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Fasting is a common phenomenon caused by environmental factors. Here, changes in growth, serum biochemical parameters, intestinal microbiota, and liver transcriptome were investigated of Pseudobagrus vachellii subjected to fasting and refeeding. Fasting resulted in a significant decrease in body weight, but a compensatory growth occurred after refeeding. Serum biochemical indices including triglycerides, glucose, urea nitrogen, aspartate transaminase, and alanine transaminase were strongly affected by fasting and refeeding. Large amounts of glucose and fat were utilised during fasting, and liver functions can be returned to normal in P. vachellii after refeeding. 16 S rDNA analysis showed that fasting altered intestinal microbiota homeostasis and decreased intestinal α-diversity. At the phylum level, the dominant phyla were Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota. Additionally, fasting significantly increased the abundance of the genera Plesiomonas, Edwardsiella, and Barnesiellaceae, whereas Romboutsia abundance decreased, indicating an increase in opportunistic pathogen abundance. However, after 7 days of refeeding, the composition of the gut microbiota was partially recovered. Additionally, the transcriptome analysis of the liver tissues showed that most of the identified DEGs, such as ACACA, FASN, Akt3, SCDb, and FADS2, were related to energy- and metabolism-related pathways, including fatty acid metabolism, glucagon-signalling pathway, AMPK-signalling pathway, apoptosis, carbon metabolism, and oxidative phosphorylation. Many DEGs detected during fasting were restored to normal levels after refeeding. These findings provide an important theoretical basis for future investigation of the fish physiological and ecological mechanisms underlying adaptations to food restriction. [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis is the causative agent of the disease, tuberculosis. The most researched clinical strain of Mycobacterium tuberculosis is H37Rv. To identify possible therapeutic targets, in-silico analyses of the Mycobacterium tuberculosis H37Rv genome were carried out. The genome sequence was downloaded from the website of NCBI (National Center for Biotechnology Information). The DEG (Database of Essential Genes) was consulted to identify essential genes. Additionally, homology searches with the human genome were conducted using BLASTX. Out of a total of 3924 genes, 594 were determined to be essential for Mycobacterium tuberculosis, of which 366 had no sequence similarity to the human genome. Out of 366 genes, 242 potential drug targets have been found after being screened for fictitious and unidentified genes. After functional analysis of these 242 possible targets using Uniprot, 181 of them were identified as potential drug targets. Among the 181 target genes, 42 were related to amino acid biosynthesis, 22 were related to cell wall biosynthesis, 19 to translation, 12 to transcription, 7 to lipid metabolism, 7 to carbohydrate metabolism, etc. [ABSTRACT FROM AUTHOR]

Background: Neutrophil extracellular traps (NETs) are related to the prognosis of cancer patients. Nevertheless, the potential prognostic values of NETs in skin cutaneous melanoma (SKCM) remains largely unknown. Materials and methods: The NET‐related gene signature was constructed by LASSO Cox regression analysis using the TCGA‐SKCM cohort. The overall survival (OS) and immune status in SKCM patients between the high‐ and low‐NET score (high‐score, low‐score) groups were explored. The scRNA‐seq dataset GSE115978 was used to understand the role of NET score in SKCM at single cell resolution. Results: A five NET genes‐based signature (TLR2, CLEC6A, PDE4B, SLC22A4 and CYP4F3) was constructed as the NET‐related prognostic model for SKCM. The OS of SKCM patients with low‐score was better than that in patients with high‐score. Additionally, NET score was negatively associated with infiltration of some immune cells (e.g. type I Macrophages, CD8‐T cells, CD4‐T cells). Moreover, patients with high‐score had low stromal, immune and ESTIMATE scores. Furthermore, drug sensitivity analysis results showed that Lapatinib, Trametinib and Erlotinib may have better therapeutic advantages in patients with high‐score. Conclusion: We established a NET‐related five gene signature in SKCM and found that the NET‐related signature may exhibit a good predictive ability for SKCM prognosis. The NET score may not only predict the survival outcome and drug sensitivity in SKCM, but also reflect the immune conditions of SKCM patients. [ABSTRACT FROM AUTHOR]

Atherosclerosis, a lipid‐driven chronic inflammatory disorder, is a significant global health concern associated with high rates of morbidity and mortality, imposing a substantial societal burden. The purpose of this study is to investigate the possible molecular mechanisms of atherosclerosis and identify potential therapeutic targets. We conducted an integrated bioinformatics analysis using data from peripheral blood mononuclear cell and TISSUE databases obtained from the Gene Expression Omnibus, to identify key genes associated with the progression of atherosclerosis. Here, IRF8 was found to be a key gene in atherosclerosis patients. Silencing IRF8 with small interfering RNA reduced inflammation in endothelial cells. This suggests IRF8 is a crucial biomarker for immune infiltration in atherosclerosis advance. [ABSTRACT FROM AUTHOR]

Background: The genes involved in cephalopod development and their association with hatching and survival during early life stages have been extensively studied. However, few studies have investigated the paralarvae transcriptome of the East Asian common octopus (Octopus sinen sis). Objective: This study aimed to identify the genes related to embryonic development and hatching in O. sinensis using RNA sequencing (RNA-seq) and verify the genes most relevant to different embryonic stages. Methods: RNA samples from hatched and 25 days post-hatching (dph) O. sinensis paralarvae were used to construct cDNA libraries. Clean reads from individual samples were aligned to the reference O. sinensis database to identify the differentially expressed genes (DEGs) between the 0- and 25-dph paralarvae libraries. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to supplement the RNA-seq data for embryogenic developmental stages. Results: A total of 12,597 transcripts were annotated and 5,468 DEGs were identified between the 0- and 25-dph O. sinensis paralarvae, including 2,715 upregulated and 2,753 downregulated transcripts in the 25-dph paralarvae. Several key DEGs were related to transmembrane transport, lipid biosynthesis, monooxygenase activity, lipid transport, neuropeptide signaling, transcription regulation, and protein-cysteine S-palmitoyltransferase activity during the post-hatching development of O. sinensis paralarvae. RT-qPCR analysis further revealed that SLC5A3A, ABCC12, and NPC1 transcripts in 20 and/or 30 days post-fertilization (dpf) embryos were significantly higher (p < 0.05) than those in 10-dpf embryos. Conclusion: Transcriptome profiles provide molecular targets to understand the embryonic development, hatching, and survival of O. sinensis paralarvae, and enhance octopus production. [ABSTRACT FROM AUTHOR]

Background: Both bacterial and viral diseases are a major threat to farmed fish. As the antiviral immune mechanisms in lumpfish (Cyclopterus lumpus L.) are poorly understood, lumpfish leukocytes were stimulated with poly(I:C), a synthetic analog of double stranded RNA, which mimic viral infections, and RNA sequencing was performed. Methods: To address this gap, we stimulated lumpfish leukocytes with poly(I:C) for 6 and 24 hours and did RNA sequencing with three parallels per timepoint. Genome guided mapping was performed to define differentially expressed genes (DEGs). Results: Immune genes were identified, and transcriptome-wide analyses of early immune responses showed that 376 and 2372 transcripts were significantly differentially expressed 6 and 24 hours post exposure (hpe) to poly(I:C), respectively. The most enriched GO terms when time had been accounted for, were immune system processes (GO:0002376) and immune response (GO:0006955). Analysis of DEGs showed that among the most highly upregulated genes were TLRs and genes belonging to the RIG-I signaling pathway, including LGP2, STING and MX, as well as IRF3 and IL12A. RIG-I was not identified, but in silico analyses showed that genes encoding proteins involved in pathogen recognition, cell signaling, and cytokines of the TLR and RIG-I signaling pathway are mostly conserved in lumpfish when compared to mammals and other teleost species. Conclusions: Our analyses unravel the innate immune pathways playing a major role in antiviral defense in lumpfish. The information gathered can be used in comparative studies and lay the groundwork for future functional analyses of immune and pathogenicity mechanisms. Such knowledge is also necessary for the development of immunoprophylactic measures for lumpfish, which is extensively cultivated for use as cleaner fish in the aquaculture for removal of sea lice from Atlantic salmon (Salmo salar L.). [ABSTRACT FROM AUTHOR]

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Modern concepts in irreversible thermodynamics are applied to system transformation and degradation analyses. Phenomenological entropy generation (PEG) theorem is combined with the Degradation-Entropy Generation (DEG) theorem for instantaneous multi-disciplinary, multi-scale, multi-component system characterization. A transformation-PEG theorem and space materialize with system and process defining elements and dimensions. The near-100% accurate, consistent results and features in recent publications demonstrating and applying the new TPEG methods to frictional wear, grease aging, electrochemical power system cycling—including lithium-ion battery thermal runaway—metal fatigue loading and pump flow are collated herein, demonstrating the practicality of the new and universal PEG theorem and the predictive power of models that combine and utilize both theorems. The methodology is useful for design, analysis, prognostics, diagnostics, maintenance and optimization. [ABSTRACT FROM AUTHOR]

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive fungal diseases threatening global wheat production. Exploring powdery mildew resistance (Pm) gene(s) and dissecting the molecular mechanism of the host resistance are critical to effectively and reasonably control this disease. Durum wheat (Triticum turgidum L. var. durum Desf.) is an important gene donor for wheat improvement against powdery mildew. In this study, a resistant durum wheat accession W762 was used to investigate its potential resistance component(s) and profile its expression pattern in responding to Bgt invasion using bulked segregant RNA-Seq (BSR-Seq) and further qRT-PCR verification. Genetic analysis showed that the powdery mildew resistance in W762 did not meet monogenic inheritance and complex genetic model might exist within the population of W762 × Langdon (susceptible durum wheat). After BSR-Seq, 6,196 consistently different single nucleotide polymorphisms (SNPs) were called between resistant and susceptible parents and bulks, and among them, 763 SNPs were assigned to the chromosome arm 7B. Subsequently, 3,653 differentially expressed genes (DEGs) between resistant and susceptible parents and bulkswere annotated and analyzed by GeneOntology (GO), Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. The potential regulated genes were selected and analyzed their temporal expression patterns following Bgt inoculation. As a result, nine disease-related genes showed distinctive expression profile after Bgt invasion and might serve as potential targets to regulate the resistance against powdery mildew in W762. Our study could lay a foundation for analysis of the molecular mechanism and also provide potential targets for the improvement of durable resistance against powdery mildew. [ABSTRACT FROM AUTHOR]

Pecan scab is a devastating disease that causes damage to pecan (Carya illinoinensis (Wangenh.) K. Koch) fruit and leaves. The disease is caused by the fungus Venturia effusa (G. Winter) and the main management practice for controlling the disease is by application of fungicides at 2-to-3-week intervals throughout the growing season. Besides disease-related yield loss, application of fungicides can result in considerable cost and increases the likelihood of fungicide resistance developing in the pathogen. Resistant cultivars are available for pecan growers; although, in several cases resistance has been overcome as the pathogen adapts to infect resistant hosts. Despite the importance of host resistance in scab management, there is little information regarding the molecular basis of genetic resistance to pecan scab. The purpose of this study was to elucidate mechanisms of natural pecan scab resistance by analyzing transcripts that are differentially expressed in pecan leaf samples from scab resistant and susceptible trees. The leaf samples were collected from trees in a provenance collection orchard that represents the natural range of pecan in the US and Mexico. Trees in the orchard have been exposed to natural scab infections since planting in 1989, and scab ratings were collected over three seasons. Based on this data, ten susceptible trees and ten resistant trees were selected for analysis. RNA-seq data was collected and analyzed for diseased and non-diseased parts of susceptible trees as well as for resistant trees. A total of 313 genes were found to be differentially expressed when comparing resistant and susceptible trees without disease. For susceptible samples showing scab symptoms, 1,454 genes were identified as differentially expressed compared to non-diseased susceptible samples. Many genes involved in pathogen recognition, defense responses, and signal transduction were up-regulated in diseased samples of susceptible trees, whereas differentially expressed genes in pecan scab resistant samples were generally down-regulated compared to non-diseased susceptible samples. Our results provide the first account of candidate genes involved in resistance/susceptibility to pecan scab under natural conditions in a pecan orchard. This information can be used to aid pecan breeding programs and development of biotechnology-based approaches for generating pecan cultivars with more durable scab resistance. [ABSTRACT FROM AUTHOR]

Background: Frontal fibrosis alopecia (FFA) is a primary cicatricial alopecia and has received increasing attention in recent years. However, the pathogenesis of FFA has not been fully elucidated. Methods and results: Herein, we collected the transcriptome data of scalp lesions of seven patients with FFA and seven healthy controls. The differential expression analysis and weighted gene co‐expression network analysis were conducted and we identified 458 differentially expressed genes (DEGs) in two key modules. Later, we performed functional enrichment analysis and functional modules identification, revealing the participation of immune response and fatty acid metabolism. Based on the results, we processed further studies. On the one hand, we analyzed the infiltrating immune cells of FFA through CIBERSORT algorithm, indicating the activation of M1 macrophage and CD8+ T cell. On the other hand, considering lipid metabolism of FFA and oxidative stress of hair follicle cells in alopecia, we explored the potential ferroptosis of FFA. By intersection of DEGs and ferroptosis‐related genes from FerrDb database, 19 genes were identified and their expression was validated in an external dataset containing 36 FFA cases and 12 controls. Then, we used LASSO algorithms to construct a four‐gene diagnostic model, which achieved an AUC of 0.924 in validation dataset. Additionally, the immune cells were found to be related to ferroptosis in FFA. Conclusion: Taken together, this study contributed to reveal the molecular mechanisms of FFA and is expected to inspire future research on treatment. [ABSTRACT FROM AUTHOR]

The widespread use of battery-powered electronic devices creates the need to develop methods to extend their maximum operating time. This can be achieved by using ambient energy, which would otherwise be dissipated. The conversion of energy, usually mechanical energy, into electric energy takes place in energy harvesters. Energy harvester systems based on a dielectric elastomer (DE) are a relatively new field that is being constantly developed. Due to their features, dielectric elastomer generators (DEGs) may complement the currently dominant piezoelectric harvesters. The major feature of employing a hyperelastic material is that it allows relatively large displacements to be utilised for generating energy, which is impossible in the case of piezoceramics. This article presents a DEG designed to operate under uniaxial tensile loads and which has a multilayer structure, describes the general operating principles of a DEG, explains the construction and assembly process of the investigated design and shows the electric circuit necessary to properly direct current flow during the DEG operation. The experimental part consists of two series of tests based on a central composite design (CCD). The objective of the first part was to map a capacitance response surface of the DEG in the selected range of the cyclic mechanical load. The second part concerned the amount of generated energy for the specific load case as a function of operating voltages. The result of the work is the formulation of regression models that allow the characteristics of the presented DEG design to be identified. [ABSTRACT FROM AUTHOR]

Purpose COVID-19 strangely kills some youth with no history of physical weakness, and in addition to the lungs, it may even directly harm other organs. Its complex mechanism has led to the loss of any significantly effective drug, and some patients with severe forms still die daily. Common methods for identifying disease mechanisms and drug design are often time-consuming or reductionist. Here, we use a novel holistic systems biology approach to predict its molecular mechanisms (in vitro), significant molecular relations with SARS, and repurpose drugs. Methods We have utilized its relative phylogenic similarity to SARS. Using the available omics data for SARS and the fewer data for COVID-19 to decode the mechanisms and their significant relations, We applied the Cytoscape analyzer, MCODE, STRING, and DAVID tools to predict the topographically crucial molecules, clusters, protein interaction mappings, and functional analysis. We also applied a novel approach to identify the significant relations between the two infections using the Fischer exact test for MCODE clusters. We then constructed and analyzed a drug-gene network using PharmGKB and DrugBank (retrieved using the dgidb). Results Some of the shared identified crucial molecules, BPs and pathways included Kaposi sarcoma-associated herpesvirus infection, Influenza A, and NOD-like receptor signaling pathways. Besides, our identified crucial molecules specific to host response against SARS-CoV-2 included FGA, BMP4, PRPF40A, and IFI16. Conclusion We also introduced seven new repurposed candidate drugs based on the drug-gene network analysis for the identified crucial molecules. Therefore, we suggest that our newly recommended repurposed drugs be further investigated in Vitro and in Vivo against COVID-19. [ABSTRACT FROM AUTHOR]

Single cell RNA-sequencing (scRNA-seq) technology has significantly advanced the understanding of transcriptomic signatures. Although various statistical models have been used to describe the distribution of gene expression across cells, a comprehensive assessment of the different models is missing. Moreover, the growing number of features associated with scRNA-seq datasets creates new challenges for analytical accuracy and computing speed. Here, we developed a Python-based package (TensorZINB) to solve the zero-inflated negative binomial (ZINB) model using the TensorFlow deep learning framework. We used a sequential initialization method to solve the numerical stability issues associated with hurdle and zero-inflated models. A recursive feature selection protocol was used to optimize feature selections for data processing and downstream differentially expressed gene (DEG) analysis. We proposed a class of hybrid models combining nested models to further improve the model's performance. Additionally, we developed a new method to convert a continuous distribution to its equivalent discrete form, so that statistical models can be fairly compared. Finally, we showed that the proposed TensorFlow algorithm (TensorZINB) was numerically stable and that its computing speed and performance were superior to those of existing ZINB solvers. Moreover, we implemented seven hurdle and zero-inflated statistical models in Python and systematically assessed their performance using a real scRNA-seq dataset. We demonstrated that the ZINB model achieved the lowest Akaike information criterion compared with other models tested. Taken together, TensorZINB was accurate, efficient and scalable for the implementation of ZINB and for large-scale scRNA-seq data analysis with DEG identification. [ABSTRACT FROM AUTHOR]

Aim: Fetal growth restriction (FGR) can lead to short‐term and long‐term impairments in the fetus. The placenta functions as an exchanger for substance transport, playing a critical role in fetal growth. However, the mechanism from the placental standpoint is still not fully understood. In this study, we aimed to investigate the pathophysiological mechanisms in the placenta that mediated the development of FGR and sex differences. Methods: We analyzed the gene expression profiles of GSE100415 containing specific normotensive FGR placental samples and GSE114691 with canonical samples using three different methods, differentially expressed gene analysis, weighted gene co‐expression network analysis, and gene set enrichment analysis. Gene enrichment was performed, including the gene ontology and pathway from the Kyoto Encyclopedia of Genes and Genomes. The important process was then validated in pregnant Wistar rats subcutaneously administered dexamethasone (0.2 mg/kg/d) or saline from gestation Day 9 to 21. Results: Our results revealed little difference between the comparison of normal and normotensive FGR placental samples but confirmed the sex difference. Further analyses of the canonical samples identified the occurrence of vascular dysfunction, which was validated by the calculation of the vascular lumen area, showing that the vascular lumen in the FGR group was more than in the control. We also discovered 17 significantly expressed genes from the involved eigengenes. Conclusion: Our study provides an important theoretical and experimental basis to reevaluate the development of FGR from the placental standpoint and suggests a series of biomarkers for future clinical use. [ABSTRACT FROM AUTHOR]

Plants are often exposed to drought stress, and decreases in the soil water content can prevent plants from reaching their full genetic potential. Populus davidiana Dode belongs to the genus Populus, and it is a temperate deciduous tree that is cold and drought tolerant. To investigate the mechanism of P. davidiana response to drought stress, transcriptome analysis was performed on drought and control treatments of P. davidiana. We identified 10230 differentially expressed genes (DEGs). Most DEGs were enriched in pathways related to transcriptional regulation and hormone signal transduction, ROS metabolism, lignin synthesis, and the sugar metabolism process in two contrasting groups. Compared with the control condition, soluble sugars, proline, and POD activity were all increased under drought stress. In addition, Na+, K+, and Ca2+ were all higher under drought stress than in the control. These results not only revealed the mechanism of tolerance to drought stress in P. davidiana, but also promoted the development and application of drought-tolerant genetic resources in P. davidiana. [ABSTRACT FROM AUTHOR]

Background: Both bacterial and viral diseases are a major threat to farmed fish. As the antiviral immune mechanisms in lumpfish (Cyclopterus lumpus L.) are poorly understood, lumpfish leukocytes were stimulated with poly(I:C), a synthetic analog of double stranded RNA, which mimic viral infections, and RNA sequencing was performed. Methods: To address this gap, we stimulated lumpfish leukocytes with poly(I:C) for 6 and 24 hours and did RNA sequencing with three parallels per timepoint. Genome guided mapping was performed to define differentially expressed genes (DEGs). Results: Immune genes were identified, and transcriptome-wide analyses of early immune responses showed that 376 and 2372 transcripts were significantly differentially expressed 6 and 24 hours post exposure (hpe) to poly(I:C), respectively. The most enriched GO terms when time had been accounted for, were immune system processes (GO:0002376) and immune response (GO:0006955). Analysis of DEGs showed that among the most highly upregulated genes were TLRs and genes belonging to the RIG-I signaling pathway, including LGP2, STING and MX, as well as IRF3 and IL12A. RIG-I was not identified, but in silico analyses showed that genes encoding proteins involved in pathogen recognition, cell signaling, and cytokines of the TLR and RIG-I signaling pathway are mostly conserved in lumpfish when compared to mammals and other teleost species. Conclusions: Our analyses unravel the innate immune pathways playing a major role in antiviral defense in lumpfish. The information gathered can be used in comparative studies and lay the groundwork for future functional analyses of immune and pathogenicity mechanisms. Such knowledge is also necessary for the development of immunoprophylactic measures for lumpfish, which is extensively cultivated for use as cleaner fish in the aquaculture for removal of sea lice from Atlantic salmon (Salmo salar L.). [ABSTRACT FROM AUTHOR]

Early diagnosis and treatment of glaucoma are challenging. The discovery of glaucoma biomarkers based on gene expression data could potentially provide new insights for early diagnosis, monitoring, and treatment options of glaucoma. Non-negative Matrix Factorization (NMF) has been widely used in numerous transcriptome data analyses in order to identify subtypes and biomarkers of different diseases; however, its application in glaucoma biomarker discovery has not been previously reported. Our study applied NMF to extract latent representations of RNA-seq data from BXD mouse strains and sorted the genes based on a novel gene scoring method. The enrichment ratio of the glaucoma-reference genes, extracted from multiple relevant resources, was compared using both the classical differentially expressed gene (DEG) analysis and NMF methods. The complete pipeline was validated using an independent RNA-seq dataset. Findings showed our NMF method significantly improved the enrichment detection of glaucoma genes. The application of NMF with the scoring method showed great promise in the identification of marker genes for glaucoma. [ABSTRACT FROM AUTHOR]

Sometimes, for medical reasons, when a frozen tissue has already thawed, an operation by re-transplantation may be cancelled, and ovarian tissues should be re-frozen for transplantation next time. Research about the repeated cryopreservation of ovarian cells is rarely reported. It has been published that there is no difference in the follicle densities, proportions of proliferation of early preantral follicles, appearance of atretic follicles, or ultrastructural quality of frozen-thawed and re-frozen-rethawed tissue. However, the molecular mechanisms of a repeated cryopreservation effect on the developmental potential of ovarian cells are unknown. The aim of our experiments was to investigate the effect of re-freezing and re-thawing ovarian tissue on gene expression, gene function annotation, and protein–protein interactions. The morphological and biological activity of primordial, primary, and secondary follicles, aimed at using these follicles for the formation of artificial ovaries, was also detected. Second-generation mRNA sequencing technology with a high throughput and accuracy was adopted to determine the different transcriptome profiles in the cells of four groups: one-time cryopreserved (frozen and thawed) cells (Group 1), two-time cryopreserved (re-frozen and re-thawed after first cryopreservation) cells (Group 2), one-time cryopreserved (frozen and thawed) and in vitro cultured cells (Group 3), and two times cryopreserved (re-frozen and re-thawed after first cryopreservation) and in vitro cultured cells (Group 4). Some minor changes in the primordial, primary, and secondary follicles in terms of the morphology and biological activity were detected, and finally, the availability of these follicles for the formation of artificial ovaries was explored. It was established that during cryopreservation, the CEBPB/CYP19A1 pathway may be involved in regulating estrogen activity and CD44 is crucial for the development of ovarian cells. An analysis of gene expression in cryopreserved ovarian cells indicates that two-time (repeated) cryopreservation does not significantly affect the developmental potential of these cells. For medical reasons, when ovarian tissue is thawed but cannot be transplanted, it can be immediately re-frozen again. [ABSTRACT FROM AUTHOR]

Introduction: Aberrant gene expression is a key mechanism underlying pulmonary hypertension (PH) development. The alterations of genomic chromatin accessibility and their relationship with the aberrant gene expressions in PH are poorly understood. We used bulk Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) in pulmonary artery smooth muscle cells (PASMCs) of chronic hypoxia-exposed rats mimicking group 3 human PH. Methods: Adult Sprague Dawley rats were commercially obtained from Hunan SJA (Hunan SJA Laboratory Animal Co., Changsha, China) and randomizedly allocated into four groups exposing to nomobaric hypoxia or normoxia for 1 or 28 days respectively. After the assessment of pulmonary hemodynamics, smooth muscle cells were isolated from intralobular arteries and simultaneously subjected to bulk Assay of ATAC-seq and RNA-seq. Results: Hypoxic exposure for continuous 28-days, but not for 1-day, induced established PH phenotypes in rats. ATAC-seq revealed a major distribution of differential accessibility regions (DARs) annotated to the genome in out-of-promoter regions, following 1-day or 28-days hypoxia. 1188 DAR-associated genes and 378 differentially expressed genes (DEGs) were identified in rats after exposure to 1-day hypoxia, while 238 DAR-associated genes and 452 DEGs for 28-days hypoxia. Most of the DAR-associated genes or DEGs in 1-day did not overlap with that of 28-days hypoxia. A Pearson correlation analysis indicated no significant correlation between ATAC-seq and RNA-seq. Conclusions: The alterations in genomic chromatin accessibility and genes expression of PASMCs in the initial stage of hypoxia are distinct from the established stage of hypoxia-induced PH. The genomic differential accessibility regions may not be the main mechanisms directly underlying the differentially expressed genes observed either in the initial or established stages of PH. Thus the time-course alterations of gene expression and their possible indirect link with genomic chromatin accessibility warrant more attention in mechanistic study of pulmonary hypertension. [ABSTRACT FROM AUTHOR]

This document is a corrigendum published in the journal Frontiers in Immunology. It corrects an error in the acknowledgment section of a previously published article titled "Transcriptome-wide analyses of early immune responses in lumpfish leukocytes upon stimulation with poly(I:C)." The correction provides additional information about the funding received for the project and acknowledges the organizations that provided support. The authors apologize for the error and state that it does not affect the scientific conclusions of the article. The corrigendum is open access and was approved by the Frontiers Editorial Office. [Extracted from the article]

The antiparasitic drug halofuginone is important for controlling apicomplexan parasites. However, the occurrence of halofuginone resistance is a major obstacle for it to the treatment of apicomplexan parasites. Current studies have identified the molecular marker and drug resistance mechanisms of halofuginone in Plasmodium falciparum. In this study, we tried to use transcriptomic data to explore resistance mechanisms of halofuginone in apicomplexan parasites of the genus Eimeria (Apicomplexa: Eimeriidae). After halofuginone treatment of E. tenella parasites, transcriptome analysis was performed using samples derived from both resistant and sensitive strains. In the sensitive group, DEGs associated with enzymes were significantly downregulated, whereas the DNA damaging process was upregulated after halofuginone treatment, revealing the mechanism of halofuginone-induced parasite death. In addition, 1,325 differentially expressed genes (DEGs) were detected between halofuginone resistant and sensitive strains, and the DEGs related to translation were significantly downregulated after halofuginone induction. Overall, our results provide a gene expression profile for further studies on the mechanism of halofuginone resistance in E. tenella. [ABSTRACT FROM AUTHOR]

Nucleocytoplasmic transport receptors play key roles in the nuclear translocation of disease resistance proteins, but the associated mechanisms remain unclear. The Arabidopsis thaliana gene SAD2 encodes an importin β-like protein. A transgenic Arabidopsis line overexpressing SAD2 (OESAD2/Col-0) showed obvious resistance to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) compared to the wild type (Col-0), but the knockout mutant sad2-5 was susceptible. Transcriptomic analysis was then performed on Col-0, OESAD2/Col-0, and sad2-5 leaves at 0, 1, 2, and 3 days post-inoculation with Pst DC3000. A total of 1825 differentially expressed genes (DEGs) were identified as putative biotic stress defense genes regulated by SAD2, 45 of which overlapped between the SAD2 knockout and overexpression datasets. Gene Ontology (GO) analysis indicated that the DEGs were broadly involved in single-organism cellular metabolic processes and in response to stimulatory stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) biochemical pathway analysis revealed that many of the DEGs were associated with the biosynthesis of flavonoids and other specialized metabolites. Transcription factor analysis showed that a large number of ERF/AP2, MYB, and bHLH transcription factors were involved in SAD2-mediated plant disease resistance. These results provide a basis for future exploration of the molecular mechanisms associated with SAD2-mediated disease resistance and establish a set of key candidate disease resistance genes. [ABSTRACT FROM AUTHOR]

The effect of PARP1 knockout in HEK293 cells on the gene expression of DNA base excision repair (BER) proteins was studied. It was shown that the expression of all differentially expressed genes (DEGs) of BER was reduced by knockout. The expression of the DNA glycosylase gene NEIL1, which is considered to be one of the common "hubs" for binding BER proteins, has changed the most. The expression of genes of auxiliary subunits of DNA polymerases δ and ε is also significantly reduced. The PARP1 gene knockout cell line obtained is an adequate cell model for studying the activity of the BER process in the absence of PARP1 and testing drugs aimed at inhibiting repair processes. It has been found for the first time that knockout of the PARP1 gene results in a significant change in the level of expression of proteins responsible for ribosome biogenesis and the functioning of the proteasome. [ABSTRACT FROM AUTHOR]

Patients with preexisting metabolic disorders such as diabetes are at a higher risk of developing severe coronavirus disease 2019 (COVID-19). Mitochondrion, the very organelle that controls cellular metabolism, holds the key to understanding disease progression at the cellular level. Our current study aimed to understand how cellular metabolism contributes to COVID-19 outcomes. Metacore pathway enrichment analyses on differentially expressed genes (encoded by both mitochondrial and nuclear deoxyribonucleic acid (DNA)) involved in cellular metabolism, regulation of mitochondrial respiration and organization, and apoptosis, was performed on RNA sequencing (RNASeq) data from blood samples collected from healthy controls and patients with mild/moderate or severe COVID-19. Genes from the enriched pathways were analyzed by network analysis to uncover interactions among them and up- or downstream genes within each pathway. Compared to the mild/moderate COVID-19, the upregulation of a myriad of growth factor and cell cycle signaling pathways, with concomitant downregulation of interferon signaling pathways, were observed in the severe group. Matrix metallopeptidase 9 (MMP9) was found in five of the top 10 upregulated pathways, indicating its potential as therapeutic target against COVID-19. In summary, our data demonstrates aberrant activation of endocrine signaling in severe COVID-19, and its implication in immune and metabolic dysfunction. [ABSTRACT FROM AUTHOR]

Cold damage is one of the most important environmental factors influencing crop growth, development, and production. In this study, we generated a pair of near-isogenic lines (NILs), Towada and ZL31, and Towada showed more cold sensitivity than ZL31 in the rice seedling stage. To explore the transcriptional regulation mechanism and the reason for phenotypic divergence of the two lines in response to cold stress, an in-depth comparative transcriptome study under cold stress was carried out. Our analysis uncovered that rapid and high-amplitude transcriptional reprogramming occurred in the early stage of cold treatment. GO enrichment and KEGG pathway analysis indicated that genes of the response to stress, environmental adaptation, signal transduction, metabolism, photosynthesis, and the MAPK signaling pathway might form the main part of the engine for transcriptional reprogramming in response to cold stress. Furthermore, we identified four core genes, OsWRKY24, OsCAT2, OsJAZ9, and OsRR6, that were potential candidates affecting the cold sensitivity of Towada and ZL31. Genome re-sequencing analysis between the two lines revealed that only OsWRKY24 contained sequence variations which may change its transcript abundance. Our study not only provides novel insights into the cold-related transcriptional reprogramming process, but also highlights the potential candidates involved in cold stress. [ABSTRACT FROM AUTHOR]

Banana is one of the major food crops and its production is subject to many pests and diseases. Banana breeding exploits wild relatives and progenitor species for the introgression of resistant genes (R) into cultivated varieties to overcome these hurdles. With advances in sequencing technologies, whole-genome sequences are available for many Musa spp. and many of them are potential donors of disease resistance genes. Considering their potential role, R genes from these species were explored to develop an user-friendly open-access database that will be useful for studying and implementing disease resistance in bananas. MusaRgene database is complemented with complete details of 3598 R genes identified from eight Musa spp. and rice, Arabidopsis, sorghum along with its classification and separate modules on its expression under various stresses in resistant and susceptible cultivars and corresponding SSRs are also provided. This database can be regarded as the primary resource of information on R genes from bananas and their relatives. R genes from other allele mining studies are also incorporated which will enable the identification of its homolog in related Musa spp. MusaRgene database will aid in the identification of genes and markers associated, cloning of full-length R genes, and genetic transformation or gene editing of the R genes in susceptible cultivars. Multiple R genes can also be identified for pyramiding the genes to increase the level of resistance and durability. Overall, this database will facilitate the understanding of defense mechanisms in bananas against biotic or abiotic stresses leading to the development of promising disease-resistant varieties. [ABSTRACT FROM AUTHOR]

RNA-sequencing (RNA-seq) is a versatile, high-throughput technology that is being widely employed for screening differentially expressed genes (DEGs) in various diseases. Echinococcosis, a globally distributed zoonosis, has been reported to impose a heavy disease burden in pastoral areas of China. Herein we aimed to explore the molecular mechanisms underlying echinococcosis. In this study, peripheral blood samples were collected from six patients with alveolar echinococcosis (AE), six patients with cystic echinococcosis (CE), and six healthy controls. RNA-Seq (mRNA) was performed to detect gene transcript and expression levels, and DEGs were subjected to bioinformatic analyses. In comparison with healthy controls, 492 DEGs (270 upregulated, 222 downregulated) were found in the AE group and 424 DEGs (170 upregulated, 254 downregulated) were found in the CE group (|log2 (fold change)| > 1 and P < 0.05). Further, 60 genes were upregulated and 39 were downregulated in both the AE and CE groups. Gene ontology enrichment analysis indicated that DEGs were mainly involved in molecular functions, including extracellular space, extracellular region, organ and system development, and anatomical structure development. Protein–protein interaction (PPI) networks were constructed to depict the complex relationship between DEGs and interacting proteins. [ABSTRACT FROM AUTHOR]

Panicle degeneration, sometimes known as abortion, causes heavy losses in grain yield. However, the mechanism of naturally occurring panicle abortion is still elusive. In a previous study, we characterized a mutant, apical panicle abortion1331 (apa1331), exhibiting abortion in apical spikelets starting from the 6 cm stage of panicle development. In this study, we have quantified the five phytohormones, gibberellins (GA), auxins (IAA), abscisic acid (ABA), cytokinins (CTK), and brassinosteroids (BR), in the lower, middle, and upper parts of apa1331 and compared these with those exhibited in its wild type (WT). In apa331, the lower and middle parts of the panicle showed contrasting concentrations of all studied phytohormones, but highly significant changes in IAA and ABA, compared to the upper part of the panicle. A comparative transcriptome of apa1331 and WT apical spikelets was performed to explore genes causing the physiological basis of spikelet abortion. The differential expression analysis revealed a significant downregulation and upregulation of 1587 and 978 genes, respectively. Hierarchical clustering of differentially expressed genes (DEGs) revealed the correlation of gene ontology (GO) terms associated with antioxidant activity, peroxidase activity, and oxidoreductase activity. KEGG pathway analysis using parametric gene set enrichment analysis (PGSEA) revealed the downregulation of the biological processes, including cell wall polysaccharides and fatty acids derivatives, in apa1331 compared to its WT. Based on fold change (FC) value and high variation in expression during late inflorescence, early inflorescence, and antherdevelopment, we predicted a list of novel genes, which presumably can be the potential targets of inflorescence development. Our study not only provides novel insights into the role of the physiological dynamics involved in panicle abortion, but also highlights the potential targets involved in reproductive development. [ABSTRACT FROM AUTHOR]

Thyroid hormone has pleiotropic regulatory effects on growth, development, and metabolism. It also regulates cell proliferation, differentiation, and apoptosis. In the present study, differentially expressed genes (DEG) and their related pathways involved in TH regulation during gestation were identified in the placenta tissues of high thyroid-induced mice by RNA sequencing. The levels of TSH, FT3, and FT4 in blood showed an increasing tendency in the high thyroid-induced mice with intragastric administration of 0.250 or 0.500 μg•μL-1 L-T4, respectively. Compared to CG9d mice, one DEG and 10 DEGs were identified in the LG9d and HG9d groups, respectively. There were 32 DEGs identified between the LG9d and HG9d, 22 of which were up-regulated DEGs and 10 were down-regulated. Several GO annotations and signaling pathways were associated with embryonic development and TH synthesis and metabolism, including the Wnt signaling pathway and the TH signaling pathway. The expressions of nine randomly selected DEGs were re-quantified by quantitative real-time PCR (qPCR) and showed a consistent tendency with the results of RNA-sequencing, which suggests that reliable data are obtained in the transcriptome assay. These findings provide insights into the mechanism of the dynamic regulation of the TH balance during pregnancy in mammals. [ABSTRACT FROM AUTHOR]

To guide analysts to select the right tool and parameters in differential gene expression analyses of single-cell RNA sequencing (scRNA-seq) data, we developed a novel simulator that recapitulates the data characteristics of real scRNA-seq datasets while accounting for all the relevant sources of variation in a multi-subject, multi-condition scRNA-seq experiment: the cell-to-cell variation within a subject, the variation across subjects, the variability across cell types, the mean/variance relationship of gene expression across genes, library size effects, group effects, and covariate effects. By applying it to benchmark 12 differential gene expression analysis methods (including cell-level and pseudo-bulk methods) on simulated multi-condition, multi-subject data of the 10x Genomics platform, we demonstrated that methods originating from the negative binomial mixed model such as glmmTMB and NEBULA-HL outperformed other methods. Utilizing NEBULA-HL in a statistical analysis pipeline for single-cell analysis will enable scientists to better understand the cell-type-specific transcriptomic response to disease or treatment effects and to discover new drug targets. Further, application to two real datasets showed the outperformance of our differential expression (DE) pipeline, with unified findings of differentially expressed genes (DEG) and a pseudo-time trajectory transcriptomic result. In the end, we made recommendations for filtering strategies of cells and genes based on simulation results to achieve optimal experimental goals. [ABSTRACT FROM AUTHOR]

Osteoporosis is one of the most common metabolic skeletal diseases, which affects more than 200 million people worldwide, especially elderly and postmenopausal women. One of the main processes of osteoporosis is attenuated bone formation. Abundant evidence has confirmed that overactivated osteoclasts are responsible for the attenuated bone formation. This study aims at identifying novel methylation-associated biomarkers and therapeutic targets in osteoclasts by integrally analyzing methylation profiles and gene expression data. DNA methylation profile and gene expression data were obtained from the Gene Expression Omnibus (GEO) database. Subsequently, we integrated the two sets of data to screen for differentially expressed genes with differential methylation level (DM-DEGs) between osteoclasts and CD14+ monocytes from donors. Then, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to uncover the enriched functions and pathways of identified DM-DEGs. In addition, by combining protein-protein interaction analysis and receiver-operator characteristic analysis, we finally identified four hub DM-DEGs. Gene Set Enrichment Analysis was utilized to validate and investigate the potential biological functions of the four hub DM-DEGs. Finally, Real-time quantitative PCR (QPCR) was performed to validate the mRNA expression level of the four identified hub DM-DEGs during osteoclast differentiation. CCRL2, CCL18, C1QB, and SELL were highly correlated with osteoclastic differentiation and osteoporosis phenotype. QPCR revealed that the expression of CCRL2, CCL18, and C1QB was increased during osteoclast differentiation, whereas the expression of SELL was decreased. The present study indicated a connection between gene expression and DNA methylation during osteoclast differentiation and that four hub DM-DEGs in osteoclastogenesis and osteoporosis pathogenesis might be potential candidates for intensive research and therapeutic targets for the treatment of osteoporosis. [ABSTRACT FROM AUTHOR]

The beef fatty acid (FA) profile has the potential to impact human health, and displays polygenic and complex features. This study aimed to identify the transcriptomic FA profile in the longissimus thoracis muscle in Nellore beef cattle finished in feedlot. Forty‐four young bulls were sampled to assess the beef FA profile by considering 14 phenotypes and including differentially expressed genes (DEG), co‐expressed (COE), and differentially co‐expressed genes (DCO) analyses. All samples (n = 44) were used for COE analysis, whereas 30 samples with extreme phenotypes for the beef FA profile were used for DEG and DCO. A total of 912 DEG were identified, and the polyunsaturated (n = 563) and unsaturated ω‐3 (n = 346) FA sums groups were the most frequently observed. The COE analyses identified three modules, of which the blue module (n = 1776) was correlated with eight of 14 FA phenotypes. Also, 759 DCO genes were listed, and the oleic acid (n = 358) and monounsaturated fatty acids sum (n = 120) were the most frequent. Furthermore, 243 and 13, 319 and seven, and 173 and 12 gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were enriched respectively for the DEG, COE, and DCO analyses. Combining the results, we highlight the unexplored GIPC2, ASB5, and PPP5C genes in cattle. Besides LIPE and INSIG2 genes in COE modules, the ACSL3, ECI1, DECR2, FITM1, and SDHB genes were signaled in at least two analyses. These findings contribute to understand the genetic mechanisms underlying the beef FA profile in Nellore beef cattle finished in feedlot. [ABSTRACT FROM AUTHOR]

Introduction: Spermatozoa cryopreservation is an important technique to preserve fertility for males. This study aimed at exploring the stability of epigenetics information in human spermatozoa, manipulated by two different technologies, freezing and vitrification. Methods: Spermatozoa samples were distributed into three groups: 1. Fresh spermatozoa (control group), 2. Frozen spermatozoa, 3. Vitrified spermatozoa. Epigenetic differences of fresh and cryopreserved spermatozoa were evaluated using high-throughput RNA sequencing. Results: Differentially expressed genes (DEGs) in frozen (1103 genes) and vitrified (333 genes) spermatozoa were evaluated. The bioinformatical analysis identified 8 and 15 significant pathways in groups of frozen and vitrified spermatozoa, respectively. The majority of these pathways are most relevant to immune and infectious diseases. The DEGs of the fertilization process are not detected during vitrification. The freezing process induces more down-regulation of genes and is relevant to apoptosis changes and immune response. Conclusion: Cryopreservation of human spermatozoa is an epigenetically safe method for male fertility preservation. Cryoprotectant-free vitrification can induce more minor biological changes in human spermatozoa, in comparison with conventional freezing. [ABSTRACT FROM AUTHOR]

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Wheat powdery mildew, caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), is a destructive disease leading to huge yield losses in production. Host resistance can greatly contribute to the control of the disease. To explore potential genes related to the powdery mildew (Pm) resistance, in this study, we used a resistant genotype YD588 to investigate the potential resistance components and profiled its expression in response to powdery mildew infection. Genetic analysis showed that a single dominant gene, tentatively designated PmYD588 , conferred resistance to powdery mildew in YD588. Using bulked segregant RNA-Seq (BSR-Seq) and single nucleotide polymorphism (SNP) association analysis, two high-confidence candidate regions were detected in the chromosome arm 2B, spanning 453,752,054-506,356,791 and 584,117,809-664,221,850 bp, respectively. To confirm the candidate region, molecular markers were developed using the BSR-Seq data and mapped PmYD588 to an interval of 4.2 cM by using the markers YTU588-004 and YTU588-008. The physical position was subsequently locked into the interval of 647.1–656.0 Mb, which was different from those of Pm6 , Pm33 , Pm51 , Pm52 , Pm63 , Pm64, PmQ , PmKN0816 , MlZec1 , and MlAB10 on the same chromosome arm in its position, suggesting that it is most likely a new Pm gene. To explore the potential regulatory genes of the R gene, 2,973 differentially expressed genes (DEGs) between the parents and bulks were analyzed using gene ontology (GO), clusters of orthologous group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Based on the data, we selected 23 potential regulated genes in the enriched pathway of plant-pathogen interaction and detected their temporal expression patterns using an additional set of wheat samples and time-course analysis postinoculation with Bgt. As a result, six disease-related genes showed distinctive expression profiles after Bgt invasion and can serve as key candidates for the dissection of resistance mechanisms and improvement of durable resistance to wheat powdery mildew. [ABSTRACT FROM AUTHOR]

Introduction: A vaccine for malaria is urgently required but no vaccine has yet shown satisfactory protective efficacy especially for Plasmodium falciparum. P. falciparum infection can progress to cerebral malaria (CM), a neurological syndrome with exceedingly high mortality. Designing effective P. falciparum vaccines require more understanding of the protective immune response while the host immune response to CM and the mechanisms are still elusive. Here, we aim to identify host gene responses to CM and host gene networks associated with CM pathogenesis. Methods: An innovative genomic analysis strategy, the weighted gene coexpression network analysis (WGCNA) combined with differential gene expression analysis, was used in this study. Data for analysis contain 93 whole blood samples, derived from two previous public transcriptome datasets. Results: This approach led to the identification of numerous differentially expressed human transcripts and dozens of coexpression gene modules. We further identified nine key genes, including MBP, SAMSN1, PSMF1, SLC39A8, EIF3B, SMPDL3A, FABP5, SPSB3, and SHARPIN, of which the last four genes were first identified to be related to CM in the present study. Conclusion: The results provided a comprehensive characterization of host gene expression profiles in CM and offered some new insight into malaria vaccine design. These identified key genes could be potential targets or immune modulators for novel therapeutic interventions of CM. [ABSTRACT FROM AUTHOR]

Context: Wool is one of the most important animal fibres for the textile industry, and its diameter directly affects its economic value. However, the molecular mechanisms underlying wool fibre diameter (FD) in sheep have not been fully elucidated. Aims: The aims of the work were to make an initial comparison of skin transcriptomes from sheep with wool of high and low FD, and to identify key genes affecting FD. Methods: High-throughput RNA-Seq technology was employed to explore the skin transcriptome, using three sheep with fine wool (FD <21.0 μm) and three sheep with coarse wool (FD >27.0 μm). Key results: We obtained 28 607 228 bp of clean sequence data, 78.9% (±3.8%) of which uniquely aligned to the reference genome across the six samples. In total, 19 914 mRNA transcripts were expressed (FPKM >0) in the six skin samples, among which were certain well-known genes involved in the skin–hair cycle, such as KRTAP7 - 1 , KRT14 , Wnt10b , Wnt2b , β- catenin and FGF5. Furthermore, 467 genes were significantly differentially expressed between the fine-wool and coarse-wool groups, including 21 genes with upregulated and 446 genes with downregulated expression in the sheep with lower FD. These differentially expressed genes were particularly enriched in the gene ontology processes related to lipid metabolism, skin development, differentiation and immune function (P < 0.05). The biological processes were involved in collagen catabolism, negative regulation of macromolecule metabolism, steroid hormone stimulation and lipid metabolism. A significant Kyoto Encyclopedia of Genes and Genomes pathway involving the metabolism of lipids and lipoproteins was also enriched, revealing that lipid metabolism might be one of the key factors affecting FD. The expression of these differentially expressed genes that were involved in the metabolism of lipids and lipoproteins pathway was verified by quantitative real-time PCR (qPCR). The correlation between the mRNA expression level from qPCR and RNA-Seq data was 0.999 (P < 0.001). Conclusions: The 467 differentially expressed genes, especially those involved in lipid metabolism and immune function, may play key roles in wool follicle metabolism and the expression of wool FD. Implications: This study provided valuable data for future studies aimed at elucidating the mechanisms that underlie wool follicle metabolism and wool FD. The work may also have implications for studies of the human hair follicle. Wool fibre diameter is one of the most important economic traits of sheep wool. In the present study, we discovered 467 differentially expressed genes between fine- and coarse-wool sheep, a large proportion of which are related to lipid metabolism and the immune system. Further study of these genes will help to elucidate mechanisms underlying wool follicle metabolism and wool fibre diameter. [ABSTRACT FROM AUTHOR]

Despite countless papers on plant tissue culture, few have assessed the transcriptional changes that occur in a developing explant from the moment it is cut and plated, and during early stages of development. In this study, the mRNA profile of in vitro potato (Solanum tuberosum L.) plantlets derived from internode stems was assessed via four comparisons during five time intervals (0 h, 24 h, 48 h, 1 week, and 4 weeks) using the Kyoto Encyclopedia of Genes and Genomes (KEGG) classification. After screening KEGG metabolic groups, 35 processes were shown to be either up- or down-regulated. The vast majority (28 processes) were related to growth or development. The expression intensity of 40,430 genes was assessed and 158, 107, 163, and 142 sequences were either significantly up- or down-regulated at 0 h vs 24 h, 24 h vs 48 h, 48 h vs 1 week, and 1 week vs 4 weeks, respectively. A total of 10 DEGs coding for transcription factors were significantly down-regulated, including five ethylene-responsive transcription factors, and two probable WRKY transcription factors. RT-qPCR was used to validate RNA-seq data: Spearman and Pearson correlation coefficients between SeqMonk LFC and RT-qPCR LFC were 0.748 and 0.879, respectively. To the best of our knowledge, this is the first transcriptomic assessment of the changes taking place in the mRNA profile of a developing potato stem explant. [ABSTRACT FROM AUTHOR]

Sesame (Sesamum indicum L.), is rich source of oil, protein and potent antioxidants with wide applications. Molecular approach can be of great use for trait improvement as well more availability for this crop. The present work aims at tissue specific transcriptome profiling along with biochemical pathway analysis and genic region putative marker discovery. We report 14389, 9465 and 5490 DEGs in root, leaf and flower-bud tissues, respectively. 135, 113 and 120 cellular metabolic or signaling pathways having common 118 pathways were found in root-leaf (RL), leaf-flower (LF) and flower-root (FR), respectively. 218, 170 and 180 transcription factors were identified in root, leaf and flower transcriptome, respectively. Among DEGs, microRNA targets predicted were 534, 376 and 173 in root, leaf and flower, respectively. Genic region repeat analysis revealed 379 SSR. Further variant analysis revealed 3371, 5439 and 4975 SNPs and 2257, 2403 and 2411 INDELs in root, leaf and flower, respectively. The present study will aid in understanding the major biochemical pathways operating in different tissues. Genic region putative marker discovery can be a valuable genomic resource for future crop improvement program. [ABSTRACT FROM AUTHOR]

Background: Single-cell RNA-Sequencing (scRNA-Seq) has provided single-cell level insights into complex biological processes. However, the high frequency of gene expression detection failures in scRNA-Seq data make it challenging to achieve reliable identification of cell-types and Differentially Expressed Genes (DEG). Moreover, with the explosive growth of single-cell data using 10x genomics protocol, existing methods will soon reach the computation limit due to scalability issues. The single-cell transcriptomics field desperately need new tools and framework to facilitate large-scale single-cell analysis. Results: In order to improve the accuracy, robustness, and speed of scRNA-Seq data processing, we propose a generalized zero-inflated negative binomial mixture model, "JOINT," that can perform probability-based cell-type discovery and DEG analysis simultaneously without the need for imputation. JOINT performs soft-clustering for cell-type identification by computing the probability of individual cells, i.e. each cell can belong to multiple cell types with different probabilities. This is drastically different from existing hard-clustering methods where each cell can only belong to one cell type. The soft-clustering component of the algorithm significantly facilitates the accuracy and robustness of single-cell analysis, especially when the scRNA-Seq datasets are noisy and contain a large number of dropout events. Moreover, JOINT is able to determine the optimal number of cell-types automatically rather than specifying it empirically. The proposed model is an unsupervised learning problem which is solved by using the Expectation and Maximization (EM) algorithm. The EM algorithm is implemented using the TensorFlow deep learning framework, dramatically accelerating the speed for data analysis through parallel GPU computing. Conclusions: Taken together, the JOINT algorithm is accurate and efficient for large-scale scRNA-Seq data analysis via parallel computing. The Python package that we have developed can be readily applied to aid future advances in parallel computing-based single-cell algorithms and research in various biological and biomedical fields. [ABSTRACT FROM AUTHOR]

Previous studies have suggested potential signature genes for lung cancer, however, due to factors such as sequencing platform, control, data selection and filtration conditions, the results of lung cancer-related gene expression analysis are quite different. Here, we performed a meta-analysis on existing lung cancer gene expression results to identify Meta-signature genes without noise. In this study, functional enrichment, protein-protein interaction network, the DAVID, String, TfactS, and transcription factor binding were performed based on the gene expression profiles of lung adenocarcinoma and non-small cell lung cancer deposited in the GEO database. As a result, a total of 574 differentially expressed genes (DEGs) affecting the pathogenesis of lung cancer were identified (207 up-regulated expression and 367 down-regulated expression in lung cancer tissues). A total of 5,093 interactions existed among the 507 (88.3%) proteins, and 10 Meta-signatures were identified: AURKA, CCNB1, KIF11, CCNA2, TOP2A, CENPF, KIF2C, TPX2, HMMR, and MAD2L1. The potential biological functions of Meta-signature DEGs were revealed. In summary, this study identified key genes involved in the process of lung cancer. Our results would help the developing of novel biomarkers for lung cancer. [ABSTRACT FROM AUTHOR]

In this study, we used RNA-seq to analyze the muscle and liver tissues of black carps (Mylopharyngodon piceus) of different growth rates from the same batch to evaluate their growth traits. We have two groups; they are the black carp group with fast-growth rate and the slow-growth rate. A total of 23,132 genes were enriched in the Gene Ontology analysis, and 285 related pathways were found in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The KEGG pathway analysis showed significant differences in the expression of some genes involved in growth- and development-related metabolic pathways such as the FoxO signaling pathway, p53 signaling pathway, PI3K-Akt signaling pathway, apoptosis, TGF-β signaling pathway, and insulin signaling pathway. The numbers of differentially expressed genes in muscle and liver are 1913 and 1775. Nine of the differently expressed genes involved in the different growth traits and accuracy of the transcriptome data were validated using quantitative real-time PCR. We found that the expression levels of some growth-related genes were significantly higher in the fast-growth rate black carps than in the slow-growth rate black carps. The large number of transcriptome sequences obtained in this study has enriched the black carp gene resources, and the obtained differentially expressed genes and related pathway analysis provide valuable information for understanding the growth traits of the black carp. [ABSTRACT FROM AUTHOR]

As an economically important marine seaweed, Pyropia yezoensis can be asexually reproduced via archeospores. However, the molecular mechanism of archeospore formation remains unclear. In this study, we characterized the transcriptomes of two strains of Py. yezoensis, which are strain W′ with abundant archeospores and strain W with scarce archeospores. The 25- and 35-day-old gametophytic blades of both strains were sampled for RNA sequencing. Based on comparative transcriptomic analysis, a large number of differential expressed genes (DEGs) of four pairwise groups between samples were generated. In an effort to identify the genes related to archeospore formation, 415 consensus DEGs reflecting the difference between two strains were investigated. Gene ontology and KEGG analysis revealed that the function for these DEGs was enriched in various processes, such as translation, ribosome assembly, RNA methylation, vesicles assembly, intracellular localization of organelles, and endocytosis. According to functional analysis on 80 selected DEGs, it indicated that genes involved in calcium and MAPK signaling pathway, cytoskeletal movement, and cell wall degradation were related to the formation of archeospores. The accuracy of RNA-seq results was validated by quantitative real-time PCR of 8 selected DEGs. These findings suggest that the molecular mechanism of archeospore formation in Py. yezoensis is sophisticated and our results will serve as an essential foundation for further studies. [ABSTRACT FROM AUTHOR]

The molecular mechanisms of adrenocortical carcinoma (ACC) carcinogenesis and progression remain unclear. In the present study, three microarray datasets from the Gene Expression Omnibus database were screened, which identified a total of 96 differentially expressed genes (DEGs). A protein-protein interaction network (PPI) was established for these DEGs and module analysis was performed using STRING and Cytoscape. A total of eight hub genes were identified from the most significant module; namely, calponin 1 (CNN1), myosin light chain kinase (MYLK), cysteine and glycine rich protein 1 (CSRP1), myosin heavy chain 11 (MYH11), fibulin extracellular matrix protein 2 (EFEMP2), fibulin 1 (FBLN1), microfibril associated protein 4 (MFAP4) and fibulin 5 (FBLN5). The biological functions of these hub genes were analyzed using the DAVID online tool. Changes in the expression of hub genes did not affect overall survival; however, downregulated EFEMP2 decreased disease-free survival. CSRP1 and MFAP4 expression levels were associated with adverse clinicopathological features. In conclusion, although all eight hub genes were downregulated in ACC, they appeared to have important functions in ACC carcinogenesis and progression. Identification of these genes complements the genetic expression profile of ACC and provides insight for the diagnosis, treatment and prognosis of ACC. [ABSTRACT FROM AUTHOR]

Purpose: Bladder cancer is one of the leading causes of cancer death all over the world, and half of patients are diagnosed at advanced stages with poor therapeutic response. Thus, developing new biomarkers for bladder cancer diagnosis and prognosis is urgently needed. Materials and Methods: Bioinformatic and gene ontology (GO) analysis were employed to screen highly upregulated and secretory tumor markers in the TCGA BLCA cohort. IHC in tissue microarray and ELISA in cancer cell culture medium were used to validate the expression of putative biomarkers in bladder cancer. Bisulfite sequencing was used to detect DNA methylation status in the promoter of putative genes. Results: In this study, MMP11 is first identified as one of the most differentially expressed genes (DEGs) in bladder cancer by meta-analysis in a TCGA bladder cancer cohort. The strong upregulation of MMP11 is confirmed at protein levels in both bladder cancer patients and cell lines. Mechanistic studies reveal that MMP11 promoter hypomethylation, but not genomic amplification or mutation, accounts for its enhanced expression in bladder cancer both in vitro and in vivo. Moreover, clinicopathological analysis indicates that MMP11 upregulation is associated with the tumor progression and poor survival in bladder cancer patients. Discussion: These findings suggest that MMP11, as a secretory protein, is a promising biomarker for diagnosis and prognosis in bladder cancer. [ABSTRACT FROM AUTHOR]

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive fungal diseases threatening global wheat production. Host resistance is well known to be the most efficient method to control this disease. However, the molecular mechanism of wheat powdery mildew resistance (Pm) is still unclear. To analyze the molecular mechanism of Pm , we used the resistant wheat cultivar Jimai 23 to investigate its potential resistance components and profiled its expression in response to powdery mildew infection using bulked segregant RNA-Seq (BSR-Seq). We showed that the Pm of Jimai 23 was provided by a single dominant gene, tentatively designated PmJM23 , and assigned it to the documented Pm2 region of chromosome 5DS. 3,816 consistently different SNPs were called between resistant and susceptible parents and the bulked pools derived from the combinations between the resistant parent Jimai23 and the susceptible parent Tainong18. 58 of the SNPs were assigned to the candidate region of PmJM23. Subsequently, 3,803 differentially expressed genes (DEGs) between parents and bulks were analyzed by GO, COG and KEGG pathway enrichment. The temporal expression patterns of associated genes following Bgt inoculation were further determined by RT-qPCR. Expression of six disease-related genes was investigated during Bgt infection and might serve as valuable genetic resources for the improvement of durable resistance to Bgt. [ABSTRACT FROM AUTHOR]

Background: Angioimmunoblastic T-cell lymphoma (AITL) is an aggressive disease. Most cancer diagnoses are determined by anatomical histology. Therefore, many samples are stored in FFPE blocks for H&E staining. However, RNAs extracted from the FFPE block have a high level of fragmentation, making it difficult to perform accurate DEG analysis using RNA sequencing. Objective: To overcome fragmented RNA's drawback in NGS application, we applied the NanoString nCounter® technique of hybridization method that can be used for DEG analysis without PCR amplification. Methods: We characterized the gene expression profiling of AITLs though transcriptome analysis based on the nCounter® PanCancer IO 360™ Panel and NanoString platform. To perform the analysis of differential expression gene (DEG) profiles in AITLs, we compared the NanoString data from eight AITL patients with a healthy control donor. Results: Ninety-one genes were up-regulated and six genes were down-regulated in AITLs compared to control. The Gene Ontology (GO) analysis of 97-DEGs revealed that they were closely related to cytokine, MAPK cascade, leukocyte differentiation, and immune response, suggesting that this affect the immune system. In addition, KEGG analysis revealed that AITL DEGs were found to be highly involved in cytokine–cytokine receptor interaction and PI3K-Akt signaling pathway. Conclusion: We believe that comprehensive multiplex studies, along with NanoString analysis, may be helpful to understand the molecular mechanisms of AITL, including mutations, gene expression, and protein expression studies. [ABSTRACT FROM AUTHOR]

This study investigated natural gas dehydration performance of selected glycols and sales gas characteristics of dehydrated gases with Aspen Hysys. In this study, all the relevant simulations with the selected glycols were conducted with the same scale and parameters, so that their dehydration performance and sales gas characteristics could be compared effectively. In case of circulation rate, lowest water composition was achieved by 99% ethylene-glycol (EG), highest methane composition was obtained by 90% triethylene-glycol (TEG), the highest amount of sales gas obtained by 90% tetraethylene-glycol (TREG), highest LHV (lower heating value) was achieved by 99% diethylene-glycol (DEG), highest HHV (higher heating value) was achieved by 99% DEG, highest total LHV was obtained by 95% TEG and highest total HHV was obtained by 95%-TEG. In case of both contractor pressure and stage number, lowest water composition was achieved by 95% TEG, highest methane composition was obtained by 95% TEG, the highest amount of sales gas obtained by 90% TREG, highest LHV was achieved by 95% TEG, highest HHV was achieved by 99% DEG, highest total LHV was obtained from 95% EG and highest total HHV was obtained by 90% TREG. The pressure and temperature of glycol did not show any effect on any parameter of sales gas. With glycol circulation rate, a similar changing trend of H2O and CH4 composition and amount of sales gas was found for all TEG and TREG components and higher concentration DEG and EG components, although different patterns found for lower concentration DEG and EG. Change of H2O and CH4 composition and amount of sales gas with stage number DEG and EG showed more sensitivity, and for heating values, TREG showed higher sensitivity. EG showed more sensitivity to the parameters with the change of contractor pressure. Although TEG was found as an overall better dehydrator, but its high circulation rate made EG an alternate. [ABSTRACT FROM AUTHOR]

Background: 5-Azacytidine (5-azaC) promotes the development of 'Kyoho' grape berry but the associated changes in gene expression have not been reported. In this study, we performed transcriptome analysis of grape berry at five developmental stages after 5-azaC treatment to elucidate the gene expression networks controlling berry ripening. Results: The expression patterns of most genes across the time series were similar between the 5-azaC treatment and control groups. The number of differentially expressed genes (DEGs) at a given developmental stage ranged from 9 (A3_C3) to 690 (A5_C5). The results indicated that 5-azaC treatment had not very great influences on the expressions of most genes. Functional annotation of the DEGs revealed that they were mainly related to fruit softening, photosynthesis, protein phosphorylation, and heat stress. Eight modules showed high correlation with specific developmental stages and hub genes such as PEROXIDASE 4, CAFFEIC ACID 3-O-METHYLTRANSFERASE 1, and HISTONE-LYSINE N-METHYLTRANSFERASE EZA1 were identified by weighted gene correlation network analysis. Conclusions: 5-AzaC treatment alters the transcriptional profile of grape berry at different stages of development, which may involve changes in DNA methylation. [ABSTRACT FROM AUTHOR]