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Integrated omics studies delineate the formation and dynamics of lipid droplets in Rhodococcus opacus PD630 for biofuel feedstock

ABSTRACT: Purpose: To delineate mechanisms underlying lipid storage in LDs, we compared the transcriptomes of cells cultivated under three lipid-accumulating conditions. Methods: PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform. The sequence reads were mapped by using Bowtie followed by Cufflinks. Results: Most genes were either expressed under all three conditions (6,759 genes) or under at least one condition (7,770 genes), but 1,177 genes were not expressed under any of these conditions. We observed a marked response 3 h after cells were transferred from NB to MSM; 56.99% of the genes were up-regulated and 30.32% were down-regulated, with 21.15% being up-regulated more than 2-fold and 9.36% being down-regulated more than 2-fold Conclusions: Genes in category J (translation, ribosomal structure and biogenesis) were significantly up-regulated (p-value 5.05E-20, two-tailed Chi-square test), while genes in category K (transcription), G (carbohydrate transport and metabolism) and C (energy production and conversion) were down-regulated (p-values: 6.0E-07, 8.08E-06 and 4.56E-05, respectively, two-tailed Chi-square test). Increased expression of ribosomal proteins is consistent with number of genes (56.99%) up-regulated in the MSM3 treatment. This decrease in energy production and conversion is consistent with inhibition of cell division and lipid accumulation in MSM.

ORGANISM(S): Rhodococcus opacus

PROVIDER: GSE42381 | GEO | 2013/11/04

SECONDARY ACCESSION(S): PRJNA181257

REPOSITORIES: GEO

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Integrated omics studies delineate the formation and dynamics of lipid droplets in Rhodococcus opacus PD630 for biofuel feedstock

Project description:Purpose: To delineate mechanisms underlying lipid storage in LDs, we compared the transcriptomes of cells cultivated under three lipid-accumulating conditions. Methods: PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform. The sequence reads were mapped by using Bowtie followed by Cufflinks. Results: Most genes were either expressed under all three conditions (6,759 genes) or under at least one condition (7,770 genes), but 1,177 genes were not expressed under any of these conditions. We observed a marked response 3 h after cells were transferred from NB to MSM; 56.99% of the genes were up-regulated and 30.32% were down-regulated, with 21.15% being up-regulated more than 2-fold and 9.36% being down-regulated more than 2-fold Conclusions: Genes in category J (translation, ribosomal structure and biogenesis) were significantly up-regulated (p-value 5.05E-20, two-tailed Chi-square test), while genes in category K (transcription), G (carbohydrate transport and metabolism) and C (energy production and conversion) were down-regulated (p-values: 6.0E-07, 8.08E-06 and 4.56E-05, respectively, two-tailed Chi-square test). Increased expression of ribosomal proteins is consistent with number of genes (56.99%) up-regulated in the MSM3 treatment. This decrease in energy production and conversion is consistent with inhibition of cell division and lipid accumulation in MSM. PD630 mRNA profiles of 3 different conditions (normal condition and LDs acculation conditions) were generated by deep sequencing, using Solid platform.

2013-11-04 | E-GEOD-42381 | biostudies-arrayexpress

Screen of differential expression genes on bat hibernating regulation

Project description:We report the application of the Illumina/Solexa sequencing-by-synthesis platform to analysis differential expression genes of two key tissues (brain and adipose tissue) during hibernation vs. aroused state, with a hibernating bat species (Myotis ricketti) as model. Total of 12272 genes were identified including 11291 genes in brain and 10691 genes in adipose tissue. Chi-square test indicated that 1943 and 3673 genes in brain and adipose tissues respectively reached the significant level (P â¤ 0.01), including 1243 up-regulated and 700 down-regulated genes in hibernating brain and 2621 up-regulated and 1052 down-regulated genes in hibernating adipose tissue. This study provide opportunity to in-deep analysis the molecular mechanism of hibernating regualtion.

2018-12-31 | GSE29052 | GEO

Viral Microarray - Control Set

Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy.

2010-05-24 | GSE21317 | GEO

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RNA-seq of Mycobacterium smegmatis mc2-155 SMR5 wild-type vs. a pafBC deletion strain under different growth/stress conditions

Project description:The goal of the experiment is to obtain a differential gene expression profile for Mycobacterium smegmatis mc2-155 SMR5 (Msm) wild-type in comparison to a pafBC deletion strain (MSMEG_3888 and MSMEG_3889). In addition, the gene expression is to be analyzed with respect to different growth/stress conditions. Four groups were etablished: (1) Msm wild-type under standard conditions (2) Msm delta-pafBC under standard conditions (3) Msm wild-type treated with mitomycin C (4) Msm delta-pafBC treated with mitomycin C.

2018-06-17 | E-MTAB-6497 | biostudies-arrayexpress

Viral Microarray - Cultured Virus Set

2010-05-24 | E-GEOD-21318 | biostudies-arrayexpress

Viral Microarray - Control Set

2010-05-24 | E-GEOD-21317 | biostudies-arrayexpress

A fluorescent perilipin 2 knock-in mouse model reveals a high abundance of lipid droplets in the developing and adult brain

Project description:Lipid droplets (LDs) are dynamic lipid storage organelles. They are tightly linked to metabolism and can exert protective functions, making them important players in health and disease. Most LD studies in vivo rely on staining methods, providing only a snapshot. We therefore developed a LD-reporter mouse by endogenously labelling the LD coat protein perilipin 2 (PLIN2) with tdTomato, enabling staining-free fluorescent LD visualisation in living and fixed tissues and cells. Here we validate this model under standard and high-fat diet conditions and demonstrate that LDs are highly abundant in various cell types in the healthy brain, including neurons, astrocytes, ependymal cells, neural stem/progenitor cells and microglia. Furthermore, we also show that LDs are abundant during brain development and can be visualized using live-imaging of embryonic slices. Taken together, our tdTom-Plin2 mouse serves as a novel tool to study LDs and their dynamics under both physiological and diseased conditions in all tissues expressing Plin2.

2024-05-15 | GSE267069 | GEO

Cleavage of rTLP and rCHI by Peptidases from Drosophila suzukii Larval (Peptdomics Analysis)

Project description:We produced recombinant TLP and CHI as model thermolabile wine haze proteins and applied a peptidomics strategy to investigate whether D. suzukii larval peptidases were able to digest them under acidic conditions (pH 3.5) typically found in winemaking practices.

2023-05-10 | PXD039025 | Pride

Exploring the genes associated with male sterility mutant (msm) in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq

Project description:The hybrid seed production was performed using the male sterility line, which is an important way of heterosis utilization in Chinese cabbage. A stably inherited male sterile mutant msm was obtained from a Chinese cabbage DH line ‘FT’ using the isolated microspore culture combined with 60Co γ-rays mutagenesis. Compared to the wild type ‘FT’, the msm exhibited completely degenerated stamens and no pollen phenotype, and other characters had no significant difference except for stamen. The genetic analysis indicated that the msm mutant phenotype was controlled by a single recessive nuclear gene. Cytological observation showed that the stamen abortion of msm began at the tetrad period, and tapetum cells were abnormally expanded and highly vacuolated, leading to microspore abortion. Comparative transcriptome analysis on the flower buds of ‘FT’ and msm using RNA-Seq technology revealed a total of 1,653 differentially expressed genes (DEGs). Among which, a large number of genes associated with male sterility were found, including 64 pollen development and pollen tube growth-related genes, 94 pollen wall development-related genes, 11 phytohormone-related genes and 16 transcription factor-related genes, and the overwhelming majority of these genes were down-regulated in the msm vs. ‘FT’ comparison. Furthermore, KEGG pathway analysis indicated that a variety of carbohydrate metabolic and lipid metabolic pathways were significantly enriched, which may be related to pollen abortion. The expression patterns of 24 male sterility-related genes were analyzed using qRT-PCR. In addition, a total of 24,476 single nucleotide polymorphisms and 413,073 insertion-deletion events were specifically detected in msm. These results facilitate to elucidate the regulatory mechanisms of male sterility in Chinese cabbage.

2019-01-23 | GSE125485 | GEO

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