Circular RNAs Mediate the Effects of Dietary Tryptophan on the Transformation of Muscle Fiber Types in Weaned Piglets.

The nutritional composition of the diet significantly impacts the overall growth and development of weaned piglets. The current study aimed to explore the effects and underlying mechanisms of dietary tryptophan consumption on muscle fiber type transformation during the weaning period. Thirty weaned piglets with an average body weight of 6.12 ± 0.16 kg were randomly divided into control (CON, 0.14% Trp diet) and high Trp (HT, 0.35% Trp) groups and maintained on the respective diet for 28 days. The HT group of weaned piglets exhibited highly significant improvements in growth performance and an increased proportion of fast muscle fibers. Transcriptome sequencing revealed the potential contribution of differentially expressed circular RNAs toward the transformation of myofiber types in piglets and toward the regulation of expression of related genes by targeting the microRNAs, miR-34c and miR-182, to further regulate myofiber transformation. In addition, 145 DE circRNAs were identified as potentially protein-encoding, with the encoded proteins associated with a myofiber type transformation. In conclusion, the current study greatly advances and refines our current understanding of the regulatory networks associated with piglet muscle development and myofiber type transformation and also contributes to the optimization of piglet diet formulation.

Application of Spinal Subtraction and Bone Background Fusion CTA in the Accurate Diagnosis and Evaluation of Spinal Vascular Malformations.

BACKGROUND AND PURPOSE: Accurate pretreatment diagnosis and assessment of spinal vascular malformations using spinal CTA are crucial for patient prognosis, but the postprocessing reconstruction may not be able to fully depict the lesions due to the complexity inherent in spinal anatomy. Our purpose was to explore the application value of the spinal subtraction and bone background fusion CTA (SSBBF-CTA) technique in precisely depicting and localizing spinal vascular malformation lesions. MATERIALS AND METHODS: In this retrospective study, patients (between November 2017 and November 2022) with symptoms similar to those of spinal vascular malformations were divided into diseased (group A) and nondiseased (group B) groups. All patients underwent spinal CTA using Siemens dual-source CT. Multiplanar reconstruction; routine bone subtraction, and SSBBF-CTA images were obtained using the snygo.via and ADW4.6 postprocessing reconstruction workstations. Multiple observers researched the following 3 aspects: 1) preliminary screening capability using original images with multiplanar reconstruction CTA, 2) the accuracy and stability of the SSBBF-CTA postprocessing technique, and 3) diagnostic evaluation of spinal vascular malformations using the 3 types of postprocessing images. Diagnostic performance was analyzed using receiver operating characteristic analysis, while reader or image differences were analyzed using the Wilcoxon signed-rank test or the Kruskal-Wallis rank sum test. RESULTS: Forty-nine patients (groups A and B: 22 and 27 patients; mean ages, 44.0 [SD, 14.3] years and 44.6 [SD,15.2] years; 13 and 16 men) were evaluated. Junior physicians showed lower diagnostic accuracy and sensitivity using multiplanar reconstruction CTA (85.7% and 77.3%) than senior physicians (93.9% and 90.9%, 98% and 95.5%). Short-term trained juniors achieved SSBBF-CTA image accuracy similar to that of experienced physicians (P > .05). In terms of the visualization and localization of spinal vascular malformation lesions (nidus/fistula, feeding artery, and drainage vein), both multiplanar reconstruction and SSBBF-CTA outperformed routine bone subtraction CTA (P = .000). Compared with multiplanar reconstruction, SSBBF-CTA allowed less experienced physicians to achieve superior diagnostic capabilities (comparable with those of experienced radiologists) more rapidly (P < .05). CONCLUSIONS: The SSBBF-CTA technique exhibited excellent reproducibility and enabled accurate pretreatment diagnosis and assessment of spinal vascular malformations with high diagnostic efficiency, particularly for junior radiologists.

Effects of maternal high-fat diet on fetal growth, placental nutrient transporters and circular RNA expression profiles.

Epidemiological and experimental studies suggest that there is a strong correlation between maternal high-fat diet and fetal-placental development. The current study aims to investigate the effects of maternal high-fat diet on fetal growth, placental nutrient transporters and circular RNA expression profiles in a mouse model. Forty C57BL/6 female mice were randomly assigned to two groups, fed either a control (10% fat for energy) diet (CON) or a high-fat (60% fat for energy) diet (HFD) for 4 weeks before mating and throughout pregnancy, and were killed on day 19.5 of pregnancy. The serum glucose, total cholesterol and low-density lipoprotein, the glucolipid metabolism-related hormones, and the insulin resistance index were significantly increased. High-throughput sequencing showed that differentially expressed circRNAs (DE circRNAs) in the placenta can regulate various biological processes, cellular components, and molecular functions through various energy metabolism pathways, and mmu-let-7g-5p was found to target and bind to multiple DE circRNAs. In addition, this study also predicted that various circRNAs with protein coding functions can regulate maternal placental nutrient transport. In general, the ceRNA (circRNAs-miRNAs-mRNAs) regulatory network of maternal placental nutrient transport constructed in this study is of great significance for further understanding the effect of maternal nutrition on fetal growth in the future.

Synthetic high-energy computed tomography image via a Wasserstein generative adversarial network with the convolutional block attention module.

Background: Computed tomography (CT) is now universally applied into clinical practice with its non-invasive quality and reliability for lesion detection, which highly improves the diagnostic accuracy of patients with systemic diseases. Although low-dose CT reduces X-ray radiation dose and harm to the human body, it inevitably produces noise and artifacts that are detrimental to information acquisition and medical diagnosis for CT images. Methods: This paper proposes a Wasserstein generative adversarial network (WGAN) with a convolutional block attention module (CBAM) to realize a method of directly synthesizing high-energy CT (HECT) images through low-energy scanning, which greatly reduces X-ray radiation from high-energy scanning. Specifically, our proposed generator structure in WGAN consists of Visual Geometry Group Network (Vgg16), 9 residual blocks, upsampling and CBAM, a subsequent attention block. The convolutional block attention module is integrated into the generator for improving the denoising ability of the network as verified by our ablation comparison experiments. Results: Experimental results of the generator attention module ablation comparison indicate an optimization boost to the overall generator model, obtaining the synthesized high-energy CT with the best metric and denoising effect. In different methods comparison experiments, it can be clearly observed that our proposed method is superior in the peak signal-to-noise ratio (PSNR), structural similarity index measure (SSIM) and most of the statistics (average CT value and its standard deviation) compared to other methods. Because P<0.05, the samples are significantly different. The data distribution at the pixel level between the images synthesized by the method in this paper and the high-energy CT images is also most similar. Conclusions: Experimental results indicate that CBAM is able to suppress the noise and artifacts effectively and suggest that the image synthesized by the proposed method is closest to the high-energy CT image in terms of visual perception and objective evaluation metrics.

Insight into the Neuroprotective Effect of Genistein-3'-Sodium Sulfonate Against Neonatal Hypoxic-Ischaemic Brain Injury in Rats by Bioinformatics.

Therapeutic hypothermia (TH) is the only intervention approved for the treatment of neonatal hypoxic-ischaemic encephalopathy (HIE), but its treatment window is narrow (within 6 h after birth), and its efficacy is not ideal. Thus, alternative treatments are urgently needed. Our previous studies showed that genistein-3'-sodium sulfonate (GSS), a derivative of genistein (Gen), has a strong neuroprotective effect in rats with ischaemic stroke, but its role in HIE is unclear. A hypoxia-ischaemia (HI) brain injury model was established in neonatal male Sprague‒Dawley (SD) rats. Twenty-four hours after reperfusion, rats treated with GSS were assessed for cerebral infarction, neurological function, and neuronal damage. RNA-Seq and bioinformatics analysis were used to explore differentially expressed genes (DEGs) and regulated signalling pathways, which were subsequently validated by Western blotting and immunofluorescence. In this study, we found that GSS not only significantly reduced the size of brain infarcts and alleviated nerve damage in rats with HIE but also inhibited neuronal loss and degeneration in neonatal rats with HIE. A total of 2170 DEGs, of which 1102 were upregulated and 1068 were downregulated, were identified in the GSS group compared with the HI group. In an analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) categories, the downregulated DEGs were significantly enriched in the pathways "Phagosome", "NF-κB signalling", and "Complement and coagulation cascades", amongst others. Meanwhile, the upregulated DEGs were significantly enriched in the pathways "Neurodegeneration", "Glutamatergic synapse", and "Calcium signalling pathway", amongst others. These results indicate that GSS intervenes in the process of HIE-induced brain injury by participating in multiple pathways, which suggests potential candidate drugs for the treatment of HIE.

Evaluation of atrial anatomical remodeling in atrial fibrillation with machine-learned morphological features.

PURPOSE: To elucidate the role of atrial anatomical remodeling in atrial fibrillation (AF), we proposed an automatic method to extract and analyze morphological characteristics in left atrium (LA), left atrial appendage (LAA) and pulmonary veins (PVs) and constructed classifiers to evaluate the importance of identified features. METHODS: The LA, LAA and PVs were segmented from contrast computed tomography images using either a commercial software or a self-adaptive algorithm proposed by us. From these segments, geometric and fractal features were calculated automatically. To reduce the model complexity, a feature selection procedure is adopted, with the important features identified via univariable analysis and ensemble feature selection. The effectiveness of this approach is well illustrated by the high accuracy of our models. RESULTS: Morphological features, such as LAA ostium dimensions and LA volume and surface area, statistically distinguished ([Formula: see text]) AF patients or AF with LAA filling defects (AF(def+)) patients among all patients. On the test set, the best model to predict AF among all patients had an area under the receiver operating characteristic curve (AUC) of 0.91 (95% CI, 0.8-1) and the best model to predict AF(def+) among all patients had an AUC of 0.92 (95% CI, 0.81-1). CONCLUSION: This study automatically extracted and analyzed atrial morphology in AF and identified atrial anatomical remodeling that statistically distinguished AF or AF(def+). The importance of identified atrial morphological features in characterizing AF or AF(def+) was validated by corresponding classifiers. This work provides a good foundation for a complete computer-assisted diagnostic workflow of predicting the occurrence of AF or AF(def+).

FOS gene associated immune infiltration signature in perivascular adipose tissues of abdominal aortic aneurysm.

Abdominal aortic aneurysms (AAA) are pathological dilations in local aortic wall. The inflammatory infiltrates of the perivascular adipose tissue (PAT) surrounding AAAs were associated with AAAs and have been shown to contribute vascular pathology. However, the mechanism by which PAT inflammation contributes to vascular pathology in AAA remains to be clarified. This study aimed to explore the association between immune cell infiltration and key gene expression profile in PAT of AAA. For that, a gene expression dataset of human dilated perivascular adipose tissue (dPAT), non-dilated perivascular adipose tissue (ndPAT), subcutaneous abdominal fat (SAF) and omental-visceral fat (OVF) samples, as well as another microarray dataset of the abdominal perivascular adipose tissue in peripheral artery disease patients were downloaded from GEO database for analysis in this study. The CIBERSORT algorithm, weighted gene co-expression network analysis (WGCNA) and LASSO algorithm were used for the identification of immune infiltration, immune-related genes and the development of diagnostic signature. Our data discovered a significant higher proportion of activated mast cells and follicular helper T (Tfh) cells in dPAT than ndPAT, OVT and SAF samples. Moreover, AP-1 family members (FOS, FOSB, ATF3, JUN and JUNB) were found to compose the hub genes of purple module in WGCNA. Among them, FOS gene acts as a higher efficient marker to discriminate dPAT from ndPAT, OVT and SAF in AAA. Meanwhile, the expression profiles of the AP-1 family members are all significantly positive correlated with activated mast cell, plasma cell and Tfh cell infiltration in dPAT of AAA. Therefore, in the PAT surrounding AAA, the signature of inflammatory infiltration might be represented by a FOS-dominated cell network consist of activated mast cell, plasma cell and Tfh cell. Given the complicated etiology of AAA, our results are likely to shed new light on the pathophysiologic mechanism of AAA influenced by the local dPAT.

α-Mangostin Induces Apoptosis and Inhibits Metastasis of Breast Cancer Cells via Regulating RXRα-AKT Signaling Pathway.

Mangostin, which has the function of anti-inflammatory, antioxidant, and anticancer, etc, is one of the main active ingredients of the hull of the mangosteen. The main objective of the study was to elucidate its anti-cancer function and possible mechanism. α-Mangostin was separated and structurally confirmed. MTT method was used to check the effect of mangostin on breast cancer cell proliferation. Then the effect of α-Mangostin on the transcriptional activity of RXRα was tested by dual-luciferase reporter gene assay. And Western blot (WB) was used to detect the expression of apoptosis-related proteins or cell cycle-associated proteins after treatment. Also, this study was to observe the effects of α-Mangostin on the invasion of breast cancer cell line MDA-MB-231. α-Mangostin regulates the downstream effectors of the PI3K/AKT signaling pathway by degrading RXRα/tRXRα. α-Mangostin can trigger PARP cleavage and induce apoptosis, which may be related to the induction of upregulated BAX expression and downregulation of BAD and cleaved caspase-3 expression in MDA-MB-231 cells through blockade of AKT signaling. The experiments verify that α-Mangostin have evident inhibition effects of invasion and metastasis of MDA-MB-231 cells. Cyclin D1 was involved in the anticancer effects of α-Mangostin on the cell cycle in MDA-MB-231 cells. α-Mangostin induces apoptosis, suppresses the migration and invasion of breast cancer cells through the PI3K/AKT signaling pathway by targeting RXRα, and cyclin D1 has involved in this process.

Optimized PCR-Based Enrichment Improves Coverage Uniformity and Mutation Detection in Mitochondrial DNA Next-Generation Sequencing.

Next-generation sequencing-based methods have been commonly used for detecting mutations of mitochondrial genome (mtDNA). PCR amplification is a highly effective method of mtDNA enrichment before sequencing. However, it has been observed that highly variable sequencing depth within PCR amplicons severely reduces the coverage uniformity and accuracy of mutation calling. Therefore, it is necessary to develop an optimized PCR-based strategy for mtDNA sequencing. Herein, the effect of DNA quality on the efficiency of PCR amplification was analyzed and the effects of different primer-design methods, including the number of primer pairs, overlap length of amplicons, and modification of primers, on coverage uniformity and mutation calling in mtDNA sequencing were assessed. Results showed that DNA quality significantly affected the efficiency of PCR amplification. Importantly, over- and under-representation of coverage depth at overlap regions of amplicons were observed when amplicons were not modified and overlap was shorter than two sequencing fragment sizes (800 bp). Then, under-representation was overcome by increasing the overlap length of the amplicons, and over-representation was effectively reduced by 5'-block modification of primers and sticky-end ligation of amplicons. Moreover, findings indicated that these two optimized PCR-based sequencing strategies effectively improved mutation calling in primer-binding regions. Optimized PCR-based mtDNA enrichment and sequencing approaches have been established, which laid a foundation for accurate mutation detection of mtDNA in diseases.

[Bioinformatical analysis of differently expressed genes related to mitochondrial function in systemic sclerosis].

Objective To investigate the relationship between mitochondria and systemic sclerosis (SSc) by analyzing the expression of mitochondrial function-related genes in skin biopsy samples from patients with SSc. Methods Gene chip expression profile of SSc skin biopsy in Gene Expression Omnibus (GEO) database was used, and differently expressed genes (DEGs) related to mitochondrial function were identified by t test and fold change (FC). What's more, functional annotation, functional enrichment and protein interaction network analysis were performed. Results A total of 422 significant DEGs were identified between the SSc group and the normal group. Among them, 23 DEGs were mitochondrial function-related genes. Functional annotation and enrichment analysis of 23 DEGs revealed that abnormally expressed mitochondrial function-related genes mainly affected several biological processes, such as mitochondrial energy supply and cell metabolism. Conclusion The dysregulation of mitochondrial function-related genes in SSc patients affects the function of mitochondria, suggesting that the abnormality of mitochondrial function may be associated with the development of SSc.

Prognostic significance of preoperative skeletal muscle status in patients with gastric cancer after radical gastrectomy.

BACKGROUND AND OBJECTIVES: The association between skeletal muscle status and gastric cancer (GC) prognosis remains unclear. Here, we investigated the impact of the skeletal muscle index (SMI) on overall survival (OS) in GC patients after radical gastrectomy. METHODS AND STUDY DESIGN: We divided 178 patients into four groups: adult men, adult women, elderly men and elderly women. The SMI, calculated using CT images, of patients was graded using cutoff values of group-specific tertiles. Age, body mass index, SMI grade, Charlson comorbidity index, surgical method (total vs distal gastrectomy), tumor stage, and histological type and differentiation were included in Cox regression models to assess the primary outcome parameter of OS. A new prognostic score for 3- year OS was established by combining the SMI grade and tumor stage, and receiver operating characteristic (ROC) curve analyses were used to determine its predictive reliability. RESULTS: For groups with high, medium, and low SMI grades, the 3-year OS rates were 94.04, 79.08 and 59.09% and 86.09, 70.11 and 49.11% (p<0.001) in patients undergoing distal and total gastrectomy, respectively. In the multivariate analysis, low SMI (hazard ratio (HR) 1.82, 95% confidence interval (CI) 1.14-2.9), advanced stage (HR 2.89, 95% CI 1.43-5.83), and total gastrectomy (HR 1.69, 95% CI 0.95-3.01) were independent risk factors for OS (p<0.010). The areas under the ROC curves for the prognostic score were 0.77 (range 0.61-0.93) and 0.76 (range 0.65-0.86) in patients undergoing distal and total gastrectomy, respectively. CONCLUSIONS: The preoperative SMI was an independent prognostic factor for long-term survival in GC patients after radical gastrectomy.

Translation of yes-associated protein (YAP) was antagonized by its circular RNA via suppressing the assembly of the translation initiation machinery.

Yap is the key component of Hippo pathway which plays crucial roles in tumorigenesis. Inhibition of Yap activity could promote apoptosis, suppress proliferation, and restrain metastasis of cancer cells. However, how Yap is regulated is not fully understood. Here, we reported Yap being negatively regulated by its circular RNA (circYap) through the suppression of the assembly of Yap translation initiation machinery. Overexpression of circYap in cancer cells significantly decreased Yap protein but did not affect its mRNA levels. As a consequence, it remarkably suppressed proliferation, migration and colony formation of the cells. We found that circYap could bind with Yap mRNA and the translation initiation associated proteins, eIF4G and PABP. The complex containing overexpressed circYap abolished the interaction of PABP on the poly(A) tail with eIF4G on the 5'-cap of the Yap mRNA, which functionally led to the suppression of Yap translation initiation. Individually blocking the binding sites of circYap on Yap mRNA or respectively mutating the binding sites for PABP and eIF4G derepressed Yap translation. Significantly, breast cancer tissue from patients in the study manifested dysregulation of circYap expression. Collectively, our study uncovered a novel molecular mechanism in the regulation of Yap and implicated a new function of circular RNA, supporting the pursuit of circYap as a potential tool for future cancer intervention.

The complete mitochondrial genome sequence of the Daweishan Mini chicken.

Daweishan Mini chicken is a valuable chicken breed in China. In this study, the complete mitochondrial genome sequence of Daweishan Mini chicken using PCR amplification, sequencing and assembling has been obtained for the first time. The total length of the mitochondrial genome was 16,785 bp, with the base composition of 30.26% A, 23.73% T, 32.51% C, 13.51% G. It contained 37 genes (2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes) and a major non-coding control region (D-loop region). The protein start codons are ATG, except for COX1 that begins with GTG. The complete mitochondrial genome sequence of Daweishan Mini chicken provides an important data set for further investigation on the phylogenetic relationships within Gallus gallus.

Variability of miRNA expression during the differentiation of human embryonic stem cells into retinal pigment epithelial cells.

Embryonic stem cells (ESCs) and induced pluripotent stem cells can be induced to differentiate into retinal pigment epithelium (RPE). MiRNAs have been characterized and found playing important roles in the differentiation process of ESCs, but their length and sequence heterogeneity (isomiRs), and their non-canonical forms of miRNAs are underestimated or ignored. In this report, we found some non-canonical miRNAs (dominant isomiRs) in all differentiation stages, and 27 statistically significant editing sites were identified in 24 different miRNAs. Moreover, we found marked major-to-minor arm-switching events in 14 pre-miRNAs during the hESC to RPE cell differentiation phases. Our study for the first time reports exploring the variability of miRNA expression during the differentiation of hESCs into RPE cells and the results show that miRNA variability is a ubiquitous phenomenon in the ESC differentiation.

MAPKAP1 rs10118570 polymorphism is associated with anti-infection and anti-hepatic fibrogenesis in schistosomiasis japonica.

Chronic infection with Schistosoma japonicum is an important cause of hepatic fibrosis (HF). Human 9q33.3 is one of the most important loci for stress-related diseases. We examined the potential associations of 43 single-nucleotide polymorphisms (SNPs) with S. japonicum infection and HF in epidemic region in China. We identified a SNP (rs10118570 GG in mitogen-activated protein kinase associated protein 1, MAPKAP1) contributes to anti-infection (adjusted OR = 0.35) and anti-fibrogenesis (adjusted RR = 0.44) in the discovery study. Replicative and combined studies showed consistent protective quality for this genotype (replicative: adjusted OR = 0.37 for anti-infection, and adjusted RR = 0.40 for anti-fibrogenesis; Combined: adjusted OR = 0.45 for anti-infection, and adjusted RR = 0.42 for anti-fibrogenesis). Univariate and multivariate analysis in the discovery, replicative and combined studies, suggested that durations (years), splenomegaly, serum ALB and rs10118570 were independent predictors influencing the fibrogenesis. The analysis of gene-gene interaction showed rs10118570 functions independently. We conclude that MAPKAP1 may represent a novel anti-infection and anti-fibrogenesis genomic locus in chronic schistosomiasis japonica. And rs10118570 may be a potential biomarker and target for the treatment of this life-threatening ancient disease.

Identification of novel microRNAs in primates by using the synteny information and small RNA deep sequencing data.

Current technologies that are used for genome-wide microRNA (miRNA) prediction are mainly based on BLAST tool. They often produce a large number of false positives. Here, we describe an effective approach for identifying orthologous pre-miRNAs in several primates based on syntenic information. Some of them have been validated by small RNA high throughput sequencing data. This approach uses the synteny information and experimentally validated miRNAs of human, and incorporates currently available algorithms and tools to identify the pre-miRNAs in five other primates. First, we identified 929 potential pre-miRNAs in the marmoset in which miRNAs have not yet been reported. Then, we predicted the miRNAs in other primates, and we successfully re-identified most of the published miRNAs and found 721, 979, 650 and 639 new potential pre-miRNAs in chimpanzee, gorilla, orangutan and rhesus macaque, respectively. Furthermore, the miRNA transcriptome in the four primates have been re-analyzed and some novel predicted miRNAs have been supported by the small RNA sequencing data. Finally, we analyzed the potential functions of those validated miRNAs and explored the regulatory elements and transcription factors of some validated miRNA genes of interest. The results show that our approach can effectively identify novel miRNAs and some miRNAs that supported by small RNA sequencing data maybe play roles in the nervous system.

Imaging diagnosis of hepatic ectopic pregnancy: A report of one case.

This article is about a case of hepatic ectopic pregnancy. A patient suffered from an acute abdomen with 14-day vaginal bleeding. A serum, human chorionic gonadotrophin (HCG) of 8,988 mIU/mL revealed a bit of pelvic effusion. A computed tomography (CT) plain scan displayed a polygonal, moderate density shadow of the left liver lobe. An enhanced CT had no sign of intensification. A magnetic resonance imaging (MRI) plain scan was undertaken. On a T1-weighted imaging (T1WI), the lesion appeared to be a low signal; on a T2-weighted imaging (T2WI), the lesion appeared to be a high signal. With enhanced MRI, the lesion showed an irregular mild plague-like intensification during the venous phase. It was excised by an operation and chorionic tissue was seen under a microscope. The result of pathological diagnosis was hepatic ectopic pregnancy.