scholarly journals The muscle development transcriptome landscape of ovariectomized goat

2017 ◽  
Vol 4 (12) ◽  
pp. 171415 ◽  
Author(s):  
Sihuan Zhang ◽  
Han Xu ◽  
Xinfeng Liu ◽  
Qing Yang ◽  
Chuanying Pan ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Muscle Development ◽  
Enrichment Analysis ◽  
Repeat Sequence ◽  
Cdna Libraries ◽  
Polymorphism Analysis ◽  
Rna Seq ◽  
Single Nucleotide ◽  
Almost All ◽  
Go Terms

In practical production, almost all rams and about 50% of ewes are used to fatten. Researchers have proved that ewe ovariectomy could improve the productivity significantly, but the specific molecular mechanism is still unknown. In this study, five independent cDNA libraries (three and two from ovariectomized and normal ewe longissimus dorsi samples, respectively) were constructed to thoroughly explore the global transcriptome, further to reveal how the ovariectomized ewes influence muscle development by Illumina2000 sequencing technology. As a result, 205 358 transcripts and 118 264 unigenes were generated. 15 490 simple sequence repeats (SSRs) were revealed and divided into six types, and the short repeat sequence SSR (monomers, dimers, trimers) was the domain type. Single nucleotide polymorphism analysis found that the number of transition was greater than the number of transversion among the five libraries. Furthermore, 1612 differently expressed genes (DEGs) (Log2fold_change > 1 and p  < 0.05) were revealed between ovariectomized and normal ewe groups, in which 903 genes were expressed commonly in the two groups, and 288 and 421 genes were uniquely expressed in normal and ovariectomized ewe groups, respectively. Gene Ontology (GO) analysis categorized all unigenes into 555 GO terms and 56 DEGs were significantly categorized into 43 GO terms ( p  < 0.05). KEGG enrichment analysis annotated 12 976 genes (containing 137 DEGs) to 86 pathways, among them 24 and 11 DEGs involved in development and reproduction associated pathways, respectively. To validate the reliability of the RNA-seq analysis, 22 candidate DEGs were randomly selected to perform quantitative real-time polymerase chain reaction. The result showed that 9 and 1 genes were significantly and approximately significantly expressed in control and treatment group, respectively, and the results of RNA-seq are believable in this study. Overall, these results were helpful for elucidating the molecular mechanism of muscle development of ovariectomized animals and the application of female ovariectomy in fattening.

scholarly journals Transcriptome Analysis of a Jujube (Ziziphus Jujuba Mill.) Cultivar Response to Heat Stress

2021 ◽  
Author(s):  
Lei Yang ◽  
Juan Jin ◽  
Ding-yu Fan ◽  
Qing Hao ◽  
Jianxin Niu
Keyword(s):  
Gene Ontology ◽  
Heat Stress ◽  
Stress Response ◽  
Heat Resistance ◽  
Molecular Mechanism ◽  
Cdna Libraries ◽  
Biological Processes ◽  
Rna Seq ◽  
Ziziphus Jujuba ◽  
Growth And Reproduction

Abstract Background: Heat stress (HS) is a common stress and influences the growth and reproduction of plant species. We found and bred a putative heat-resistant jujube (Ziziphus jujuba Mill.) cultivar (JHR17) in previous study. Results: In the current study, we made the seedlings of ‘JHR17’ cultivar to be under HS (45°C) for 0, 1, 3, 5 and 7 days, respectively, and the leaf samples (HR0, HR1, HR3, HR5 and HR7) were collected accordingly. Fifteen cDNA libraries from ‘JHR17’ leaves were built with a transcriptome assay. The RNA sequencing (RNA-seq) and transcriptome comparisons were performed, and the results indicated that 1642, 4080, 5160 and 2119 differentially expressed genes (DEGs) were identified in HR1 vs. HR0, HR3 vs. HR0, HR5 vs. HR0 and HR7 vs. HR0, respectively. Gene Ontology (GO) analyses of the DEGs from these comparisons were implemented. Conclusion: It revealed that a series of biological processes, involved in stress response, photosynthesis and metabolism, were enriched successfully, suggesting that lowering or up-regulating these genes of processes might play important roles in response to HS. This study may contribute to understand the molecular mechanism of ‘JHR17’ cultivar response to HS, and be beneficial for developing jujube cultivars to improve heat resistance.

scholarly journals Rearranged zebrafish genomic DNA induces zebrafish mutant after microinjection into fertilized egg and preliminary study of the mechanism

2018 ◽  
Author(s):  
Zheming Cao ◽  
Weidong Ding ◽  
Xuwen Bing ◽  
Jun Qiang ◽  
Pao Xu
Keyword(s):  
Dna Binding ◽  
Genomic Dna ◽  
Binding Proteins ◽  
Hypervariable Region ◽  
Enrichment Analysis ◽  
Dna Binding Proteins ◽  
Repeat Sequence ◽  
Regulatory Sequence ◽  
Kegg Pathways ◽  
Almost All

AbstractGenomic DNA of zebrafish was first digested incompletely with Msp I, and then the fragments were joined to form rearranged genomic DNA. This rearranged genomic DNA was incompletely digested with EcoR I, and the fragments were linked with a long adaptor. Two primers (Gmprimer1 and Gmprimer2) were designed according to the adaptor sequence for two-step amplification. The Gmprimer1-amplified products were microinjected into fertilized zebrafish eggs after purification and a red flesh mutant was observed among 42 surviving zebrafish. We obtained several introduced sequences by two-step amplification. The second set of Gmprimer2-amplified products were purified and microinjected into fertilized zebrafish eggs; all 37 surviving fish were red flesh mutants. We found that the largest amplified band from the mutant from the first microinjection was also present in the amplified pattern from six mutants from the second microinjection. The length of the sequence was 2,565 bp, but it did not encode any proteins. Microinjecting this sequence into fertilized zebrafish eggs produced the red flesh mutant. The sequences differed slightly among different individuals from the second microinjection. Most regions of these sequences were the same, with the exception of a hypervariable region. We mixed 10 such sequences equally and microinjected them into zebrafish zygotes; the findings showed that most zygotes died and the surviving zebrafish were almost all mutants. By genome walking, we found that the site of insertion of the fragment was the same, beginning at position 41,365,003 of the eighth chromosome, and that downstream of the introduced fragment is a conservative sequence of 6,536 bp (named Cao-sequence), starting from a small reverse repeat sequence, not encoding any gene, nor similar to any known regulatory sequence. It has 322 homologous sequences in the zebrafish genome, which are distributed in all chromosomes. We designed two primers within Cao-sequence and several primers specific for different locations upstream of it. Compared with normal zebrafish, we found that the amplified patterns of all mutants in Cao-sequence regions changed to varying degrees. To further understand the effect of the introduced sequence on the zebrafish genomes, we selected six mutants for whole-genome resequencing. The results showed that numerous Cao-sequences from these six mutants were partially deleted and the lengths of the deletions was mostly approximately 6,100 bp, being located at the 5′ end of Cao-sequences. Among them, 43 Cao-sequence loci were commonly deleted from the six mutants (with slightly different locations), and the other deletion sites were not identical. We think that different deletion combinations of Cao-sequence may show different mutation characteristics. The tail part from four red flesh mutants and three individuals of wild type were collected for transcriptome sequencing. TopGO analysis showed that the 4 most significant enrichment nodes were sequence specific DNA binding proteins, sequence specific transcription factors, chromatin proteins and zinc binding proteins. The results of KEGG enrichment analysis showed that the top four affected KEGG-pathways were metabolic pathways, oxidative phosphorylation, citrate cycle and 2-oxocarboxylic acid metabolism.We conclude that deletion of Cao-sequence can affect the expression of a series of transcription regulators and specific DNA binding proteins, then many basic metabolic processes were disturbed which led to mutations.

Requirements for a successful defence reaction by the CRISPR–Cas subtype I-B system

2013 ◽  
Vol 41 (6) ◽  
pp. 1444-1448 ◽  
Author(s):  
Britta Stoll ◽  
Lisa-Katharina Maier ◽  
Sita J. Lange ◽  
Jutta Brendel ◽  
Susan Fischer ◽  
...  
Keyword(s):  
Genetic Material ◽  
Repeat Sequence ◽  
Current Data ◽  
Rna Seq ◽  
Defence Mechanisms ◽  
Stem Loop ◽  
Defence Reaction ◽  
Molecular Approaches ◽  
Stem Loop Structure ◽  
Almost All

Uptake of foreign mobile genetic elements is often detrimental and can result in cell death. For protection against invasion, prokaryotes have developed several defence mechanisms, which take effect at all stages of infection; an example is the recently discovered CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) immune system. This defence system directly degrades invading genetic material and is present in almost all archaea and many bacteria. Current data indicate a large variety of mechanistic molecular approaches. Although almost all archaea carry this defence weapon, only a few archaeal systems have been fully characterized. In the present paper, we summarize the prerequisites for the detection and degradation of invaders in the halophilic archaeon Haloferax volcanii. H. volcanii encodes a subtype I-B CRISPR–Cas system and the defence can be triggered by a plasmid-based invader. Six different target-interference motifs are recognized by the Haloferax defence and a 9-nt non-contiguous seed sequence is essential. The repeat sequence has the potential to fold into a minimal stem–loop structure, which is conserved in haloarchaea and might be recognized by the Cas6 endoribonuclease during the processing of CRISPR loci into mature crRNA (CRISPR RNA). Individual crRNA species were present in very different concentrations according to an RNA-Seq analysis and many were unable to trigger a successful defence reaction. Recognition of the plasmid invader does not depend on its copy number, but instead results indicate a dependency on the type of origin present on the plasmid.

scholarly journals N-trans-Feruloyloctopamine Wakes Up BBC3, DDIT3, CDKN1A, and NOXA Signals to Accelerate HCC Cell Apoptosis

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Bin Ma ◽  
Jing Li ◽  
Wen-Ke Yang ◽  
Mei-Gui Zhang ◽  
Xiao-Dong Xie ◽  
...  
Keyword(s):  
Tumor Cell ◽  
Cell Apoptosis ◽  
Enrichment Analysis ◽  
The Novel ◽  
Rna Seq ◽  
Flow Cytometry Data ◽  
Huh7 Cells ◽  
Proliferation And Apoptosis ◽  
Go Terms ◽  
Cell Analyzer

N-trans-Feruloyloctopamine (FO), a natural compound, was reported in our previous study to inhibit a tumor cell malignant phenotype by AKT- and EMT-related signals and might be used as a promising drug for HCC treatment. However, the specific targets and detailed mechanisms still need to be clarified. Screening with RNA-Seq in Huh7 cells treated with FO revealed that 317 genes were modulated, of which 188 genes were upregulated and 129 genes were downregulated. Real-time cell analyzer and flow cytometry data reveal that tumor cell proliferation and apoptosis were impacted by FO. DAVID bioinformatic data showed that most of the biological process GO terms are related to proliferation and apoptosis. KEGG enrichment analysis showed that FO mainly regulates PI3K-AKT- and apoptosis-related signals, in which BBC3, DDIT3, NOXA, and CDKN1A on the surface serve as the novel targets of FO inducing HCC cell apoptosis. The result implied that FO might exacerbate HCC cell apoptosis by regulating BBC3, DDIT3, CDKN1A, and NOXA signals. The obstacle effect of FO can provide new targets and new credibility for the treatment of liver cancer.

scholarly journals Phenotypic Resemblance to Neuropsychiatric Disorder and Altered mRNA Profiles in Cortex and Hippocampus Underlying IL15Rα Knockout

2021 ◽  
Vol 14 ◽  
Author(s):  
Yi He ◽  
Yuxin Yu ◽  
Yanan Li ◽  
Weicheng Duan ◽  
Zuoli Sun ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Control Group ◽  
Rna Seq ◽  
Skeletal Muscle Development ◽  
Altered Expression ◽  
Y Maze

BackgroundPrevious studies of the functions of IL15Rα have been limited to immune activities and skeletal muscle development. Immunological factors have been identified as one of the multiple causes of psychosis, and neurological symptoms have been described in IL15Rα knockout (KO) mice. Seeking to explore possible mechanisms for this in the IL15Rα–/– mouse brain, we analyzed gene expression patterns in the cortex and hippocampus using the RNA-seq technique.MethodsIL15Rα KO mice were generated and littermate wildtype (WT) mice were used as a control group. A Y-maze was used to assess behavior differences between the two groups. The cortex and hippocampus of 3-month-old male mice were prepared and RNA-seq and transcriptome analysis were performed by gene set enrichment analysis (GSEA).ResultsCompared with the WT group, IL15Rα KO animals showed higher speed in the novel arm and more entrance frequency in the old arm in the Y-maze experiment. GSEA indicated that 18 pathways were downregulated and 13 pathways upregulated in both cortex and hippocampus from the GO, KEGG, and Hallmark gene sets. The downregulated pathways formed three clusters: respiratory chain and electron transport, regulation of steroid process, and skeletal muscle development.ConclusionIL15Rα KO mice exhibit altered expression of multiple pathways, which could affect many functions of the brain. Lipid biosynthesis and metabolism in the central nervous system (CNS) should be investigated to provide insights into the effect of IL15Rα on psychosis in this murine model.

scholarly journals Transcriptome profiling of laser-captured germ cells and functional characterization of zbtb40 during 17alpha-methyltestosterone-induced spermatogenesis in orange-spotted grouper (Epinephelus coioides)

2019 ◽  
Author(s):  
Xi Wu ◽  
Yang Yang ◽  
Chaoyue Zhong ◽  
Yin Guo ◽  
Shuisheng Li ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Germ Cells ◽  
Cellular Localization ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Cdna Libraries ◽  
Epinephelus Coioides ◽  
Rna Seq ◽  
Hormone Metabolism ◽  
Male Germ Cells

Abstract Background: Spermatogenesis is an intricate process regulated by a finely organized network. The orange-spotted grouper (Epinephelus coioides) is a protogynous hermaphroditic fish, but the regulatory mechanism of its spermatogenesis is not well-understood. In the present study, transcriptome sequencing of the male germ cells isolated from orange-spotted grouper was performed to explore the molecular mechanism underlying spermatogenesis. Results: In this study, the orange-spotted grouper was induced to change sex from female to male by 17alpha-methyltestosterone (MT) implantation. During the spermatogenesis, male germ cells (spermatogonia, spermatocytes, spermatids, and spermatozoa) were isolated by laser capture microdissection. Transcriptomic analysis for the isolated cells was performed. A total of 244,984,338 clean reads were generated from four cDNA libraries. Real-time PCR results of 13 genes related to sex differentiation and hormone metabolism indicated that transcriptome data are reliable. RNA-seq data showed that the female-related genes and genes involved in hormone metabolism were highly expressed in spermatogonia and spermatozoa, suggesting that these genes participate in the spermatogenesis. Interestingly, the expression of zbtb family genes showed significantly changes in the RNA-seq data, and their expression patterns were further examined during spermatogenesis. The analysis of cellular localization of Eczbtb40 and the co-localization of Eczbtb40 and Eccyp17a1 in different gonadal stages suggested that Eczbtb40 might interact with Eccyp17a1 during spermatogenesis. Conclusions: For the first time, our study investigated the transcriptome of the male germ cells from orange-spotted grouper, and identified functional genes, GO terms, and KEGG pathways involved in spermatogenesis. Furthermore, Eczbtb40 was first characterized and predicted the role during spermatogenesis. These data will contribute to future studies on the molecular mechanism of spermatogenesis in teleosts.

scholarly journals Neoadjuvant chemoradiation alters biomarkers of anticancer immunotherapy responses in locally advanced rectal cancer

2021 ◽  
Vol 9 (3) ◽  
pp. e001610
Author(s):  
Incheol Seo ◽  
Hye Won Lee ◽  
Sang Jun Byun ◽  
Jee Young Park ◽  
Hyeonji Min ◽  
...  
Keyword(s):  
Rectal Cancer ◽  
Locally Advanced ◽  
Enrichment Analysis ◽  
Advanced Rectal Cancer ◽  
Locally Advanced Rectal Cancer ◽  
Neoadjuvant Chemoradiation ◽  
Cytolytic Activity ◽  
Gene Set Enrichment Analysis ◽  
Preoperative Treatment ◽  
Rna Seq

BackgroundNeoadjuvant chemoradiation therapy (CRT) is a widely used preoperative treatment strategy for locally advanced rectal cancer (LARC). However, a few studies have evaluated the molecular changes caused by neoadjuvant CRT in these cancer tissues. Here, we aimed to investigate changes in immunotherapy-related immunogenic effects in response to preoperative CRT in LARC.MethodsWe analyzed 60 pairs of human LARC tissues before and after irradiation from three independent LARC cohorts, including a LARC patient RNA sequencing (RNA-seq) dataset from our cohort and GSE15781 and GSE94104 datasets.ResultsGene ontology analysis showed that preoperative CRT significantly enriched the immune response in LARC tissues. Moreover, gene set enrichment analysis revealed six significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways associated with downregulated genes, including mismatch repair (MMR) genes, in LARC tissues after CRT in all three cohorts. Radiation also induced apoptosis and downregulated various MMR system-related genes in three colorectal cancer cells. One patient with LARC showed a change in microsatellite instability (MSI) status after CRT, as demonstrated by the loss of MMR protein and PCR for MSI. Moreover, CRT significantly increased tumor mutational burden in LARC tissues. CIBERSORT analysis revealed that the proportions of M2 macrophages and CD8 T cells were significantly increased after CRT in both the RNA-seq dataset and GSE94104. Notably, preoperative CRT increased various immune biomarker scores, such as the interferon-γ signature, the cytolytic activity and the immune signature.ConclusionsTaken together, our findings demonstrated that neoadjuvant CRT modulated the immune-related characteristics of LARC, suggesting that neoadjuvant CRT may enhance the responsiveness of LARC to immunotherapy.

scholarly journals Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

2021 ◽  
Vol 22 (5) ◽  
pp. 2481
Author(s):  
Jodi Callwood ◽  
Kalpalatha Melmaiee ◽  
Krishnanand P. Kulkarni ◽  
Amaranatha R. Vennapusa ◽  
Diarra Aicha ◽  
...  
Keyword(s):  
Heat Stress ◽  
Molecular Mechanisms ◽  
Stomatal Closure ◽  
Enrichment Analysis ◽  
Leaf Size ◽  
Vaccinium Corymbosum ◽  
Climatic Conditions ◽  
Differentially Expressed ◽  
Transcriptomic Changes ◽  
Go Terms

Blueberries (Vaccinium spp.) are highly vulnerable to changing climatic conditions, especially increasing temperatures. To gain insight into mechanisms underpinning the response to heat stress, two blueberry species were subjected to heat stress for 6 and 9 h at 45 °C, and leaf samples were used to study the morpho-physiological and transcriptomic changes. As compared with Vaccinium corymbosum, Vaccinium darrowii exhibited thermal stress adaptation features such as small leaf size, parallel leaf orientation, waxy leaf coating, increased stomatal surface area, and stomatal closure. RNAseq analysis yielded ~135 million reads and identified 8305 differentially expressed genes (DEGs) during heat stress against the control samples. In V. corymbosum, 2861 and 4565 genes were differentially expressed at 6 and 9 h of heat stress, whereas in V. darrowii, 2516 and 3072 DEGs were differentially expressed at 6 and 9 h, respectively. Among the pathways, the protein processing in the endoplasmic reticulum (ER) was the highly enriched pathway in both the species: however, certain metabolic, fatty acid, photosynthesis-related, peroxisomal, and circadian rhythm pathways were enriched differently among the species. KEGG enrichment analysis of the DEGs revealed important biosynthesis and metabolic pathways crucial in response to heat stress. The GO terms enriched in both the species under heat stress were similar, but more DEGs were enriched for GO terms in V. darrowii than the V. corymbosum. Together, these results elucidate the differential response of morpho-physiological and molecular mechanisms used by both the blueberry species under heat stress, and help in understanding the complex mechanisms involved in heat stress tolerance.

scholarly journals Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Joseph Tomlinson ◽  
Shawn W. Polson ◽  
Jing Qiu ◽  
Juniper A. Lake ◽  
William Lee ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Specific Expression ◽  
Single Nucleotide ◽  
Allele Specific Expression ◽  
Detection Tool ◽  
Commercial Broiler ◽  
Significant Phenomenon ◽  
Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

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