Human Glial Fibrillary Acidic Protein Gene Promoter Targets Hepatic and Pancreatic Stellate Cells in Transgenic Bama Mini-Pigs

A B S T R A C T Hepatic and pancreatic stellate cells (HSCs and PSCs) have been considered to be closely associated with the pathogenesis of fibrosis, offering a hopeful therapeutic target for treating hepatic and pancreatic fibrosis. Recently, we have generated transgenic mini-pigs carrying astrocyte-specific expression of DsRed regulated by the 2.2-kb human glial fibrillary acidic protein (hGFAP) gene promoter. This study was intended to examine whether the targeted transgene expression of DsRed will be present in the porcine HSCs and PSCs. Histological fluorescent imaging showed several DsRed-expressing cells were interspersed between the parenchyma cells. Moreover, these DsRedexpressing cells were checked as indeed HSCs and PSCs by co-labeling with GFAP immunoreactivity. Thus, our results demonstrate the 2.2-kb hGFAP gene promoter holds matched regulatory elements therefore is capable of introducing specific expression of transgene in porcine HSCs and PSCs, providing a novel strategy to selectively manipulate the HSCs and PSCs in a large animal model

Tropical Forests Classification Based on Weighted Separation Index from Multi-Temporal Sentinel-2 Images in Hainan Island

Tropical forests play a vital role in biodiversity conservation and the maintenance of sustainability. Although different time-series spatial resolution satellite images have provided opportunities for tropical forests classification, the complexity and diversity of vegetation types still pose challenges, especially for distinguishing different vegetation types. In this paper, we proposed a Spectro-Temporal Feature Selection (STFS) method based on the Weighted Separation Index (WSI) using multi-temporal Sentinel-2 data for mapping tropical forests in Jianfengling area, Hainan Province. The results showed that the tropical forests were classified with an overall accuracy of 93% and an F1 measure of 0.92 with multi-temporal Sentinel-2 data. As our results also revealed, the WSI based STFS method could be efficient in tropical forests classification by using a fewer feature subset compared with Variable Selection Using Random Forest (14 features and all 40 features, respectively) to achieve the same accuracy. The analysis also showed it was not advisable to only pursue a higher WSI value while ignoring the heterogeneity and diversity of features. This study demonstrated that the WSI can provide a new feature selection method for multi-temporal remote sensing image classification

Differential Analysis of Gene Expression of Toll-like Receptors and Antimicrobial Peptides in Immune Organs and Tissues of Tibetan and Duroc-Landrace-Yorkshire pigs

【Objective】In mammals, Toll-like receptors and antimicrobial peptide genes are important components of the innate immune system, which play a crucial role in fighting against pathogen attacks. The study was conducted to explore the expression differences of Toll-like receptor and antimicrobial peptide genes between different immune organs or tissues in Tibetan pigs and Duroc-Landrace-Yorkshire pigs, with an aim to reveal the potential contribution of these genes to disease resistance and immune response and provide theoretical support for the screening of molecular markers for disease resistance.【Method】The mRNA abundance of Toll-like receptors genes (TLR1-TLR9) and two types of antimicrobial peptide genes (PBD-1 and PR-39) in lungs, mesenteric lymph nodes, inguinal lymph nodes, submandibular lymph nodes and spleens of 6-month-old Tibetan and Duroc-Landrace-Yorkshire pigs were detected by qPCR.【Result】The mRNA expression of Tolllike receptors and antimicrobial peptide genes in most of the immune organs or tissues of Tibetan pigs was significantly higher than that of Duroc-Landrace-Yorkshire pigs. Among them, the mRNA expression of TLR1 and TLR2 in lungs was increased by about 50%, and PR-39 was increased by 2.6 times; the expression of TLR4 in mesenteric lymph nodes was increased by 40%, and the expression of TLR1 and PR-39 was increased by 88% and 3 times, respectively. In the inguinal lymph nodes, the expression of TLR1 and TLR2 was increased by about 2 times, and the expression of TLR9 and PR-39 was increased by 70%, especially, the expression of PR-39 increasing by 7 times; The expression of TLR1, TLR2, TLR4 and TLR7 in submandibular lymph nodes was increased by more than 2 times, and the expression of PR-39 was increased by nearly 7 times, which was similar to that in inguinal lymph nodes; the expression of TLR1 in the spleen rose by 3.5 times, which was similar to that in submandibular lymph nodes. The expression of TLR4 and TLR9 increased by about 50%, and the expression of PR-39 increased by 2.5 times.【Conclusion】Tibetan pigs show higher expression levels of Toll-like receptors and antimicrobial peptide genes in multiple immune organs or tissues compared to Duroc-Landrace-Yorkshire pigs. It is implied that Tibetan pigs may possess stronger innate immunity and be able to generate more effective local or systemic immune responses against pathogenic microbial infections. The results of this study provide important theoretical support for the identification of disease resistance molecular markers and are expected to provide a scientific basis for further improvement of disease resistance in Tibetan pigs and other pig breeds

Genome-wide analysis of the intrinsic apoptotic pathway in the tropical sea cucumber Holothuria leucospilota

To date, studies on apoptosis in echinoderms mainly focus on the caspase-dependent extrinsic apoptotic pathway, while knowledges regarding the intrinsic apoptotic pathway is still limited. In this study, 55 genes belong to 7 families of the intrinsic apoptotic pathway, namely, Bcl-2, caspase, AIF, Cyt c, Apaf-1, Smac, HTRA2 and Endo G, were identified by screening of the genomic database of the tropical sea cucumber Holothuria leucospilota. The Bcl-2 family showed significant gene expansion in H. leucospilota but not in other echinoderms, while the pro-apoptotic factor Endo G is generally lost in echinoderms. Transcriptomic data showed that the genes of the intrinsic apoptotic pathway were ubiquitously expressed in all tissues, and all embryonic and larval developmental stages of H. leucospilota. The gene numbers and functional domains of the caspase family and AIF family were further clarified and showed conserved with their counterparts in vertebrates. In primary coelomocytes, the transcript expression of different caspases showed different responses to pathogenic challenges of vibrio and pathogen-associated molecular patterns, and environmental challenges of heave metal and reactive oxygen species. Overall, this study indicates that the intrinsic apoptotic pathway is conserved between vertebrates and echinoderms by using the sea cucumber H. leucospilota as a model. This study may contribute in increasing the knowledge of development and innate immunity in ancestral deuterostomia species

Identifying Stage II Colorectal Cancer Recurrence Associated Genes by Microarray Meta-Analysis and Building Predictive Models with Machine Learning Algorithms

Background. Stage II colorectal cancer patients had heterogeneous prognosis, and patients with recurrent events had poor survival. In this study, we aimed to identify stage II colorectal cancer recurrence associated genes by microarray meta-analysis and build predictive models to stratify patients’ recurrence-free survival. Methods. We searched the GEO database to retrieve eligible microarray datasets. The microarray meta-analysis was used to identify universal recurrence associated genes. Total samples were randomly divided into the training set and the test set. Two survival models (lasso Cox model and random survival forest model) were trained in the training set, and AUC values of the time-dependent receiver operating characteristic (ROC) curves were calculated. Survival analysis was performed to determine whether there was significant difference between the predicted high and low risk groups in the test set. Results. Six datasets containing 651 stage II colorectal cancer patients were included in this study. The microarray meta-analysis identified 479 recurrence associated genes. KEGG and GO enrichment analysis showed that G protein-coupled glutamate receptor binding and Hedgehog signaling were significantly enriched. AUC values of the lasso Cox model and the random survival forest model were 0.815 and 0.993 at 60 months, respectively. In addition, the random survival forest model demonstrated that the effects of gene expression on the recurrence-free survival probability were nonlinear. According to the risk scores computed by the random survival forest model, the high risk group had significantly higher recurrence risk than the low risk group (HR = 1.824, 95% CI: 1.079–3.084, p = 0.025). Conclusions. We identified 479 stage II colorectal cancer recurrence associated genes by microarray meta-analysis. The random survival forest model which was based on the recurrence associated gene signature could strongly predict the recurrence risk of stage II colorectal cancer patients

Machine Learning‐Assisted Microfluidic Synthesis of Perovskite Quantum Dots

The quality and property control of nanomaterials are center themes to guarantee and promote their applications. Different synthesis methods and reaction parameters are control factors for their properties. However, the vast combination number of the factors with multilevels leads to the obstacle that trying all‐through the data space is nearly impossible. Herein, the combination of microfluidic synthesis method with machine learning (ML) models to address this challenge in case of perovskite quantum dots (PQDs) with tunable photoluminescence (PL) is reported. The ML‐assisted synthesis not only helps to elucidate the nucleation growth‐ripening mechanisms, but also successfully guides to synthesize PQDs with precise wavelength and full width of half maximum (FWHM) of the PL by optimizable conditions to match the time‐saving, energy‐saving, and minimal environmental pressure goals

FOLFOX treatment response prediction in metastatic or recurrent colorectal cancer patients via machine learning algorithms

Abstract Early identification of metastatic or recurrent colorectal cancer (CRC) patients who will be sensitive to FOLFOX (5‐FU, leucovorin and oxaliplatin) therapy is very important. We performed microarray meta‐analysis to identify differentially expressed genes (DEGs) between FOLFOX responders and nonresponders in metastatic or recurrent CRC patients, and found that the expression levels of WASHC4, HELZ, ERN1, RPS6KB1, and APPBP2 were downregulated, while the expression levels of IRF7, EML3, LYPLA2, DRAP1, RNH1, PKP3, TSPAN17, LSS, MLKL, PPP1R7, GCDH, C19ORF24, and CCDC124 were upregulated in FOLFOX responders compared with nonresponders. Subsequent functional annotation showed that DEGs were significantly enriched in autophagy, ErbB signaling pathway, mitophagy, endocytosis, FoxO signaling pathway, apoptosis, and antifolate resistance pathways. Based on those candidate genes, several machine learning algorithms were applied to the training set, then performances of models were assessed via the cross validation method. Candidate models with the best tuning parameters were applied to the test set and the final model showed satisfactory performance. In addition, we also reported that MLKL and CCDC124 gene expression were independent prognostic factors for metastatic CRC patients undergoing FOLFOX therapy

Evaluation of SARS-CoV-2-Neutralizing Nanobody Using Virus Receptor Binding Domain-Administered Model Mice

Due to the rapid spread of coronavirus disease 2019 (COVID-19), there is an urgent requirement for the development of additional diagnostic tools for further analysis of the disease. The isolated nanobody Nb11-59 binds to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor-binding domain (RBD) with high affinity to neutralize the virus and block the angiotensin-converting enzyme 2- (ACE2-) RBD interaction. Here, we introduce a novel nanobody-based radiotracer named 68Ga-Nb1159. The radiotracer retained high affinity for the RBD and showed reliable radiochemical characteristics both in vitro and in vivo. Preclinical positron emission tomography (PET) studies of 68Ga-Nb1159 in mice revealed its rapid clearance from circulation and robust uptake into the renal and urinary systems. Fortunately, 68Ga-Nb1159 could specifically reveal the distribution of the RBD in mice. This study also helped to evaluate the pharmacodynamic effects of the neutralizing nanobody. Moreover, 68Ga-Nb1159 may be a promising tool to explore the distribution of the RBD and improve the understanding of the virus. In particular, this study identified a novel molecular radioagent and established a reliable evaluation method for specifically investigating the RBD through noninvasive and visual PET technology