iMarmot: an integrative platform for comparative and functional genomics of marmots

Liu, Baoning; Bai, Liang; Yu, Qingqing; Hu, Fang; Wu, Jing; Song, Zhao; Wang, Rong; Wang, Weirong; Tao, Yuanqing; Fan, Jianglin; Liu, Enqi

doi:10.1186/s12864-020-6697-7

Cited by 3 publications

(2 citation statements)

References 33 publications

(38 reference statements)

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“…Subsequently, alignment of clean reads with the mouse reference genome (GRCm38) was conducted utilizing TopHat. Quantification and normalization of gene expression were conducted by Cufflinks in RPKM (reads per million per kilo bases) [ 26 ]. The DESeq software was utilized to analyze DEGs through a comparison between the Ad-GFP and Ad-SFRP4 cohorts [ 27 ].…”

Section: Methodsmentioning

confidence: 99%

SFRP4 Reduces Atherosclerosis Plaque Formation in ApoE Deficient Mice

Guan

Liu

et al. 2023

Cardiology Research and Practice

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Secreted frizzled related protein 4 (SFRP4), a member of the SFRPs family, contributes to a significant function in metabolic and cardiovascular diseases. However, there is not enough evidence to prove the antiatherosclerosis effect of SFRP4 in ApoE knock-out (KO) mice. ApoE KO mice were fed a western diet and injected adenovirus (Ad)-SFRP4 through the tail vein for 12 weeks. Contrasted with the control cohort, the area of atherosclerotic plaque in ApoE KO mice overexpressing SFRP4 was reduced significantly. Plasma high-density lipoprotein cholesterol was elevated in the Ad-SFRP4 group. RNA sequence analysis indicated that there were 96 differentially expressed genes enriched in 10 signaling pathways in the mRNA profile of aortic atherosclerosis lesions. The analysis data also revealed the expression of a number of genes linked to metabolism, organism system, and human disease. In summary, our data demonstrates that SFRP4 could play an important role in improving atherosclerotic plaque formation in the aorta.

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Section: Methodsmentioning

confidence: 99%

SFRP4 Reduces Atherosclerosis Plaque Formation in ApoE Deficient Mice

Guan

Liu

et al. 2023

Cardiology Research and Practice

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“…The Perl script was employed over 0.25% low-quality bases (Phred quality score < 20) or over 10% Ns for trimming the reads with contaminated adapters. The alignment of clean reads with the mouse reference genome (GRCm38) was subsequently performed using TopHat, whereas the quantification and normalization of gene expression were performed by Cufflinks in RPKM (reads per million per kilobases) [ 19 ]. Moreover, DESeq software was used to analyze DEGs and draw a comparison between the Ad-GFP and Ad-C1QL1 cohorts [ 20 ], with the false discovery rate (FDR) being employed to set a significant threshold for the p -value in various tests.…”

Section: Methodsmentioning

confidence: 99%

C1QL1/CTRP14 Is Largely Dispensable for Atherosclerosis Formation in Apolipoprotein-E-Deficient Mice

Guan

Shi

Liu

et al. 2022

JCDD

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The purpose of this study was to investigate the influence of C1QL1 on atherosclerosis as well as the transcriptomic alteration of the aorta. While complement C1ql-like 1 (C1QL1) is one of the C1q/tumor-necrosis-factor-related protein (CTRP) family members, also known as CTRP14, and is synthesized and secreted mainly by the brain and adipose tissues, the functional properties of the C1QL1/CTRP14 protein outside the brain and adipocytes remain, however, unknown. In this regard, apolipoprotein E (ApoE) knockout (KO) mice were fed a Western diet and injected with adenovirus (Ad) green fluorescent protein or Ad-C1QL1 through the tail vein for 12 weeks. In contrast with the control cohort, the area of atherosclerotic plaque in ApoE KO mice overexpressing C1QL1 showed no significant difference, and the RNA sequence revealed that there were only 111 differentially expressed genes (DEGs) enriched in 26 signaling pathways of the mRNA profile in the aortic atherosclerosis lesions. This analysis also revealed the expression of several genes related to metabolism, organismal system, and human diseases such as type II diabetes, which are not associated with the formation of atherosclerosis in the aorta. These findings illustrate that C1QL1 is largely dispensable for atherosclerosis formation in ApoE-deficient mice and does not improve atherosclerotic plaque formation in the aorta.

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Comparative genomic analysis of Halomonas campaniensis wild-type and ultraviolet radiation-mutated strains reveal genomic differences associated with increased ectoine production

Wang

Gao

et al. 2023

Int Microbiol

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Ectoine is a natural amino acid derivative and one of the most widely used compatible solutes produced by Halomonas species that affects both cellular growth and osmotic equilibrium. The positive effects of UV mutagenesis on both biomass and ectoine content production in ectoine-producing strains have yet to be reported. In this study, the wild-type H. campaniensis strain XH26 (CCTCCM2019776) was subjected to UV mutagenesis to increase ectoine production. Eight rounds of mutagenesis were used to generate mutated XH26 strains with different UV-irradiation exposure times. Ectoine extract concentrations were then evaluated among all strains using high-performance liquid chromatography analysis, alongside whole genome sequencing with the PacBio RS II platform and comparison of the wild-type strain XH26 and the mutant strain G8-52 genomes. The mutant strain G8-52 (CCTCCM2019777) exhibited the highest cell growth rate and ectoine yields among mutated strains in comparison with strain XH26. Further, ectoine levels in the aforementioned strain significantly increased to 1.51 ± 0.01 g L−1 (0.65 g g−1 of cell dry weight), representing a twofold increase compared to wild-type cells (0.51 ± 0.01 g L−1) when grown in culture medium for ectoine accumulation. Concomitantly, electron microscopy revealed that mutated strain G8-52 cells were obviously shorter than wild-type strain XH26 cells. Moreover, strain G8-52 produced a relatively stable ectoine yield (1.50 g L−1) after 40 days of continuous subculture. Comparative genomics analysis suggested that strain XH26 harbored 24 mutations, including 10 nucleotide insertions, 10 nucleotide deletions, and unique single nucleotide polymorphisms. Notably, the genes orf00723 and orf02403 (lipA) of the wild-type strain mutated to davT and gabD in strain G8-52 that encoded for 4-aminobutyrate-2-oxoglutarate transaminase and NAD-dependent succinate-semialdehyde dehydrogenase, respectively. Consequently, these genes may be involved in increased ectoine yields. These results suggest that continuous multiple rounds of UV mutation represent a successful strategy for increasing ectoine production, and that the mutant strain G8-52 is suitable for large-scale fermentation applications.

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iMarmot: an integrative platform for comparative and functional genomics of marmots

Cited by 3 publications

References 33 publications

SFRP4 Reduces Atherosclerosis Plaque Formation in ApoE Deficient Mice

SFRP4 Reduces Atherosclerosis Plaque Formation in ApoE Deficient Mice

C1QL1/CTRP14 Is Largely Dispensable for Atherosclerosis Formation in Apolipoprotein-E-Deficient Mice

Comparative genomic analysis of Halomonas campaniensis wild-type and ultraviolet radiation-mutated strains reveal genomic differences associated with increased ectoine production

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