Project description:Transcriptome profiling of three models with impaired insulin/IGF1 signaling. 1. Deep sequencing of endogenous mRNA from Caenorhabditis elegans N2 var. Bristol (wildtype) and daf-2(e1370) mutant; 2. Deep sequencing of endogenous mRNA from murine embryonic fibroblasts (MEF) wildtype and irs1-/- knockout; 3. Deep sequencing of endogenous mRNA from murine embryoinic fibroblast (MEF) insr+/- -lox and insr+/- knockout 14 samples examined: C. elegans N2 var. Bristol (wildtype) vs. daf-2(e1370) mutant; MEF wildtype vs. irs1-/- knockout; MEF insr+/- -lox vs. insr +/- knockout
Project description:<p>Paris polyphylla var. yunnanensis is a widely cultivated rhizomatous perennial woody plant known for producing the highly valued steroidal saponins. Steroidal saponins serve as the primary active component and exhibit a variety of pharmacological effects. However, the accumulation of secondary metabolites and the related functional genes involved in plant biosynthesis varies across different developmental stages. In this study, we collected samples of P. polyphylla var. yunnanensis aged 3-8 years for metabolome and transcriptome sequencing analysis. A total of 1510 metabolites and 270.65 Gb of clean data were identified from these samples. This research aims to provide a theoretical foundation for understanding the internal mechanisms governing the accumulation of secondary metabolites and the formation of quality in P. polyphylla var. yunnanensis, thereby establishing a basis for its efficient cultivation and increased saponin yield.</p>
Project description:The major virulence factor of Plasmodium falciparum parasites, PfEMP1 is expressed by a multigene family, termed var genes. Here selection linked integration (SLI) was utilized to modify var genes in P. falciparum parasites to select for parasite populations expressing a single var gene. Bulk RNA was isolated from ring stage parasites of these SLI parasite populations and analyzed with next generation sequencing. The proportion of exon 2 transcripts of var genes normalized to transcripts per million was determined per cell line to confirm the predominant expression of the desired var gene.
Project description:We have investigated the effect of RRP6 depletion on the transcriptome of S2 cells using Illumina deep RNA sequencing. We have also carried out Illumina ChIP-seq analysis of RRP6 genome occupancy in control S2 cells (GFP-KD) and in cells depleted of SU(VAR)3-9.
Project description:Epigenetic regulation of mutually exclusive transcription within the var gene family is important for infection and pathogenesis of the malaria parasite Plasmodium falciparum. var genes are kept transcriptionally silent via heterochromatic clusters located at the nuclear periphery; however, only a few proteins have been shown to play a direct role in var gene transcriptional regulation. Importantly, the chromatin components that contribute to var gene nuclear organization remain unknown. Here, we adapted a CRISPR-based immunoprecipitation-mass spectrometry approach for de novo identification of factors associated with specific transcriptional regulatory sequences of var genes. Tagged, catalytically inactive Cas9 (“dCas9”) was targeted to var gene promoters or introns, cross-linked, and immunoprecipitated with all DNA, proteins, and RNA associated with the targeted locus. Chromatin immunoprecipitation followed by sequencing demonstrated that genome-wide dCas9 binding was specific and robust. Proteomics analysis of dCas9-immunoprecipitates identified specific proteins for each target region, including known and novel factors such as DNA binding proteins, chromatin remodelers, and structural proteins. We also demonstrate the ability to immunoprecipitate RNA that is closely associated to the targeted locus. Our CRISPR/dCas9 study establishes a new tool for targeted purification of specific genomic loci and advances understanding of virulence gene regulation in the human malaria parasite.
Project description:Transcriptome profiling of three models with impaired insulin/IGF1 signaling. 1. Deep sequencing of endogenous mRNA from Caenorhabditis elegans N2 var. Bristol (wildtype) and daf-2(e1370) mutant; 2. Deep sequencing of endogenous mRNA from murine embryonic fibroblasts (MEF) wildtype and irs1-/- knockout; 3. Deep sequencing of endogenous mRNA from murine embryoinic fibroblast (MEF) insr+/- -lox and insr+/- knockout Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
Project description:Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars, B. juncea and B. nigra, for salinity tolerance. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52. We report transcriptome sequencing of two-weeks-old seedlings of B. juncea var. CS52 under normal growth conditions (CTRL) and in response to salinity stress (SS) using Illumina paired-end sequencing
Project description:<p>Objective:</p><p>Metabolic associated fatty liver disease (MAFLD) affects approximately 25% of the global population, posing a serious threat to public health, and its pathogenesis remains largely unknown. Gut fungi play a significant role in the development of liver diseases, but the gut microbial community and its functions in MAFLD patients are not yet clear.</p><p>Methods:</p><p>We performed fungal ITS sequencing on fecal samples from 107 MAFLD patients and 120 healthy control (HC), matched for region, ethnicity, age, and sex. A high-fat diet-induced MAFLD mouse model was established and multi-omics techniques such as Liver transcriptome sequencing, qPCR, Western blot, and immunofluorescence were employed to validate the molecular mechanisms of key gut fungi involved in MAFLD. </p><p>Results:</p><p>MAFLD patients exhibited reduced species richness and diversity compared to HC. The gut microbiome of MAFLD patients was characterized by an increase in the harmful fungal genus Rhizopus, specifically the harmful fungi Rhizopus microsporus var. rhizopodiformis and Rhizopus microsporus var. chinensis, which positively correlated with the degree of steatosis and BMI. Transplantation of fecal microbiota from MAFLD subjects into ABX mice led to the onset of MAFLD-like symptoms, whereas B amphotericin (AMP) administration alleviated disease progression. Gavage with Rhizopus microsporus var. rhizopodiformis significantly exacerbates gut microbiota dysbiosis and metabolic disorders, disrupted the intestinal barrier and activated liver SREBP-1c, thereby upregulating key lipid synthesis enzymes ACC1 and FASN. This activation occurred through a pro-inflammatory cascade involving the liver macrophage LPS-TLR4-NF-κB axis, amplification of inflammatory signals, and neutrophil degranulation.</p><p>Conclusion:</p><p>Rhizopus microsporus var. rhizopodiformis promotes hepatic lipid synthesis by upregulating hepatic neutrophil degranulation and facilitating SREBP-1c activation pathway.</p>
Project description:<p>Objective:</p><p>Metabolic associated fatty liver disease (MAFLD) affects approximately 25% of the global population, posing a serious threat to public health, and its pathogenesis remains largely unknown. Gut fungi play a significant role in the development of liver diseases, but the gut microbial community and its functions in MAFLD patients are not yet clear.</p><p>Methods:</p><p>We performed fungal ITS sequencing on fecal samples from 107 MAFLD patients and 120 healthy control (HC), matched for region, ethnicity, age, and sex. A high-fat diet-induced MAFLD mouse model was established and multi-omics techniques such as Liver transcriptome sequencing, qPCR, Western blot, and immunofluorescence were employed to validate the molecular mechanisms of key gut fungi involved in MAFLD. </p><p>Results:</p><p>MAFLD patients exhibited reduced species richness and diversity compared to HC. The gut microbiome of MAFLD patients was characterized by an increase in the harmful fungal genus Rhizopus, specifically the harmful fungi Rhizopus microsporus var. rhizopodiformis and Rhizopus microsporus var. chinensis, which positively correlated with the degree of steatosis and BMI. Transplantation of fecal microbiota from MAFLD subjects into ABX mice led to the onset of MAFLD-like symptoms, whereas B amphotericin (AMP) administration alleviated disease progression. Gavage with Rhizopus microsporus var. rhizopodiformis significantly exacerbates gut microbiota dysbiosis and metabolic disorders, disrupted the intestinal barrier and activated liver SREBP-1c, thereby upregulating key lipid synthesis enzymes ACC1 and FASN. This activation occurred through a pro-inflammatory cascade involving the liver macrophage LPS-TLR4-NF-κB axis, amplification of inflammatory signals, and neutrophil degranulation.</p><p>Conclusion:</p><p>Rhizopus microsporus var. rhizopodiformis promotes hepatic lipid synthesis by upregulating hepatic neutrophil degranulation and facilitating SREBP-1c activation pathway.</p>
Project description:We have investigated the effect of RRP6 depletion on the transcriptome of S2 cells using Affymetrix whole-genome tiling arrays. We have also carried out Illumina ChIP-seq analysis of RRP6 genome occupancy in control S2 cells (GFP-KD) and in cells depleted of SU(VAR)3-9.