The process of solid-state fermentation of soybean meal: antimicrobial activity, fermentation heat generation and nitrogen solubility index

BACKGROUND

Bacillus amyloliquefaciens has excellent protease production ability and holds great prospects for application in the solid-state fermentation of soybean meal (SBM).

RESULTS

Among eight strains of bacteria, Bacillus amyloliquefaciens subsp. plantarum CICC 10265, which exhibited higher protease production, was selected as the fermentation strain. The protease activity secreted by this strain reached 106.41 U mL-1 . The microbial community structure differed significantly between natural fermentation and inoculation-enhanced fermented soybean meal (FSBM), with the latter showing greater stability and inhibition of miscellaneous bacterial growth. During fermentation, the temperature inside the soybean meal increased, and the optimal environmental temperature for FSBM was found to be between 35 and 40 °C. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis and nitrogen solubility index (NSI) results demonstrated that solid-state fermentation had a degrading effect on highly denatured proteins in SBM, resulting in an NSI of 67.1%.

CONCLUSION

Bacillus amyloliquefaciens subsp. plantarum CICC 10265 can enhance the NSI of SBM in solid-state fermentation and inhibit the growth of miscellaneous bacteria. © 2023 Society of Chemical Industry.

scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding

Dynamic compartmentalization of eukaryotic DNA into active and repressed states enables diverse transcriptional programs to arise from a single genetic blueprint, whereas its dysregulation can be strongly linked to a broad spectrum of diseases. While single-cell Hi-C experiments allow for chromosome conformation profiling across many cells, they are still expensive and not widely available for most labs. Here, we propose an alternate approach, scENCORE, to computationally reconstruct chromatin compartments from the more affordable and widely accessible single-cell epigenetic data. First, scENCORE constructs a long-range epigenetic correlation graph to mimic chromatin interaction frequencies, where nodes and edges represent genome bins and their correlations. Then, it learns the node embeddings to cluster genome regions into A/B compartments and aligns different graphs to quantify chromatin conformation changes across conditions. Benchmarking using cell-type-matched Hi-C experiments demonstrates that scENCORE can robustly reconstruct A/B compartments in a cell-type-specific manner. Furthermore, our chromatin confirmation switching studies highlight substantial compartment-switching events that may introduce substantial regulatory and transcriptional changes in psychiatric disease. In summary, scENCORE allows accurate and cost-effective A/B compartment reconstruction to delineate higher-order chromatin structure heterogeneity in complex tissues.

Application of Hyperspectral Imaging as a Nondestructive Technology for Identifying Tomato Maturity and Quantitatively Predicting Lycopene Content

Maturity is a crucial indicator in assessing the quality of tomatoes, and it is closely related to lycopene content. Using hyperspectral imaging, this study aimed to monitor tomato maturity and predict its lycopene content at different maturity stages. Standard normal variable (SNV) transformation was applied to preprocess the hyperspectral data. Then, using competitive adaptive reweighted sampling (CARS), the characteristic wavelengths were selected to simplify the calibration models. Based on the full and characteristic wavelengths, a support vector classifier (SVC) model was developed to determine tomato maturity qualitatively. The results demonstrated that the classification accuracy using the characteristic wavelength led to the obtention of better results with an accuracy of 95.83%. In addition, the support vector regression (SVR) and partial least squares regression (PLSR) models were utilized to predict lycopene content. With a coefficient of determination for prediction (R2P) of 0.9652 and a root mean square error for prediction (RMSEP) of 0.0166 mg/kg, the SVR model exhibited the best quantitative prediction capacity based on the characteristic wavelengths. Following this, a visual distribution map was created to evaluate the lycopene content in tomato fruit intuitively. The results demonstrated the viability of hyperspectral imaging for detecting tomato maturity and quantitatively predicting the lycopene content during storage.

Enhancer Coamplification and Hijacking Promote Oncogene Expression in Liposarcoma

SIGNIFICANCE

Comprehensive profiling of the enhancer landscape and 3D genome structure in liposarcoma identifies extensive enhancer-oncogene coamplification and enhancer hijacking events, deepening the understanding of how oncogenes are regulated in cancer.

Structural Characteristics of Reaction Tissue in Plants

To maintain or adjust posture under the challenges of gravity and increased self-weight, or the effects of light, snow, and slope, plants have the ability to develop a special type of tissue called reaction tissue. The formation of reaction tissue is a result of plant evolution and adaptation. The identification and study of plant reaction tissue are of great significance for understanding the systematics and evolution of plants, the processing and utilization of plant-based materials, and the exploration of new biomimetic materials and biological templates. Trees' reaction tissues have been studied for many years, and recently, many new findings regarding these tissues have been reported. However, reaction tissue requires further detailed exploration, particularly due to their complex and diverse nature. Moreover, the reaction tissues in gymnosperms, vines, herbs, etc., which display unique biomechanical behavior, have also garnered the attention of research. After summarizing the existing literature, this paper provides an outline of the reaction tissues in woody plants and non-woody plants, and lays emphasis on alternations in the cell wall structure of the xylem in softwood and hardwood. The purpose of this paper is to provide a reference for the further exploration and study of reaction tissues with great diversity.

MEK1-dependent MondoA phosphorylation regulates glucose uptake in response to ketone bodies in colorectal cancer cells

The Mondo family transcription factor MondoA plays a pivotal role in sensing metabolites, such as glucose, glutamine, and lactic acid, to regulate glucose metabolism and cell proliferation. Ketone bodies are important signals for reducing glucose uptake. However, it is unclear whether MondoA functions in ketone body-regulated glucose transport. Here we reported that ketone bodies promoted MondoA nuclear translocation and binding to the promoter of its target gene TXNIP. Ketone bodies reduced glucose uptake, increased apoptosis and decreased proliferation of colorectal cancer cells, which was impeded by MondoA knockdown. Moreover, we identified MEK1 as a novel component of the MondoA protein complex using a proteomic approach. Mechanistically, MEK1 interacted with MondoA and enhanced tyrosine 222, but not serine or threonine, phosphorylation of MondoA, inhibiting MondoA nuclear translocation and transcriptional activity. Ketone bodies decreased MEK1-dependent MondoA phosphorylation by blocking MondoA and MEK1 interaction, leading to MondoA nuclear translocation, TXNIP transcription, and inhibition of glucose uptake. Therefore, our study not only demonstrated that ketone bodies reduce glucose uptake, promote apoptosis, and inhibit cell proliferation in colorectal cancer cells by regulating MondoA phosphorylation but also identified MEK1-dependent phosphorylation as a new mechanism to manipulate MondoA activity.

Cytohesin-4 Upregulation in Glioma-Associated M2 Macrophages Is Correlated with Pyroptosis and Poor Prognosis

Cytohesin-4 (CYTH4) is a member of the PSCD family. Members of this family appear to mediate the regulation of protein sorting and membrane trafficking. In previous studies, CYTH4 has been linked with multiple brain diseases, but not glioma, the most common type of brain tumor. We utilized multiple glioma single-cell RNA sequencing datasets and bulk data from the TCGA and CGGA and conducted GSEA and KEGG and GO analyses. Biomarker potential was tested via ROC curve analysis. Radar plots were used to study TMB and MSI correlations. Immune cell studies were conducted using CIBERSORT. All statistical analyses were performed in R software and GraphPad Prism 9. CYTH4 was overexpressed in the glioma macrophage population in several single-cell RNA sequencing datasets and was most correlated with M2 macrophages. CYTH4 expression was higher in tumor tissues and was correlated with survival and WHO grade. ROC curves suggested CYTH4 overexpression to be a potential glioma biomarker. GSEA results indicated a relationship between CYTH4 and apoptosis, and PPI analysis supported a pyroptosis correlation. KEGG and GO analysis results linked CYTH4 with antigen processing and presentation and neutrophil activities. In summary, the study identified a CYTH4/pyroptosis/M2 macrophage axis. CYTH4 was upregulated in M2 macrophages in glioma and affected pyroptosis. CYTH4 overexpression is a potential biomarker predicting a poor prognosis.

CTNI-37. REPEATED OPENING OF THE BLOOD-BRAIN BARRIER WITH THE SKULL-IMPLANTABLE SONOCLOUD-9 (SC9) DEVICE: PHASE 1 TRIAL OF NAB-PACLITAXEL AND SC9 IN RECURRENT GLIOBLASTOMA

BACKGROUND

The blood-brain barrier (BBB) is a major impediment to pharmacological treatment of gliomas. Low-intensity pulsed ultrasound with concomitant administration of intravenous microbubbles (LIPU/MB), temporarily opens the BBB. Here we investigate the pharmacokinetics and safety of this approach of repeated delivery of albumin-bound paclitaxel (Abraxane®, ABX) to the peri-tumoral brain. To perform LIPU/MB-based BBB opening prior to ABX infusions, we used a novel 6 x 6 cm device with 9 ultrasound emitters (SC9) that is implanted in a skull window after tumor resection.

METHODS

A Phase 1 dose-escalation trial using Bayesian adaptive design was conducted (NCT04528680). Patients with recurrent operable glioblastoma, a WHO PS ≤ 2 and adequate bone marrow and organ function were eligible. After tumor resection and implantation of SC9, repeated cycles of BBB opening by LIPU/MB immediately followed by ABX, was performed every 3 weeks. Intraoperative LIPU/MB and low dose ABX was given prior to tumor resection allowed for investigation tissue concentrations and pharmacokinetics.

RESULTS

Seventeen patients have been treated at six escalating ABX dose levels (40-260 mg/m2). At dose of 260 mg/m2, a grade 3 reversible taxane-associated dose limiting encephalopathy was observed in one patient. The patient continued treatment at a lower dose in subsequent cycles. A second patient exhibited encephalopathy on cycle 2. One patient developed grade 2 cumulative peripheral neuropathy. Intraoperative pharmacokinetic studies showed that ABX tissue concentrations in non-enhancing peri-tumoral brain were increased 3.7-fold after LIPU/MB. sc-RNA-sequencing showed transcriptional dysregulation of membrane transporters, pathways related to trans-cytosis as well as cell-cell and cell-matrix adhesion.

CONCLUSIONS

The LIPU/MB using skull-implantable ultrasound enhances the penetration of ABX in large regions of the brain. The procedure can be performed repeatedly and safely. LIPU-based BBB opening leads to transcriptional alterations in brain endothelium. Funding: NIH/NCI 1R01CA245969-01A1, CarThera (SC9 devices), BMS/Celgene (Abraxane®).

Subtype-specific 3D genome alteration in acute myeloid leukaemia

Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases1-5. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.

EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps

The Hi-C technique has been shown to be a promising method to detect structural variations (SVs) in human genomes. However, algorithms that can use Hi-C data for a full-range SV detection have been severely lacking. Current methods can only identify interchromosomal translocations and long-range intrachromosomal SVs (>1 Mb) at less-than-optimal resolution. Therefore, we develop EagleC, a framework that combines deep-learning and ensemble-learning strategies to predict a full range of SVs at high resolution. We show that EagleC can uniquely capture a set of fusion genes that are missed by whole-genome sequencing or nanopore. Furthermore, EagleC also effectively captures SVs in other chromatin interaction platforms, such as HiChIP, Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET), and capture Hi-C. We apply EagleC in more than 100 cancer cell lines and primary tumors and identify a valuable set of high-quality SVs. Last, we demonstrate that EagleC can be applied to single-cell Hi-C and used to study the SV heterogeneity in primary tumors.

Abstract 2953: Subtype-specific and structure variation induced 3D genome alteration in acute myeloid leukemia

Acute myeloid leukemia (AML) represents a set of heterogeneous myeloid malignancies hallmarked by mutations in epigenetic modifiers, transcription factors, and kinases that can cause epigenetic reshaping. It is unclear to what extent AML mutations drive chromatin 3D structure alteration and contribute to myeloid transformation. We first performed Hi-C and whole-genome sequencing in 25 AML patient samples and seven healthy donor samples, and identified recurrent alterations of A/B compartments, TADs, and chromatin loops that are unique to different subtypes. To investigate how altered chromatin organization contributes to transcriptional misregulation, we performed RNA-Seq, ATAC-Seq and CUT&ag for CTCF, H3K27ac, and H3K27me3 in the same AML samples. We identified extensive and recurrent AML-specific promoter-enhancer and promoter-repressor loops. We performed both CRISPR deletion and interference experiments and validated two repressor loops that downregulated cancer related genes IKZF2 and RTTN. Furthermore, by using our recently developed algorithm, we identified structural variation-induced enhancer-hijacking and repressor-hijacking events in AML samples. We further demonstrated the role of hijacked enhancers in AML cell growth by CRISPR screening, and the role of hijacked repressors by CRISPR de-repression. We performed whole-genome bisulfite sequencing in 20 AML and normal samples, and showed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Finally, by treating the AML cells with the DNA hypomethylating agent and performing triple knockdown of DNMT1/3A/3B, we demonstrated the impact of altered DNA methylation on gene expression and 3D genome organization. Overall this study provides an invaluable resource for leukemia studies and also highlighted the role of repressor-loops and hijacked cis-elements in gene regulation and human diseases.

Citation Format: Jie Xu, Fan Song, Baozhen Zhang, Huijue Lyu, Mikoto Kobayashi, Ziyu Zhao, Ye Hou, Xiaotao Wang, Yu Luan, Bei Jia, Lena Stasiak, Qixuan Wang, Qi Jin, Qiushi Jin, Yihao Fu, Ross C. Hardison, Sinisa Dovat, Leonidas C. Platanias, Yue Yang, Tomoko Yamada, Aaron D. Viny, Ross L. Levine, David F. Claxton, James R. Broach, Hong Zheng, Feng Yue. Subtype-specific and structure variation induced 3D genome alteration in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2953.

A bivalent Tim-3/PD-1 bispecific antibody for the treatment of PD-1 antibody resistant or refractory NSCLC

e14597

Background: Immune checkpoint inhibitors (ICI) PD-1/PD-L1 antibody are key drugs for the treatment of non-small cell lung cancer (NSCLC). Bispecific antibody is one of the strategies aimed at the clinical needs for NSCLC patients who are resistant to or refractory from ICI treatment. Tim-3, one of the next generation of ICB targets, is co-expressed on exhausted T cells with PD-1. It is also expressed by innate immune populations, including NK and DC. Dual blocking PD-1 and Tim-3 not only on T cells but also on DC, NK cells may achieve better clinical benefit. Methods: A bivalent to both Tim-3 and PD-1 bispecific antibody (Bis5) was developed and is in Phase I clinical trials for NSCLC patients who are resistant to or refractory from PD-1 antibody treatment. Results: Bis5 showed affinity of 5-8 nM to both Tim-3 and PD-1. Moreover, Bis5 showed better cell activity than Tim-3 and PD-1 antibody combination to activated T cell as well as NK and DC. Bis5 showed 77%-88% tumor inhibition which is close to PD-1 antibody alone in MC38 model. Neither PD-1 antibody or PD-1 and Tim-3 antibody combination show any activity in CT26 model while Bis5 showed significant tumor inhibition activity and doubled the survival rate. The highest non-severe toxicity dose (HNSTD) was 200mpk in monkeys. ADA were 33.3% (2/6), 83.3% (5/6), and 0.0% (0/6) at doses of 2, 10, and 50 mpk, respectively. The T1/2 were 31.7-66.5 h for doses 2-50 mpk. Conclusions: A Phase I, multicenter, open-label study to evaluate the safety, tolerability, pharmacokinetics, pharmacodynamics, immunogenicity and preliminary efficacy of Bis5 in patients with advanced and/or metastatic solid tumors has started. Seven cohorts (0.1, 0.3, 1, 3, 6, 10, 15 mg/kg) are planned to be enrolled sequentially in the dose escalation part. In the expansion part, a cohort group of 10 patients is planned for post PD-1 treated NSCLC as the second or third line treatment.

A peptide fused to CLDN18.2 antibody targeting the tumor antigen associated CD8+T cells for the treatment of pancreatic cancers

e16240

Background: PD-1/PD-L1-targeted immunotherapies have become critical roles in the treatment for many tumors. However, there is limited progress in gastrointestinal cancers, especially in pancreatic ductal adenocarcinoma (PDAC). PDAC is low immunogenicity. PDAC microenvironment is immunosuppressive. More than 70% PDACs have few or no CD8+ T cells around the tumor cell or in the tumor microenvironment. Therefore, immunotherapy like PD-1/PD-L1 antibody alone is rarely effective for PDACs. Methods: Some cytokine or analogs may activate CD8+ T cells. An analog specifically activating tumor antigen associated (TAA) CD8+ T cells was fused to anti-CLDN18.2 antibody. Results: The specific bi-functional molecule (Bis2) has high affinity to human anti-CLDN18.2 (14pM) and CD8+T cells. Bis2 shows significant in vivo efficacy at 0.1 mpk. The efficacy lasts for more than 24 days, only given two doses at day 1 and day 3, respectively. IHC shows that the tumor infiltrated CD8+T cells significantly increased and IFNγ secretion enhanced as well. The IHC results are consistent with the mechanism that Bis2 induces TAA CD8+ T cell proliferation and prevents CD8+T cells from IFNγ-mediated apoptosis. Moreover, Bis2 also shows 100% tumor inhibition in combination with either chem (L-OHP+5FU) or PD-1 antibody in vivo which is better than chem in combination with PD-1 antibody. Bis2 also shows 60% tumor inhibition at 1mpk in CLDN18.2 negative cell based in vivo model. Bis2 shows ADA in monkeys in two weeks by dosing weekly. The repeated doses toxicity study shows an increase of MONO and %MONO and decrease in RBC, HGB, HCT, and MCHC. The HNSTD was 3mpk. The T1/2 was 40h. Conclusions: The Phase I study in advanced solid tumors is ongoing. The study uses accelerated titration starting from 0.01mpk combined with a BOIN design, maximum patient size of 36. In the expansion part, two cohorts of 10 CLDN18.2+ pancreatic cancer patients are planned for the treatment of Bis2 alone or Bis2 in combination with chemotherapy, respectively.

Repeated opening of the blood-brain barrier with the skull-implantable SonoCloud-9 (SC9) device: Phase 1 trial of nab-paclitaxel and SC9 in recurrent glioblastoma

2016

Background: The blood-brain barrier (BBB) is a major impediment to pharmacological treatment of gliomas, a diffuse tumor infiltrating the peri-tumoral normal brain. Low-intensity pulsed ultrasound directed at the brain with concomitant administration of intravenous microbubbles (LIPU/MB), temporarily opens the BBB. This technique was previously shown with a first generation of the device in combination with carboplatin chemotherapy (Idbaih et al. 2019). Here we investigate the pharmacokinetics and safety of this approach in the context of repeated delivery of albumin-bound paclitaxel (ABX) to the peri-tumoral brain. To perform LIPU/MB-based BBB opening prior to ABX infusions, we used a novel 6 x 6 cm device with 9 ultrasound emitters (SC9) that is implanted in a skull window after tumor resection. Methods: A Phase 1 dose-escalation trial using Bayesian adaptive design was initiated at our institution (NCT04528680). Patients with recurrent operable glioblastoma, a WHO PS ≤ 2 and normal bone marrow and organ function were eligible. After tumor resection and implantation of SC9, repeated cycles of BBB opening by LIPU/MB immediately followed by ABX, was performed every 3 weeks. Intraoperative LIPU/MB and low dose ABX was given prior to tumor resection for investigation of pharmacokinetics. Results: Seventeen patients have been enrolled and six dose levels of ABX were used (40-260 mg/m2). Severe, reversible taxane-associated encephalopathy was observed in one patient at the max. planned dose level (260 mg/m2). The patient continued treatment at a lower dose in subsequent cycles. One patient developed grade 2 cumulative peripheral neuropathy. Other mild to moderate and reversible toxicities for ABX including myelosuppression, fatigue, alopecia were observed as expected. Intraoperative sonication and pharmacokinetic studies showed that ABX tissue concentrations in non-enhancing peri-tumoral brain were increased several-fold after LIPU/MB. On electron microscopy, sonicated tissue showed ultra-structural alterations in brain capillary endothelial cells. Molecular studies showed transcriptional dysregulation of membrane transporters, pathways related to trans-cytosis, cell permeability as well as cell-cell and cell-matrix adhesion. Updated results will be presented. Conclusions: The LIPU/MB using skull-implantable ultrasound enhances the penetration of large chemotherapeutic drugs such as ABX in large regions of the brain, a procedure that can be performed repeatedly and safely. LIPU-based BBB opening leads to ultrastructural and transcriptional alterations in brain endothelial cells. A Phase 2 clinical trial is planned to investigate efficacy of this approach. Funding: NIH/NCI 1R01CA245969-01A1, Carthera (SC9 devices), Celgene/BMS, Malnati Brain Tumor Institute, Moceri Family Foundation. Clinical trial information: NCT04528680.

Enhancer selection dictates gene expression responses in remote organs during tissue regeneration

Acute trauma stimulates local repair mechanisms but can also impact structures distant from the injury, for example through the activity of circulating factors. To study the responses of remote tissues during tissue regeneration, we profiled transcriptomes of zebrafish brains after experimental cardiac damage. We found that the transcription factor gene cebpd was upregulated remotely in brain ependymal cells as well as kidney tubular cells, in addition to its local induction in epicardial cells. cebpd mutations altered both local and distant cardiac injury responses, altering the cycling of epicardial cells as well as exchange between distant fluid compartments. Genome-wide profiling and transgenesis identified a hormone-responsive enhancer near cebpd that exists in a permissive state, enabling rapid gene expression in heart, brain and kidney after cardiac injury. Deletion of this sequence selectively abolished cebpd induction in remote tissues and disrupted fluid regulation after injury, without affecting its local cardiac expression response. Our findings suggest a model to broaden gene function during regeneration in which enhancer regulatory elements define short- and long-range expression responses to injury.

A finite element model to predict the double hearing protector effect on an in-house acoustic test fixture

The sound attenuation of double hearing protectors (DHPs), earplugs combined with earmuffs, generally falls short of the sum of each single protector's attenuation when used independently. This phenomenon, referred to as the DHP effect, is found to be related to structure-borne sound transmission involving the outer ear and can also be observed on acoustic test fixtures (ATFs). At present, it still remains not fully understood, and no available model can help demonstrate the associated sound transmission mechanisms. In this work, a finite element model is proposed to study the DHP effect on an ATF between 100 Hz and 5 kHz. Power balances are calculated with selected configurations of the ATF in order to (i) quantify the contribution of each sound path, and study the effects of (ii) the artificial skin and (iii) acoustic excitation on the ATF exterior boundaries. The DHP effect is shown to originate from the structure-borne sound power injected from the ATF boundaries and/or earmuff cushion. The important influence of earcanal wall vibration is highlighted when the skin is accounted for. The simulation results allow for gaining more insight into the sound transmission through a DHP/ATF system.

Pan-Cancer Analysis and Validation Reveals that D-Dimer-Related Genes are Prognostic and Downregulate CD8+ T Cells via TGF-Beta Signaling in Gastric Cancer

Background: Cancer is considered one of the most lethal diseases worldwide. Venous thromboembolism (VTE) is the second leading cause of death in cancer patients. As one of the most reproducible predictors of thromboembolism, the D-dimer level is commonly considered by oncologists. Previous studies have demonstrated that the most correlated genes at the D-dimer level are F3, F5 and FGA.

Methods: Using data from TCGA and multiple webtools, including GEPIA2, UALCAN, TIMER2.0, Kaplan-Meier Plotter and CIBERSORTx, we analyzed the tumor mutation burden (TMB), microsatellite instability (MSI) and functions of D-dimer-related genes in cancer. Validation was conducted via quantitative real-time polymerase chain reaction (qRT-PCR) and independent GEO + GTEx cohort. All statistical analyses were performed in R software and GraphPad Prism 9.

Results: F3, F5 and FGA were expressed differently in multiple cancer types. TMB, MSI and anti-PD1/PDL1 therapy responses were correlated with D-dimer-related gene expression. D-Dimer-related genes expression affect the survival of cancer patients. F3 and F5 functioned in TGF-beta signaling. F3 and F5 were related to immunity and affected the fraction of CD8⁺ T cells by upregulating the TGF-beta signaling pathway, forming an F3, F5/TGF-beta signaling/CD8+ T cell axis.

Conclusion: F3, F5 and FGA serve as satisfactory GC multibiomarkers and potentially influence the immune microenvironment and survival of cancer patients by influencing TGF-beta signaling.

Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation

Inherited noncoding genetic variants confer significant disease susceptibility to childhood acute lymphoblastic leukemia (ALL) but the molecular processes linking germline polymorphisms with somatic lesions in this cancer are poorly understood. Through targeted sequencing in 5,008 patients, we identified a key regulatory germline variant in GATA3 associated with Philadelphia chromosome-like ALL (Ph-like ALL). Using CRISPR-Cas9 editing and samples from patients with Ph-like ALL, we showed that this variant activated a strong enhancer that upregulated GATA3 transcription. This, in turn, reshaped global chromatin accessibility and three-dimensional genome organization, including regions proximal to the ALL oncogene CRLF2. Finally, we showed that GATA3 directly regulated CRLF2 and potentiated the JAK-STAT oncogenic effects during leukemogenesis. Taken together, we provide evidence for a distinct mechanism by which a germline noncoding variant contributes to oncogene activation, epigenetic regulation and three-dimensional genome reprogramming.

A Robust and Wearable Triboelectric Tactile Patch as Intelligent Human-Machine Interface

The human-machine interface plays an important role in the diversified interactions between humans and machines, especially by swaping information exchange between human and machine operations. Considering the high wearable compatibility and self-powered capability, triboelectric-based interfaces have attracted increasing attention. Herein, this work developed a minimalist and stable interacting patch with the function of sensing and robot controlling based on triboelectric nanogenerator. This robust and wearable patch is composed of several flexible materials, namely polytetrafluoroethylene (PTFE), nylon, hydrogels electrode, and silicone rubber substrate. A signal-processing circuit was used in this patch to convert the sensor signal into a more stable signal (the deviation within 0.1 V), which provides a more effective method for sensing and robot control in a wireless way. Thus, the device can be used to control the movement of robots in real-time and exhibits a good stable performance. A specific algorithm was used in this patch to convert the 1D serial number into a 2D coordinate system, so that the click of the finger can be converted into a sliding track, so as to achieve the trajectory generation of a robot in a wireless way. It is believed that the device-based human-machine interaction with minimalist design has great potential in applications for contact perception, 2D control, robotics, and wearable electronics.

Abstract 2118: Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemia

Inherited non-coding genetic variants confer significant disease susceptibility in many cancers. However, the molecular processes of by which germline variants contribute to somatic lesions are poorly understood. We performed targeted sequencing in 5,008 patients and identified a key regulatory germline variant in GATA3 strongly associated with Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL). By creating an isogenic cellular model with CRISPR-Cas9 system, we showed that this variant activated a strong enhancer that significantly upregulated GATA3 transcription, which in turn reshaped the global chromatin accessibility and 3D genome organization. Remarkably, this genotype switch induced a chromatin loop between the CRLF2 oncogene and a distal enhancer, similar to the somatically acquired super-enhancer hijacking event in patients. GATA3 genotype-related alterations in transcriptional control and 3D chromatin organization were further validated in Ph-like ALL patients. Finally, we showed that GATA3 directly regulates CRLF2 and potentiates the oncogenic effects of JAK-STAT signaling in leukemogenesis. Altogether, our results provide evidence for a novel mechanism by which a germline non-coding variant contributes to oncogene activation epigenetic regulation and 3D genome reprogramming.

Citation Format: Hongbo Yang, Hui Zhang, Yu Luan, Tingting Liu, Kathryn Roberts, Mao-xiang Qian, Bo Zhang, Wenjian Yang, Virginia Perez-Andreu, Jie Xu, Sriranga lyyanki, Da Kuang, Shalini Reshmi, Julie Gastier-Foster, Colton Smith, Ching-Hon Pui, William Evans, Stephen Hunger, Stephen Hunger, Leonidas Platanias, Mary Relling, Charles Mullighan, Mignon Loh, Feng Yue, Jun Yang. Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2118.

Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer

Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival. Transcriptionally, FOXA1, GATA3, and PPARG are shown to be essential for luminal subtype-specific gene regulation and subtype switching, while TP63, STAT3, and TFAP2 family members are critical for regulation of basal subtype-specific genes. Despite these advances, the underlying epigenetic mechanisms and 3D chromatin architecture responsible for subtype-specific regulation in bladder cancer remain unknown. RESULT: We determine the genome-wide transcriptome, enhancer landscape, and transcription factor binding profiles of FOXA1 and GATA3 in luminal and basal subtypes of bladder cancer. Furthermore, we report the first-ever mapping of genome-wide chromatin interactions by Hi-C in both bladder cancer cell lines and primary patient tumors. We show that subtype-specific transcription is accompanied by specific open chromatin and epigenomic marks, at least partially driven by distinct transcription factor binding at distal enhancers of luminal and basal bladder cancers. Finally, we identify a novel clinically relevant transcription factor, Neuronal PAS Domain Protein 2 (NPAS2), in luminal bladder cancers that regulates other subtype-specific genes and influences cancer cell proliferation and migration. CONCLUSION: In summary, our work identifies unique epigenomic signatures and 3D genome structures in luminal and basal urinary bladder cancers and suggests a novel link between the circadian transcription factor NPAS2 and a clinical bladder cancer subtype.

Gene mapping reveals the association between tyrosine protein kinase Abl1 and the silk yield of Bombyx mori

The Z chromosome of the silkworm contains a major gene that influences silk yield. This major locus on chromosome Z accounts for 35.10% of the phenotypic variance. The location and identification of the gene have been a focus of silkworm genetics research. Unfortunately, identification of this gene has been difficult. We used extreme phenotype subpopulations and selected from a backcross population, BC₁ M, which was obtained using the high-yield strain 872B and the low-yield strain IS-Dazao as parents, for mapping the gene on the chromosome Z. The candidate region was narrowed down to 134 kb at the tip of the chromosome. BmAbl1 in this region correlated with silk gland development by spatiotemporal expression analysis. This gene was differentially expressed in the posterior silk glands of the high- and low-yield strains. In BmAbl1, an insertion-deletion (indel) within the 10th exonic region and an SNP within the 6th intronic region were detected and shown to be associated with cocoon shell weight in 84 Bombyx mori strains with different yields. Nucleotide diversity analysis of BmAbl1 and its 50 kb flanking regions indicated that BmAbl1 has experienced strong artificial selection during silkworm domestication. This study is the first to identify the genes controlling silk yield in the major QTL of the Z chromosome using forward genetics.

A proof-of-concept study of an automated solution for clinical metagenomic next-generation sequencing

AIMS

Metagenomic next-generation sequencing (mNGS) has been utilized for diagnosing infectious diseases. It is a culture-free and hypothesis-free nucleic acid test for diagnosing all pathogens with known genomic sequences, including bacteria, fungi, viruses and parasites. While this technique greatly expands the clinical capacity of pathogen detection, it is a second-line choice due to lengthy procedures and microbial contaminations introduced from wet-lab processes. As a result, we aimed to reduce the hands-on time and exogenous contaminations in mNGS.

METHODS AND RESULTS

We developed a device (NGSmaster) that automates the wet-lab workflow, including nucleic acid extraction, PCR-free library preparation and purification. It shortens the sample-to-results time to 16 and 18·5 h for DNA and RNA sequencing respectively. We used it to test cultured bacteria for validation of the workflow and bioinformatic pipeline. We also compared PCR-free with PCR-based library prep and discovered no differences in microbial reads. Moreover we analysed results by automation and manual testing and found that automation can significantly reduce microbial contaminations. Finally, we tested artificial and clinical samples and showed mNGS results were concordant with traditional culture.

CONCLUSION

NGSmaster can fulfil the microbiological diagnostic needs in a variety of sample types.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study opens up an opportunity of performing in-house mNGS to reduce turnaround time and workload, instead of transferring potentially contagious specimen to a third-party laboratory.

The Role of Mondo Family Transcription Factors in Nutrient-Sensing and Obesity

In the past several decades obesity has become one of the greatest health burdens worldwide. Diet high in fats and fructose is one of the main causes for the prevalence of metabolic disorders including obesity. Promoting brown or beige adipocyte development and activity is regarded as a potential treatment of obesity. Mondo family transcription factors including MondoA and carbohydrate response element binding protein (ChREBP) are critical for nutrient-sensing in multiple metabolic organs including the skeletal muscle, liver, adipose tissue and pancreas. Under normal nutrient conditions, MondoA and ChREBP contribute to maintaining metabolic homeostasis. When nutrient is overloaded, Mondo family transcription factors directly regulate glucose and lipid metabolism in brown and beige adipocytes or modulate the crosstalk between metabolic organs. In this review, we aim to provide an overview of recent advances in the understanding of MondoA and ChREBP in sensing nutrients and regulating obesity or related pathological conditions.

A map of cis-regulatory elements and 3D genome structures in zebrafish

The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species¹. However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.

Synthesis and application of gas diffusion cathodes in an advanced type of undivided electrochemical cell

This paper reports the oxidation of Remazol black B dye by employing iron ions catalyst based gas diffusion cathodes, (GDCs). A GDC was synthesized by using a layer of carbon black and iron ions catalyst for oxygen reduction to hydrogen peroxide. The results demonstrated around 97% decolorization of Remazol black-B dye for 50 min by iron ions catalyst based GDC. The degradation study was performed under electrogenerated hydrogen peroxide at a constant voltage of - 0.6 V vs Hg/HgSO4 in which the rate of degradation was correlated with hydrogen peroxide production. Overall, the GDC's found to be effective method to degrade the dyes via electro-Fenton.

[Correlation analysis between prostate imaging report and data system score and pathological results of prostate cancer]

Objective: To explore the correlation between prostate imaging report and data system (PI-RADS) score and international society of uological pathology (ISUP) grade of prostate cancer (PCa) and the role of PI-RADS score in predicting the pathological features of clinically significant PCa (csPCa), positive surgical margin and pathological upgrade. Methods: The pathologically positive patients with multi-parameter magnetic resonance image (mpMRI) were included in this study. The patients with prostate specific antigen (PSA)<100 μg/L were divided into two groups: biopsy group (n=523) and RP group (n=215). The correlation between PI-RADS score and ISUP grade and the accuracy of predicting csPCa in the two groups were evaluated. In the RP group, the correlation between PI-RADS score and postoperative pathological grade or degradation and positive incisal margin was further discussed. The patients with PSA≥100 μg/L (171cases in biopsy group and 6 cases in RP group) were not included in the statistical analysis, and the results were simply described. Results: The age, prostate volume, and PSA level of biopsy group and RP group was (72±8) years vs (68±7) years, 48.3 (32-57) cm(3) vs 47.2 (32-54) cm(3), and 26.3(10.2-34.2)μg/L vs 21.7 (9.24-23.95)μg/L, respectively. The PI-RADS scores ≤ 3,4, and 5 in the biopsy group were 109,97, and 317 respectively, and those in the RP group were 61,55, and 99 respectively. There were significant differences in the composition of ISUP grades of different PI-RADS scores between the two groups (P<0.001), and there was a positive correlation between the two groups (r=0.493 in the biopsy group, r=0.671 in the RP group, both P<0.001). Using PI-RADS score to predict csPCa, biopsy group (AUC=0.764, P<0.001, 95%CI:0.710-0.819) and RP group (AUC=0.807, P<0.001, 95%CI:0.735-0.879) had certain accuracy. The PI-RADS score combined with PSA could improve the accuracy of csPCa prediction in the biopsy group (AUC=0.795,P<0.001, 95% CI:0.746-0.843) and the RP group (AUC=0.852, P<0.001, 95%CI:0.789-0.915). Compared with the pathological results of biopsy in the RP group, 52.6% of the patients showed upgrade and degrade of ISUP, and there was insignificant difference in the composition of PI-RADS scores between upgraded and degraded patients (P>0.05). However, 41.7%(27/65) of the patients with ISUP grade 1 biopsies had pathological upgrades that the patients with PI-RADS ≤ 3 accounted for 33.3%, while the patients with PI-RADS>3 accounted for 66.7%, and there was significant difference between the two groups (P<0.05). After RP, 43.3% of the patients had positive surgical margins, and the patients with PI-RADS score ≤ 3, 4 and 5 were 13 (14%), 24 (25.8%) and 56 (60.2%), respectively, while the PI-RADS scores of patients with negative surgical margin were 48 (39.3%), 31(25.4%) and 43(35.2%), respectively. There was significant difference between the two groups (P<0.001). The higher the PI-RADS score, the greater the possibility of the positive surgical margin. For the patients with PSA ≥ 100 μg/L, 98.8% (169/171) patients in the biopsy group had a PI-RADS score 5. The pathological results of all patients were csPCa, of which 85.4% (146/171) had ISUP grade ≥ 4. Among them, 6 cases underwent RP, 5 cases had ISUP grade ≥ 4, all surgical margin were positive, 5 cases had seminal vesicle invasion, 3 cases had capsule invasion and 3 cases had positive pelvic lymph nodes. Conclusion: ThePI-RADS score is correlated with the ISUP grade of PCa. Combined with PSA can accurately predict csPCa. At the same time, the higher PI-RADS score, the more likely the patients with positive incisal margin after RP and Gleason score of 3+3=6 at the time of puncture will be upgraded pathologically.

LncRNAs are regulated by chromatin states and affect the skeletal muscle cell differentiation

Objective

This study aims to clarify the mechanisms underlying transcriptional regulation and regulatory roles of lncRNAs in skeletal muscle cell differentiation.

Methods

We analysed the expression patterns of lncRNAs via time‐course RNA‐seq. Then, we further combined the ATAC‐seq and ChIP‐seq to investigate the governing mechanisms of transcriptional regulation of differentially expressed (DE) lncRNAs. Weighted correlation network analysis and GO analysis were conducted to identify the transcription factor (TF)‐lncRNA pairs related to skeletal muscle cell differentiation.

Results

We identified 385 DE lncRNAs during C2C12 differentiation, the transcription of which is determined by chromatin states around their transcriptional start sites. The TF‐lncRNA correlation network showed substantially concordant changes in DE lncRNAs between C2C12 differentiation and satellite cell rapid growth stages. Moreover, the up‐regulated lncRNAs showed a significant decrease following the differentiation capacity of satellite cells, which gradually declines during skeletal muscle development. Notably, inhibition of the lncRNA Atcayos and Trp53cor1 led to the delayed differentiation of satellite cells. Those lncRNAs were significantly up‐regulated during the rapid growth stage of satellite cells (4‐6 weeks) and down‐regulated with reduced differentiation capacity (8‐12 weeks). It confirms that these lncRNAs are positively associated with myogenic differentiation of satellite cells during skeletal muscle development.

Conclusions

This study extends the understanding of mechanisms governing transcriptional regulation of lncRNAs and provides a foundation for exploring their functions in skeletal muscle cell differentiation.

Scheduling algorithm for the picture configuration for secondary tasks of a digital human–computer interface in a nuclear power plant

Secondary tasks of a digital human–computer interface in a nuclear power plant increase the mental workloads of operators and decrease their accident performance. To reduce the adverse effects of secondary tasks on operators, a picture configuration scheduling algorithm of secondary tasks is proposed. Based on the research background and operator interviews, a scheduling algorithm process is established, and variables and constraint conditions of the scheduling process are defined. Based on the scheduling process and variables definitions, this article proposes a picture feature extraction method, a method for counting identical keywords, an arrangement method of queues in a buffer pool and a picture configuration scheduling algorithm of secondary tasks. The results of simulation experiments demonstrate that the algorithm realizes satisfactory performance in terms of the number of replacements, the average waiting time, and the accuracy.

An eco-friendly fluorometric polymer nanoparticle for selectively monitoring sulfadiazine in tap water

An eco-friendly fluorescence polymer nanoparticle based on carbon quantum dots and poly(methyl methacrylate) nanoparticles is successfully fabricated to detect sulfadiazine. By making use of the abundant functional group of carbon quantum dots and poly(methyl methacrylate) nanoparticles, without any extra modification, the synthetic process of the fluorescence nanoparticles is reduced and the unnecessary chemical molecules are avoided being brought into the reaction system. The investigation of the fluorescence property of carbon quantum dots shows that the prepared carbon quantum dots are the excitation independent. In addition, the morphology of the synthesized fluorescence polymer nanoparticle is tested by the scanning electron microscope and shows that the fluorescence sensor possesses a good spherical core-shell structure. Moreover, under the optimized condition, the prepared fluorescence polymer nanoparticle possesses a good selectivity in the detection of sulfadiazine under a mixture solution. Moreover, the limit of detection is 4 μmol.l^-1 within the detective range from 10 μmol.l^-1 to 60 μmol.l^-1. Meanwhile, the fluorescence quenching mechanism is considered with the photoinduced electron transfer mechanism. Finally, the practical research on the detection of sulfadiazine in tap water shows that the recovery range and relative standard deviation are 97.5% - 105.1% and 2.1%-4.5%, respectively.

A sensitive electrochemical sensor modified with multi-walled carbon nanotubes doped molecularly imprinted silica nanospheres for detecting chlorpyrifos

A highly sensitive and convenient electrochemical sensor, based on surface molecularly imprinted polymers and multiwalled carbon nanotubes, was successfully developed to detect chlorpyrifos in real samples. In order to solve the problems like uneven shapes, poor size accessibility, and low imprinting capacity, the layer of the molecularly imprinted polymer was prepared on the surface of silica nanospheres. Moreover, the doping of multiwalled carbon nanotubes greatly improved the electrical properties of developed sensor. Under the optimal conductions, the electrochemical response of the sensor is linearly proportional to the concentration of chlorpyrifos in the range of 5.0 × 10^-12 -5.0 × 10^-8  mol/L with a low detection limit of 8.1 × 10^-13  mol/L. The prepared sensor exhibited multiple advantages such as low cost, simple preparation, convenient use, excellent selectivity, and good reproducibility. Finally, the prepared sensor was successfully used to detect chlorpyrifos in vegetable and fruit.

A Transfer Matrix Model of the IEC 60318-4 Ear Simulator: Application to the Simulation of Earplug Insertion Loss

The IEC 60318-4 ear simulator is used to measure the insertion loss (IL) of earplugs in the ear canal of an acoustical test fixture (ATF) and is designed to represent an average acoustic impedance (in a reference plane) of the human ear. The ear simulator is usually modeled using a lumped parameter model (LPM) which has frequency limitations and inadequately accounts for the thermo-viscous effects in the simulator. The simulator numerical models that can better deal with the thermo-viscous phenomena often lack essential geometric details. Most related studies also suffer from the lack of experimental validation of the models. Therefore, a transfer matrix (TM) model of the IEC 60318-4 simulator is proposed based on a direct assessment of its geometric dimensions. Such a model is of particular interest for designing artificial ear simulators. The variability in the simulator impedance due to the geometric uncertainties is quantified using the Monte Carlo method. The TM model is validated using i) a finite element (FE) model of the simulator and ii) impedance measurements with a sound intensity probe. It is found to better describe the simulator impedance above 3 kHz compared to the LPM. The TM model is then coupled to a FE model of an occluded ATF ear canal to simulate the IL of an earplug in the frequency range [100 Hz, 10 kHz]. In the model, the simulator is considered as a cylindrical cavity terminated by an equivalent tympanic impedance which is determined from the TM model to simulate the sound pressure measured at the real microphone position (not at the reference plane) in the ATF ear canal. The simulated IL is validated against i) that obtained with a complete FE model of the corresponding system and ii) measurements using an ATF. The TM model is shown to better agree with the simulator FE model than the LPM above 6 kHz regarding the earplug IL simulated using this method.

Tailored Plasmons in Pentacene/Graphene Heterostructures with Interlayer Electron Transfer

van der Waals (vdW) heterostructures, which are produced by the precise assemblies of varieties of two-dimensional (2D) materials, have demonstrated many novel properties and functionalities. Here we report a nanoplasmonic study of vdW heterostructures that were produced by depositing ordered molecular layers of pentacene on top of graphene. We find through nanoinfrared (IR) imaging that surface plasmons formed due to the collective oscillations of Dirac Fermions in graphene are highly sensitive to the adjacent pentacene layers. In particular, the plasmon wavelength declines systematically but nonlinearly with increasing pentacene thickness. Further analysis and density functional theory (DFT) calculations indicate that the observed peculiar thickness dependence is mainly due to the tunneling-type electron transfer from pentacene to graphene. Our work unveils a new method for tailoring graphene plasmons and deepens our understanding of the intriguing nano-optical phenomena due to interlayer couplings in novel vdW heterostructures.

[Effect of multimodal analgesia using periprostatic nerve block anesthesia combined with flurbiprofen in transperineal template-guided prostate biopsy]

Objective: To evaluate the effect of multimodal analgesia using periprostatic nerve block anesthesia (PNB) combined with flurbiprofen in patients undergoing transperineal template-guided prostate biopsy (TTPB). Methods: Totally 166 patients (aged (68.2±9.1) years, range: 47 to 81 years) who received TTPB from October 2017 to June 2018 at Department of Urology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University were enrolled prospectively. All the patients were randomly divided into 2 groups. The observation group (n=79) was given flurbiprofen axetil 1 mg/kg intravenously for half an hour before operation and lidocaine was used for PNB before the biopsy. The control group (n=87) was given normal saline combined with PNB. A visual analog scale (VAS) and visual numeric scale (VNS) were used to assess the patients' pain and quantify their satisfaction at two time points: VAS-1 and VNS-1: during biopsy procedure, VAS-2 and VNS-2: 30 min after the procedure. The date were compared by t test, χ(2) test, Fisher exact test and two-way repeated measures anova analysis between the 2 groups. Results: The age, total prostate volume, serum prostate-specific antigen and the number of cores were comparable among the 2 groups (P>0.05). The VAS-1 scores of the control group and the observation group were 2.8±1.7, 1.9±1.2, respectively, and the VNS-1 were 3.1±0.7, 3.4±0.3, respectively. The VAS-1 were significantly lower in observation group than in control group (F=3.904, P=0.000). Conversely, the VNS-1 were higher in observation group (F=3.526, P=0.000). At 30-minute postoperative, the VAS-2 and VNS-2 were 0.7±0.4 and 3.7±0.2 in the control group, respectively. The VAS-2 and VNS-2 were 0.6±0.5 and 3.8±0.1 in the observation group, respectively. There were no significant differences in the pain scores or the satisfaction scores between the 2 groups (F=1.429, 2.825; P=0.136, 0.083). The incidence of overall complications was 26.4% (23/87) in the control group and 25.3% (20/79) in the observation group, with no statistical difference between the 2 groups (χ(2)=0.027, P=0.869). And the complications had no statistically significant difference among the 2 groups including hematuria, urinary retention, infection, hematospermia, vascular and neurological reactions, nausea, vomiting, dizziness, headache, and respiratory depression (P>0.05). Conclusion: The multimodal analgesia induced by PNB and flurbiprofen could effectively relieve the pain for patients who received TTPB.

Quantification of allelic differential expression using a simple Fluorescence primer PCR-RFLP-based method

Allelic differential expression (ADE) is common in diploid organisms, and is often the key reason for specific phenotype variations. Thus, ADE detection is important for identification of major genes and causal mutations. To date, sensitive and simple methods to detect ADE are still lacking. In this study, we have developed an accurate, simple, and sensitive method, named fluorescence primer PCR-RFLP quantitative method (fPCR-RFLP), for ADE analysis. This method involves two rounds of PCR amplification using a pair of primers, one of which is double-labeled with an overhang 6-FAM. The two alleles are then separated by RFLP and quantified by fluorescence density. fPCR-RFLP could precisely distinguish ADE cross a range of 1- to 32-fold differences. Using this method, we verified PLAG1 and KIT, two candidate genes related to growth rate and immune response traits of pigs, to be ADE both at different developmental stages and in different tissues. Our data demonstrates that fPCR-RFLP is an accurate and sensitive method for detecting ADE on both DNA and RNA level. Therefore, this powerful tool provides a way to analyze mutations that cause ADE.

[Precision evaluation of immune status and its significance in sepsis after burns or trauma]

Sepsis induced by major burns, trauma, and hemorrhage, remains a major cause of death of patients in intensive care units, and it may result in both the widespread activation and dysfunction of the innate as well as adaptive responses in host immune system. A large amount of information concerning subsets of innate and adaptive immune cells in sepsis has implicated that these cells, including neutrophils, macrophages, dendritic cells, T lymphocytes, regulatory T lymphocytes, and natural killer cells, have profound effects on immunoreactivity during acute insults or sepsis through modulating multiple receptor expressions or cytokine secretion, in turn contributing to the development and outcome of sepsis. It is of great significance that precision monitoring of immune function and the related indicators might help to assess the risk of secondary infection, the prognosis of septic patients, and guide the treatment of septic complications.

Ratiometric fluorescence nanosensors based on core-shell structured carbon/CdTe quantum dots and surface molecularly imprinted polymers for the detection of sulfadiazine

Sulfadiazine is an environmental pollutant derived from abuse of antibiotics. Its content in environmental water is closely related to human health. Thus, a novel dual-emission surface molecularly imprinted nanosensor is designed for the specific adsorption and detection of sulfadiazine. In the system, blue emissive carbon quantum dots wrapped with silica served as the internal reference signal for eliminating background interference, while red emissive thioglycolic acid modified CdTe quantum dots (CdTe QDs), which are low dimensional semiconductor materials by the combination of cadmium and tellurium with excellent optical properties, were encapsulated in the imprinted layer to offer recognition signal. The fluorescence of CdTe quantum dots was quenched and the fluorescence quenching degree of carbon quantum dots was inconspicuous with the increase of concentration of sulfadiazine, thereby reflecting the color change. The detection of sulfadiazine was successfully achieved in a concentration range of 0.25-20 μmol/L with detection limit of 0.042 μmol/L and nanosensors had specific recognition for sulfadiazine over its analogues. Compared to single-emission fluorescence sensors, ratiometric fluorescence nanosensors had wider linear range and higher detection accuracy. Furthermore, the nanosensors were also successfully applied for the determination of sulfadiazine in real water and milk samples with acceptable recoveries. The study provides a feasible method for the detection of sulfadiazine and a reference for the detection of sulfonamides.

Human tissue kallikrein 1 ameliorates erectile function via modulation of macroautophagy in aged transgenic rats

Previously, we have demonstrated that human tissue kallikrein 1 (hKLK1) improves age-related erectile dysfunction (ED). Autophagy has been implicated in age-related diseases, including ED. However, the molecular mechanisms underlying hKLK1-mediated amelioration of age-related ED via regulation of autophagy remains unknown. To explore the potential mechanism, male wild-type Sprague-Dawley rats (WTR) and transgenic rats harboring human KLK1 (TGR) were bred till 4 or 18 months of age and divided into three groups: young WTR (yWTR) as the control group, aged WTR (aWTR) group, and aged TGR (aTGR) group. The erectile function of each rat was evaluated using cavernous nerve electrostimulation. The ratio of intracavernous pressure/mean arterial pressure (ICP/MAP) and total ICP were also measured. Western blotting, immunohistochemistry, and transmission electron microscopy were performed to detect the levels of autophagy. The expression levels of related signaling pathways were determined by western blotting and immunohistochemistry. We found that hKLK1 improved the impaired erectile function of aged rats. Compared to the yWTR and aTGR groups, the aWTR group showed reduced smooth muscle/collagen ratio, fewer autophagosomes, and lower expression of Beclin 1 and LC3-II, which indicate impaired smooth muscle function and low level of autophagy in the smooth muscle cells. Moreover, the PI3K/Akt/mTOR signaling pathway, which is considered to be a negative regulator of autophagy, was upregulated in the aWTR group. hKLK1 may partially restore erectile function in aged transgenic rats by upregulating protective autophagy via the PI3K/Akt/mTOR pathway. These observations indicate that hKLK1 is a potential gene therapy candidate for age-related ED.

Use of Torulaspora delbrueckii Co-fermentation With Two Saccharomyces cerevisiae Strains With Different Aromatic Characteristic to Improve the Diversity of Red Wine Aroma Profile

The use of selected Saccharomyces and non-Saccharomyces strains as mixed starters has advantages over pure fermentation due to achieving wine products with distinctive and diversified aroma expected by consumers. To obtain a way to improve the aroma diversity and increase the differentiation of wine product, in this study, the aromatic effect of multi-culture of indigenous Torulaspora delbrueckii (TD12), simultaneous and sequential inoculation with two Saccharomyces strains (indigenous icewine yeast SC45 and commercial yeast BDX) with different enological characteristics were investigated in laboratory-scale 20 L fermenter, respectively. The results showed that T. delbrueckii co-fermented with different S. cerevisiae strain could generate diversified physicochemical and aromatic quality of wine as evidenced by PCA. Mixed fermentation of SC45/TD12 produced higher contents of higher alcohol (3-methyl-1-pentanol and phenylethyl alcohol), ethyl esters (ethyl decanoate and ethyl butanoate), terpenes and phenylacetaldehyde with less fatty acids (hexanoic acid, octanoic acid) and acetic acid, while BDX/TD12 generated more C₆ alcohol (1-hexanol) and acetate esters (ethyl acetate and isoamyl acetate). Compared to simultaneous inoculation, sequential inoculation could achieve higher aroma diversity, and generate higher intensity of fruity, flowery and sweet attributes of wine as assessed by calculating the odor activity values. The different S. cerevisiae strain and inoculation method in alcoholic fermentation could further influence the formations of aromatic compounds in malolactic fermentation. Our results highlighted the importance of S. cerevisiae strain in shaping the aromatic quality of wine in mixed fermentation, and also suggested that using different S. cerevisiae strains with distinct aromatic characteristics co-fermentation with specific non-Saccharomyces strain is a potential way to increase the aromatic diversity and quality of wine product, which could provide an alternative way to meet the requirement of wine consumers for diversified aromatic quality.