescent emission peak from t-MWNTs blue shifts slightly to short-wavelength. Luminescence from MWNTs could be related to the trapping of excitation energy at defect sites and the energy bandgap between the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO). Treating MWNTs with concentrated nitric acid could introduce more defects on MWNTs and make MWTNs trap more excitation energy, leading to a fluorescence enhancement of t-MWTNs; in addition, the energy bandgap between LUMO and HOMO increases with length decreasing of MWNT, and the shortening of MWNT caused by concentrated nitric acid treatment could make energy bandgap between LUMO and HOMO increase, resulting in a slight blue shift of fluorescent emission peak of t-MWTNs to short wavelength.

[Soluble expression of AiiA protein and analysis of its antimicrobial activity].

AHLs are signaling molecules produced by Gram-negative bacterium during their proliferation. These molecules are closely related with bacteria pathogenicity. AiiA protein, functioning as a intracellular lactonase, hydrolyses AHLs at lactone loop in the molecule to reduce its biological activity and also dramatically reduces pathogenicity of bacterium at the same time. In this study, DNA fragment encoding aiiA gene was amplified from the plasmid derived from Bacillus thuringiensis by PCR. Expression vector, pET29a-aiiA, was constructed and transformed into bacteria strain of E. coli BL21 (DE3) for expression of AiiA protein. After 25 h induction with 0.8 mmol/L IPTG at 20 degrees C, the protein AiiA expressed in soluble form by recombinant strain reached about 54.4 microg/mL. The recombinant protein was purified with Ni-affinity chromatography. Biological activity analysis showed that AiiA protein had a capability to hydrolyse AHLs, and strong antimicrobial activity for Eriwinia carotovora.