Systems biology applied to the study of papaya fruit ripening: the influence of ethylene / Biologia de sistemas aplicada ao estudo do amadurecimento de mamões: a influência do etileno

Fruit ripening is a biochemical process that results in flavor, odor, texture, and color suitable for human consumption, in addition to providing access to important nutrients. Although ripening promotes sensory and nutritional increases in fruits, there is also an increased susceptibility to physical damage, as is the case with papaya. These transformations occur due to changes in gene expression patterns at different stages of maturity, whose control and coordination result from the combined action of plant hormones, especially ethylene. As the action of this hormone in the regulation of gene expression is still elusive, this dissertation sought to address the global analysis of the transcriptome in an overview study of molecular processes involved in the ripening of ethylene-treated and non-treated papaya. Transcription factors related to ethylene synthesis and signaling had increased activity towards exogenous-ethylene treatment. Consequently, ethylene-induced enzymes had their coding genes differentially expressed, like genes related to the synthesis of carotenoids, linalool, and vitamins, which increase color, aroma, and antioxidant activity, respectively. Metabolic pathways related to the synthesis of sugars were suppressed while genes encoding the enzyme responsible for sucrose synthesis maintained a basal expression, showing that the accumulation of sugars occurs before the ripening process. The firmness of the peel and pulp of the fruits were strongly influenced by the treatment with ethylene and by the time of the experiment, suffering the action of numerous enzymes related to the degradation of the cell wall. The main enzyme responsible for softening the pulp was polygalacturonase, together with the activity of other pectinases and cellulases. In contrast to the need for the pre-climacteric action of pectate lyase and pectinesterase reported in other fleshy fruits, such as tomatoes and strawberries, papaya did not show a significant difference in their expression. The meta-analysis of several papaya ripening transcriptomes confirmed the expression profile observed in the previous RNA-seq, besides providing statistical enrichment to the biological narratives. Finally, the present study gathered a range of robust information on the gene regulation of the papaya ripening process, which opens possibilities for future approaches to transcriptomic analysis and validates the use of papaya as a model for such studies

O amadurecimento de frutos é um processo bioquímico que resulta em sabor, odor, textura e cor adequados para o consumo humano, além de propiciar o acesso a nutrientes importantes. Apesar do amadurecimento promover incrementos sensoriais e nutricionais nos frutos, ocorre também um aumento da suscetibilidade a danos físicos, como é o caso do mamão. Essas transformações ocorrem devido às alterações nos padrões de expressão gênica nos diferentes estádios de amadurecimento, cujo controle e coordenação decorrem da ação combinada de hormônios vegetais, principalmente do etileno. Como a ação deste hormônio na regulação da expressão gênica ainda é elusiva, a presente dissertação buscou abordar a análise global do transcriptoma em um amplo estudo dos processos moleculares envolvidos no amadurecimento de mamões tratados e não tratados com etileno. Os fatores de transcrição relacionados com a síntese e a sinalização do etileno tiveram sua atividade aumentada perante o tratamento exógeno com etileno. Consequentemente, as enzimas reguladas por esse hormônio tiveram seus genes de codificação expressos diferencialmente, como foi o caso de genes relacionados à síntese de carotenoides, linalool e vitaminas, que atuam no aumento da cor, aroma e atividade antioxidante, respectivamente. Vias metabólicas relacionadas com à síntese de açúcares foram reprimidas enquanto genes codificantes da enzima responsável pela síntese de sacarose mantiveram uma expressão basal, evidenciando que o acúmulo de açúcares ocorre antes do processo de amadurecimento. A firmeza da casca e da polpa dos frutos foram fortemente influenciadas pelo tratamento com etileno e pelo tempo de experimento, sofrendo ação de inúmeras enzimas relacionadas com a degradação da parede celular. A principal enzima responsável pelo amolecimento da polpa foi a poligalacturonase, em conjunto com a atividade de outras pectinases e celulases. Em contraste com a necessidade da ação pré-climatérica da pectato liase e da pectinesterase relatada em outras frutas carnosas, como tomates e morangos, o mamão não apresentou uma diferença significativa na expressão das mesmas. A meta-análise de diversos transcriptomas do amadurecimento do mamão reafirmaram o perfil de expressão observado no RNA-seq, além de prover enriquecimento estatístico às narrativas biológicas. Por fim, o presente estudo reuniu uma gama de informações robustas sobre a regulação gênica do processo de amadurecimento do mamão papaia, o que abrange a possibilidade para futuras abordagens de análise transcriptomica e valida o uso do mamão como modelo para tais estudos

Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda

The fall armyworm (FAW), Spodoptera frugiperda, is a destructive pest native to America and has recently become an invasive insect pest in China. Because of its rapid spread and great risks in China, understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies. Here, we assembled a chromosome-level genome of a male FAW (SFynMstLFR) and compared re-sequencing results of the populations from America, Africa, and China. Strain identification of 163 individuals collected from America, Africa and China showed that both C and R strains were found in the American populations, while only C strain was found in the Chinese and African populations. Moreover, population genomics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations. Taken together, FAWs invaded into China were most likely originated from Africa. Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW, of which 283 genes are specific to FAW. Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles, and several detoxification genes such as AOX, UGT and GST specially responded to the pesticides. These findings will be useful in developing effective strategies for management of FAW in China and other invaded areas.

Screening of reference genes for quantitative real-time PCR in Artemisia argyi / 中国中药杂志

Artemisia Argyi Folium, a traditional Chinese medicine of important medicinal and economic value, sees increasing demand in medicinal and moxibustion product market. Screening stable and reliable reference genes for quantitative real-time PCR(qRT-PCR) is a prerequisite for the analysis of gene expression in Artemisia argyi. In this study, eight commonly used reference genes, Actin, 18s, EF-1α, GAPDH, SAND, PAL, TUA, and TUB, from the transcriptome of A. argyi, were selected as candidate genes. The expression of each gene in different tissues(roots, stems, and leaves) of A. argyi and in leaves of A. argyi after treatment with methyl jasmonate(MeJA) for different time(0, 4, 8, 12 h) was detected by qRT-PCR. Then, geNorm, NormFinder, BestKeeper, ΔCT, and RefFinder were employed to evaluate their expression stability. The results demonstrated that Actin was the most stable reference gene in different tissues and in leaves treated with MeJA, and coming in the second was SAND. Furthermore, the expression of DXS and MCT which are involved in terpenoid backbone biosynthesis was detected in different tissues and after MeJA treatment. The results showed that the expression patterns of DXS and MCT in different tissues and under MeJA treatment calculated with Actin and SAND as internal reference genes were consistent, which validated the screening results. In conclusion, Actin is the most suitable reference gene for the analysis of gene expression in different tissues of A. argyi and after MeJA treatment. This study provides valuable information for gene expression analysis in A. argyi and lays a foundation for further research on molecular mechanism of quality formation of Artemisia Argyi Folium.

PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing datasets as illustrated by application to COVID-19 / 医学前沿

Pathogenic microbes can induce cellular dysfunction, immune response, and cause infectious disease and other diseases including cancers. However, the cellular distributions of pathogens and their impact on host cells remain rarely explored due to the limited methods. Taking advantage of single-cell RNA-sequencing (scRNA-seq) analysis, we can assess the transcriptomic features at the single-cell level. Still, the tools used to interpret pathogens (such as viruses, bacteria, and fungi) at the single-cell level remain to be explored. Here, we introduced PathogenTrack, a python-based computational pipeline that uses unmapped scRNA-seq data to identify intracellular pathogens at the single-cell level. In addition, we established an R package named Yeskit to import, integrate, analyze, and interpret pathogen abundance and transcriptomic features in host cells. Robustness of these tools has been tested on various real and simulated scRNA-seq datasets. PathogenTrack is competitive to the state-of-the-art tools such as Viral-Track, and the first tools for identifying bacteria at the single-cell level. Using the raw data of bronchoalveolar lavage fluid samples (BALF) from COVID-19 patients in the SRA database, we found the SARS-CoV-2 virus exists in multiple cell types including epithelial cells and macrophages. SARS-CoV-2-positive neutrophils showed increased expression of genes related to type I interferon pathway and antigen presenting module. Additionally, we observed the Haemophilus parahaemolyticus in some macrophage and epithelial cells, indicating a co-infection of the bacterium in some severe cases of COVID-19. The PathogenTrack pipeline and the Yeskit package are publicly available at GitHub.

Drug target inference by mining transcriptional data using a novel graph convolutional network framework

A fundamental challenge that arises in biomedicine is the need to characterize compounds in a relevant cellular context in order to reveal potential on-target or off-target effects. Recently, the fast accumulation of gene transcriptional profiling data provides us an unprecedented opportunity to explore the protein targets of chemical compounds from the perspective of cell transcriptomics and RNA biology. Here, we propose a novel Siamese spectral-based graph convolutional network (SSGCN) model for inferring the protein targets of chemical compounds from gene transcriptional profiles. Although the gene signature of a compound perturbation only provides indirect clues of the interacting targets, and the biological networks under different experiment conditions further complicate the situation, the SSGCN model was successfully trained to learn from known compound-target pairs by uncovering the hidden correlations between compound perturbation profiles and gene knockdown profiles. On a benchmark set and a large time-split validation dataset, the model achieved higher target inference accuracy as compared to previous methods such as Connectivity Map. Further experimental validations of prediction results highlight the practical usefulness of SSGCN in either inferring the interacting targets of compound, or reversely, in finding novel inhibitors of a given target of interest.

Cancer biology deciphered by single-cell transcriptomic sequencing

Tumors are complex ecosystems in which heterogeneous cancer cells interact with their microenvironment composed of diverse immune, endothelial, and stromal cells. Cancer biology had been studied using bulk genomic and gene expression profiling, which however mask the cellular diversity and average the variability among individual molecular programs. Recent advances in single-cell transcriptomic sequencing have enabled a detailed dissection of tumor ecosystems and promoted our understanding of tumorigenesis at single-cell resolution. In the present review, we discuss the main topics of recent cancer studies that have implemented single-cell RNA sequencing (scRNA-seq). To study cancer cells, scRNA-seq has provided novel insights into the cancer stem-cell model, treatment resistance, and cancer metastasis. To study the tumor microenvironment, scRNA-seq has portrayed the diverse cell types and complex cellular states of both immune and non-immune cells interacting with cancer cells, with the promise to discover novel targets for future immunotherapy.

Role of circular RNAs in immune-related diseases / 南方医科大学学报

Objective Circular RNAs (circRNAs) are non-coding RNAs (ncRNA) circularized without a 3' polyadenylation [poly-(A)] tail or a 5' cap, resulting in a covalently closed loop structure. circRNAs were first discovered in RNA viruses in the 1970s, but only a small number of circRNAs were discovered at that time due to limitations in traditional polyadenylated transcriptome analyses. With the development of specific biochemical and computational methods, recent studies have shown the presence of abundant circRNAs in eukaryotic transcriptomes. circRNAs play vital roles in many physiological and pathological processes, such as acting as miRNA sponges, binding to RNA-binding proteins (RBPs), acting as transcriptional regulatory factors, and even serving as translation templates. Current evidence has shown that circRNAs can be potentially used as excellent biomarkers for diagnosis, therapeutic effect evaluation, and prognostic assessment of a variety of diseases, and they may also provide effective therapeutic targets due to their stability and tissue and development-stage specificity. This review focuses on the properties of circRNAs and their immune relationship to disease, and explores the role of circRNAs in immune-related diseases and the directions of future research.

Comparative transcriptome analysis of candidate genes involved in chlorogenic acid biosynthesis during fruit development in three pear varieties of Xinjiang Uygur Autonomous Region / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Pear is one of the main fruits with thousands of years of cultivation history in China. There are more than 2000 varieties of pear cultivars around the world, including more than 1200 varieties or cultivars in China (Legrand et al., 2016). Xinjiang Uygur Autonomous Region is an important pear production region in China with 30 of varieties or cultivars. Pyrus sinkiangensis is the most popular variety, which is mainly distributed in Xinjiang (Zhou et al., 2018). Chlorogenic acid (CGA), p-coumaric acid, and arbutin are the main polyphenols in pear fruit, and their levels show great differences among different varieties (Li et al., 2014). CGA is a potential chemo-preventive agent, which possesses many important bioactivities including antioxidant, diabetes attenuating, and anti-obesity (Wang et al., 2021). Therefore, the specific CGA content of a variety is considered the embodiment of the functional nutritional value of pears.

Establishment and Validation of Immune Risk Score for Predicting Survival of Patients with Acute Myeloid Leukemia / 中国实验血液学杂志

OBJECTIVE@#To establish an immune gene prognostic model of acute myeloid leukemia (AML) and explore its correlation with immune cells in bone marrow microenvironment.@*METHODS@#Gene expression profile and clinical data of TCGA-AML were downloaded from TCGA database. Immune genes were screened by LASSO analysis to construct prognosis prediction model, and prediction accuracy of the model was quantified by receiver operating characteristic curve and area under the curve. Survival analysis was performed by Log-rank test. Enriched pathways in the different immune risk subtypes were evaluated from train cohort. The relationship between immune prediction model and bone marrow immune microenvironment was verified by flow cytometry in the real world.@*RESULTS@#Patients with low-risk score of immune gene model had better prognosis than those with high-risk score. Multivariate analysis showed that the immune gene risk model was an independent prognostic factor. The risk ratio for AML patients in the training concentration was HR=24.594 (95%CI: 6.180-97.878), and the AUC for 1-year, 3-year, and 5-year overall survival rate was 0.811, 0.815, and 0.837, respectively. In addition, enrichment analysis of differential gene sets indicated activation of immune-related pathways such as cytokines and chemokines as well as autoimmune disease-related pathways. At the same time, real world data showed that patients with high immune risk had lower numbers of CD8+T cells and B lymphocytes compared with low immune risk patients.@*CONCLUSION@#We constructed a stable prognostic model for AML, which can not only predict the prognosis of AML, but also reveal the dysregulation of immune microenvironment.

Characteristics of N6-methyladenosine modification patterns in t(8;21) acute myeloid leukemia / 南方医科大学学报

OBJECTIVE@#To investigate the relationship between AML1-ETO (AE) fusion gene and intracellular N6-methyladenosine (m6A) modification pattern in t(8;21) acute myeloid leukemia (AML).@*METHODS@#RNA m6A sequencing was performed in SKNO-1 and AE knockdown SKNO-1 (SKNO-1 siAE) cells using RNA-protein co-immunoprecipitation and high-throughput sequencing (methylated RNA immunoprecipitation sequencing, MeRIP-Seq) to analyze the changes in m6A modification of the entire transcriptome. Transcriptome sequencing (RNA-seq) was performed using high-throughput sequencing. The differentially modified mRNAs were further functionally annotated by Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The changes in m6A-related enzyme expressions were detected using real-time PCR.@*RESULTS@#A total of 26 441 genes were identified in AE knockdown AML cells and AE-expressing cells, containing 72 036 m6A peaks. AE knockdown caused a reduction of the number of intracellular m6A peaks from 37 042 to 34 994, among which 1278 m6A peaks were significantly elevated and 1225 were significantly decreased; 1316 genes with newly emerged m6A modification were detected and 1830 genes lost m6A modification after AE knockdown. The differential peaks were mainly enriched in pathways involving cancer and human T-lymphocytic leukemia virus I. RNA-seq results showed that 2483 genes were up-regulated and 3913 genes were down-regulated after AE knockdown. The combined analysis of MeRIP-Seq and RNA-Seq results revealed relatively high expression levels of m6A-modified genes as compared with the genes without m6A modification (SKNO-1: 0.6116±1.263 vs 2.010±1.655, P < 0.0001; SKNO-1 siAE: 0.5528±1.257 vs 2.067±1.686, P < 0.0001). The m6A modified genes located in the 3'UTR or 5 'UTR had significantly higher expression levels than those located in exonic regions (SKNO-1: 2.177± 1.633 vs 1.333 ± 1.470 vs 2.449 ± 1.651, P < 0.0001; SKNO-1 siAE: 2.304 ± 1.671 vs 1.336 ± 1.522 vs 2.394 ± 1.649, P < 0.05). Analysis of RNA-seq data identified 3 m6A-related enzymes that showed significantly elevated mRNA expression after AE knockdown, namely WTAP, METTL14, and ALKBH5 (P < 0.05), but the results of real-time PCR showed that the expressions of WTAP and ALKBH5 were significantly increased while the expression of METTL14 was lowered after AE knockdown (P < 0.05).@*CONCLUSION@#AE knockdown results in differential expressions of m6A-associated enzymes, suggesting that the AE fusion gene regulates the expression of one or more m6A-associated enzymes to control cellular methylation levels.

Whole-transcriptome sequencing analysis of placental differential miRNA expression profile in Down syndrome / 南方医科大学学报

OBJECTIVE@#To identify new biomarkers and molecular pathogenesis of Down syndrome (DS) by analyzing differentially expressed miRNAs in the placentas and their biological pathways.@*METHODS@#Whole transcriptome sequencing was used to identify the differentially expressed miRNAs in DS (n=3) and normal placental samples (n=3) diagnosed by prenatal diagnosis. The target genes were predicted using miRWalk, Targetscan and miRDB, and GO and KEGG pathway analyses were performed for gene enrichment studies.@*RESULTS@#We identified a total of 82 differentially expressed miRNAs in the placental tissues of DS, including 29 up-regulated miRNAs (fold change ≥2, P < 0.05) and 15 down-regulated miRNAs (fold change ≥2, P < 0.05), among which 10 miRNAs with relatively high expression abundance were selected for further analysis, including 4 up-regulated and 6 down-regulated miRNAs. These selected miRNAs shared the common target genes BTBD3 and AUTS2, both of which were associated with neurodevelopment. GO analysis showed that the target genes of the selected miRNAs were mainly enriched in protein binding, hydrolytic enzymes, metal ion binding protein combining, transferase activity, nucleotide, cytoplasmic constituents, nucleus composition, transcriptional regulation, RNA metabolism regulation, DNA-dependent RNA polymerase Ⅱ promoter transcriptional regulation, eye development, and sensory organ development. KEGG enrichment analysis showed that the target genes of these differentially expressed miRNAs were involved in the signaling pathways including tumor-related signaling pathway, PI3K-Akt signaling pathway, Ras signaling pathway, Rap1 signaling pathway, cytoskeletal regulatory signaling pathway, purine metabolization-related signaling pathway and P53 signaling pathway.@*CONCLUSION@#The differentially expressed miRNAs may play important roles in placental damage and pregnancy pathology in DS and provide clues for the prevention and treatment of mental retardation-related diseases.

Transcriptomic analysis of the ΔPaLoc mutant of Clostridioides difficile and verification of its toxicity / 中华预防医学杂志

Objective: Comparative analyses of wild-type Clostridioides difficile 630 (Cd630) strain and pathogenicity locus (PaLoc) knockout mutant (ΔPaLoc) by using RNA-seq technology. Analysis of differential expression of Cd630 wild-type strain and ΔPaLoc mutant strain and measurement of its cellular virulence changes. Lay the foundation for the construction of an toxin-attenuated vaccine strain against Clostridioides difficile. Methods: Analysis of Cd630 and ΔPaLoc mutant strains using high-throughput sequencing (RNA-seq). Clustering differentially expressed genes and screening differentially expressed genes by DESeq software. Further analysis of differential genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Finally, cytotoxicity assays of ΔPaLoc and Cd630 strains were performed in the African monkey kidney epithelial cell (Vero) and the human colonic cell (Caco-2) lines. Results: The transcriptome data showed that the ΔPaLoc mutant toxin genes tcdA and tcdB were not transcribed. Compared to the wild-type strain, CD630_36010, CD630_020910,CD630_02080 and cel genes upregulated 17.92,11.40,8.93 and 7.55 fold, respectively. Whereas the hom2 (high serine dehydrogenase), the CD630_15810 (spore-forming protein), CD630_23230 (zinc-binding dehydrogenase) and CD630_23240 (galactitol 1-phosphate 5-dehydrogenase) genes were down-regulated by 0.06, 0.075, 0.133 and 0.183 fold, respectively. The GO and KEGG enrichment analyses showed that the differentially transcribed genes in ΔPaLoc were enriched in the density-sensing system, ABC transport system, two-component system, phosphotransferase (PTS) system, and sugar metabolism pathway, as well as vancomycin resistance-related pathways. Cytotoxicity assays showed that the ΔPaLoc mutant strain lost its virulence to Vero and Caco-2 cells compared to the wild-type Cd630 strain. Conclusion: Transcriptional sequencing analysis of the Cd630 and ΔPaLoc mutant strains showed that the toxin genes were not transcribed. Those other differential genes could provide a reference for further studies on the physiological and biochemical properties of the ΔPaLoc mutant strain. Cytotoxicity assays confirmed that the ΔPaLoc mutant lost virulence to Vero and Caco-2 cells, thus laying the foundation for constructing an toxin-attenuated vaccine strain against C. difficile.

Application of single-cell transcriptome sequencing in mechanistic toxicology / 中华预防医学杂志

Traditional bulk RNA sequencing assesses the average expression level of genes in tissues rather than the differences in cellular responses. Accordingly, it is hard to differentiate sensitive responding cells, leading to inaccurate identification of toxicity pathways. Single-cell RNA sequencing (scRNA-seq) isolated single cells from tissue and subjected them to cell subtypes-specific transcriptome analysis. This technique in toxicological studies realizes the heterogeneous cellular responses in the tissue microenvironment upon chemical exposure. Thus it helps to identify sensitive responding cells and key molecular events, providing a powerful tool and a new perspective for exploring the mechanisms of toxicity and the modes of action. This review summarizes the development, principle, method, application and limitations of scRNA-seq in mechanistic toxicological researches, and discusses the prospect of multi-directional applications.

Transcriptome-wide identification and expression pattern analysis for Dof gene family in Panax ginseng from Jilin / 中国中药杂志

Dof(DNA binding with one finger), a unique class of transcription factors in plants, play an important role in seed development, tissue differentiation, and metabolic regulation. To identify the number and function of Dof gene family members in Panax ginseng, this study identified the members of Dof gene family in P. ginseng and systematically analyzed their structures, evolution, functional differentiation, expression patterns, and interactions using bioinformatics methods at the transcriptome level. At the same time, the association analysis of Dof genes from P. ginseng with key enzyme genes for ginsenoside synthesis was carried out to screen the candidate PgDof genes involved in the regulation of ginsenoside biosynthesis. The results showed that there were 54 genes belonging to the Dof gene family in P. ginseng from Jilin. All PgDof genes had Zf-Dof conserved motifs, implying that they were evolutionarily conserved and could be divided into five groups. Expression pattern analysis confirmed that the expression of PgDof gene family members in different tissues, different year-old P. ginseng, and different farm varieties varied significantly. Simultaneously, as revealed by "gene-saponin content" and "gene-gene" linkage analysis, an important candidate PgDof14-1 gene involved in the regulation of ginsenoside biosynthesis was obtained. From the established genetic transformation system of this gene in the hairy roots of P. ginseng, a positive hairy root clone was determined. This study has laid a theoretical foundation for the study of Dof gene family in P. ginseng.

Transcriptome analysis reveals the role of withering treatment in flavor formation of oolong tea (Camellia sinensis) / 生物工程学报

Oolong tea is a semi-fermented tea with strong flavor, which is widely favored by consumers because of its floral and fruity aroma as well as fresh and mellow taste. During the processing of oolong tea, withering is the first indispensable process for improving flavor formation. However, the molecular mechanism that affects the flavor formation of oolong tea during withering remains unclear. Transcriptome sequencing was used to analyze the difference among the fresh leaves, indoor-withered leaves and solar-withered leaves of oolong tea. A total of 10 793 differentially expressed genes were identified from the three samples. KEGG enrichment analysis showed that the differentially expressed genes were mainly involved in flavonoid synthesis, terpenoid synthesis, plant hormone signal transduction and spliceosome pathways. Subsequently, twelve differentially expressed genes and four differential splicing genes were identified from the four enrichment pathways for fluorescence quantitative PCR analysis. The results showed that the expression patterns of the selected genes during withering were consistent with the results in the transcriptome datasets. Further analysis revealed that the transcriptional inhibition of flavonoid biosynthesis-related genes, the transcriptional enhancement of terpenoid biosynthesis-related genes, as well as the jasmonic acid signal transduction and the alternative splicing mechanism jointly contributed to the flavor formation of high floral and fruity aroma and low bitterness in solar-withered leaves. The results may facilitate better understanding the molecular mechanisms of solar-withering treatment in flavor formation of oolong tea.

Arbuscular mycorrhizal fungi enhanced cadmium uptake in Photinia frase through altering root transcriptomes and root-associated microbial communities / 生物工程学报

As a non-essential metal, cadmium (Cd) pollution poses severe threats to plant growth, environment, and human health. Phytoextraction using nursery stocks prior to their transplantation is a potential useful approach for bioremediation of Cd contaminated soil. A greenhouse pot experiment was performed to investigate the growth, Cd accumulation, profiles of transcriptome as well as root-associated microbiomes of Photinia frase in Cd-added soil, upon inoculation of two types of arbuscular mycorrhizal fungi (AMF) Sieverdingia tortuosa and Funneliformis mosseae. Compared with the control, inoculation of F. mosseae increased Cd concentrations in root, stem and leaf by 57.2%, 44.1% and 71.1%, respectively, contributing to a total Cd content of 182 μg/plant. KEGG pathway analysis revealed that hundreds of genes involved in 'Mitogen-activated protein kinase (MAPK) signaling pathway', 'plant hormone signal transduction', 'biosynthesis of secondary metabolites' and 'glycolysis/gluconeogenesis' were enriched upon inoculation of F. mosseae. The relative abundance of Acidobacteria was increased upon inoculation of S. tortuosa, while Chloroflexi and Patescibacteria were increased upon inoculation of F. mosseae, and the abundance of Glomerales increased from 23.0% to above 70%. Correlation analysis indicated that ethylene-responsive transcription factor, alpha-aminoadipic semialdehyde synthase, isoamylase and agmatine deiminase related genes were negatively associated with the relative abundance of Glomerales operational taxonomic units (OTUs) upon inoculation of F. mosseae. In addition, plant cysteine oxidase, heat shock protein, cinnamoyl-CoA reductase and abscisic acid receptor related genes were positively associated with the relative abundance of Patescibacteria OTUs upon inoculation of F. mosseae. These finding suggested that AMF can enhance P. frase Cd uptake by modulating plant gene expression and altering the structure of the soil microbial community. This study provides a theoretical basis for better understanding the relationship between root-associated microbiomes and root transcriptomes of P. frase, from which a cost-effective and environment-friendly strategy for phytoextraction of Cd in Cd-polluted soil might be developed.

Transcriptome analysis in fetal lungs of SRC1/SRC2 double-knockout mice / 生理学报

Steroid receptor coactivators (SRCs) significantly increase the transcriptional activity of various steroid hormone receptors, and play an important regulatory role in a variety of physiological functions such as food intake, sleep, stress response and reproduction. Previous studies have found that pregnant mice carrying fetuses with SRC1/2 double-knockout (dKO) manifested delayed labor, partly due to the hypoplasia of fetal lungs and the decreased secretion of pulmonary surfactant protein-A (SP-A) and platelet activating factor (PAF). However, there is still a lack of systematic analysis of the changes in gene expression at the whole transcriptome level in the fetal lungs of SRC1/2 dKO mice. In this study, the SRC1KO, SRC2KO, SRC1/2 dKO and wild-type (WT) mouse fetal lung samples were collected at 18.5 days post coitus. The Illumina platform was employed for transcriptome mRNA sequencing, and then the differentially expressed genes (DEGs) were annotated and analyzed by GO and KEGG analysis. The results showed that the proportion of quality score of the sequencing data above Q30 in all samples was more than 92% and passed the quality control. Compared with WT fetal lungs, SRC1KO and SRC2KO fetal lungs had 61 and 32 DEGs, respectively; SRC1/2 dKO fetal lungs had 480, 11 and 901 DEGs compared with WT, SRC1KO and SRC2KO fetal lungs, respectively. Among these genes, Aspg, Crispld2, Eln, Ntsr2, Slc10a6 and Vgll3 were the unique DEGs of SRC1/2 dKO fetal lungs compared with other genotype mice. Real-time PCR and Western blotting verified the reliability of transcriptome sequencing results. The GO analysis of the DEGs between SRC1/2 dKO and WT mouse fetal lungs showed that the DEGs were significantly enriched in the extracellular space, extracellular region, and extracellular matrix in terms of cellular component. In the biological process, they were significantly enriched in the term of development of multiple organs. KEGG pathway analysis showed that the DEGs were mainly enriched in signaling pathways such as the complement system, extracellular matrix-receptor interactions, and protein digestion and absorption. In summary, this study comprehensively revealed the changes of gene expression in the fetal lungs of SRC1/2 dKO mice at the transcriptome level, which provides a new theoretical basis for the study of the developmental regulatory mechanism of the fetal lung during pregnancy, and the fetus-derived signals that affect the initiation of labor.

Mechanisms of Dangua Recipe in Improving Glycolipid Metabolic Disorders Based on Transcriptomics / 中国结合医学杂志

OBJECTIVE@#To explore the mechanisms of Dangua Recipe (DGR) in improving glycolipid metabolism based on transcriptomics.@*METHODS@#Sprague-Dawley rats with normal glucose level were divided into 3 groups according to a random number table, including a conventional diet group (Group A), a DGR group (Group B, high-calorie diet + 20.5 g DGR), and a high-calorie fodder model group (Group C). After 12 weeks of intervention, the liver tissue of rats was taken. Gene sequence and transcriptional analysis were performed to identify the key genes related to glycolipid metabolism reflecting DGR efficacy, and then gene or protein validation of liver tissue were performed. Nicotinamide phosphoribosyl transferase (Nampt) and phosphoenolpyruvate carboxykinase (PEPCK) proteins in liver tissues were detected by enzyme linked immunosorbent assay, fatty acid synthase (FASN) protein was detected by Western blot, and fatty acid binding protein 5 (FABP5)-mRNA was detected by quantitative real-time polymerase chain reaction. Furthermore, the functional verification was performed on the diabetic model rats by Nampt blocker (GEN-617) injected in vivo. Hemoglobin A@*RESULTS@#Totally, 257 differential-dominant genes of Group A vs. Group C and 392 differential-dominant genes of Group B vs. Group C were found. Moreover, 11 Gene Ontology molecular function terms and 7 Kyoto Encyclopedia of Genes and Genomes enrichment pathways owned by both Group A vs. Group C and Group C vs. Group B were confirmed. The liver tissue target validation showed that Nampt, FASN, PEPCK protein and FABP5-mRNA had the same changes consistent with transcriptome. The in vivo functional tests showed that GEN-617 increased body weight, HbA@*CONCLUSION@#Nampt activation was one of the mechanisms about DGR regulating glycolipid metabolism.

Gene expression signature analysis of peripheral blood mononuclear cells from patients with for high altitude pulmonary hypertension and value for potential drug selection / 中华心血管病杂志

Objective: To investigate the gene expression characteristics of peripheral blood mononuclear cells from patients with high altitude pulmonary hypertension (HAPH) in Naxi residents living in Lijiang, Yunnan, and to explore the underlying pathogenesis and value for potential drug selection. Methods: This is a case-control study. Six patients with HPAH (HPAH group) and 4 normal subjects (control group) were selected from the Naxi residents who originally lived in Lijiang, Yunnan Province. The general clinical data of the two groups were collected, and the related indexes of pulmonary artery pressure were collected. Peripheral blood mononuclear cells of the subjects were collected for RNA sequencing. The differences on gene expression, regulatory network of transcription factors and drug similarity between the two groups were compared. The results were compared with the public data of idiopathic pulmonary arterial hypertension (IPAH). Biological processes and signal pathways were analyzed and compared between HPAH and IPAH patients. Results: The age of 6 patients with HAPH was (68.1±8.3) years old, and there were 2 males (2/6). The age of 4 subjects in the control group was (62.3±10.9) years old, and there were 2 males (2/4). Tricuspid regurgitation velocity, tricuspid pressure gradient and pulmonary systolic pressure in HAPH group were significantly higher than those in control group (all P<0.05). The results of RNA sequencing showed that compared with the control group, 174 genes were significantly upregulated and 169 genes were downregulated in peripheral blood mononuclear cells of HAPH group. These differentially expressed genes were associated with 220 biological processes, 52 molecular functions and 23 cell components. A total of 21 biological processes and 2 signal pathways differed between HPAH and IPAH groups, most of which were related to inflammation and immune response. ZNF384, SP1 and STAT3 were selected as highly correlated transcription factors by transcription factor prediction analysis. Trichostatin A and vorinostat were screened out as potential drugs for the treatment of HAPH by drug similarity analysis. Conclusions: There are significant differences in gene expression in peripheral blood monocytes between HAPH patients and normal population, and inflammation and immune dysfunction are the main pathogenic factors. Trichostatin A and Vorinostat are potential drugs for the treatment of HAPH.

Molecular characterization and functional analysis of scavenger receptor class B from black tiger shrimp (Penaeus monodon)

BACKGROUND: Scavenger receptor class B (SRB) is a multifunctional protein in animals that participates in physiological processes, including recognition of a wide range of ligands. Astaxanthin is a major carotenoid found in shrimp. However, the molecular mechanism of astaxanthin and SRB protein binding has not been reported. RESULTS: In the present study, a member of the SRB subfamily, named PmSRB, was identified from the transcriptome of black tiger shrimp (Penaeus monodon). The open reading frame of PmSRB was 1557 bp in length and encoded 518 amino acids. The structure of PmSRB included a putative transmembrane structure at the N-terminal region and a CD36 domain. Multiple sequence alignment indicated that the CD36 domain were conserved. Phylogenetic analysis showed four separate branches (SRA, SRB, SRC, and croquemort) in the phylogenetic tree and that PmSRB was clustered with SRB of Eriocheir sinensis. Quantitative real-time polymerase chain reaction showed that the PmSRB gene was widely expressed in all tissues tested, with the highest expression level observed in the lymphoid organ and brain. Subcellular localization analysis revealed that PmSRB-GFP (green fluorescent protein) fusion proteins were predominantly localized in the cell membrane. The recombinant proteins of PmSRB showed binding activities against astaxanthin in vitro. CONCLUSIONS: PmSRB was identified and characterized in this study. It is firstly reported that PmSRB may take as an important mediator of astaxanthin uptake in shrimp.