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PRODID:-//Biomedical Mathematics Group - ECPv6.15.20//NONSGML v1.0//EN
CALSCALE:GREGORIAN
METHOD:PUBLISH
X-ORIGINAL-URL:https://www.ibs.re.kr/bimag
X-WR-CALDESC:Events for Biomedical Mathematics Group
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X-PUBLISHED-TTL:PT1H
BEGIN:VTIMEZONE
TZID:Asia/Seoul
BEGIN:STANDARD
TZOFFSETFROM:+0900
TZOFFSETTO:+0900
TZNAME:KST
DTSTART:20210101T000000
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BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20221021T150000
DTEND;TZID=Asia/Seoul:20221021T170000
DTSTAMP:20260426T082529
CREATED:20220930T035045Z
LAST-MODIFIED:20221019T070546Z
UID:6641-1666364400-1666371600@www.ibs.re.kr
SUMMARY:Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level
DESCRIPTION:We will discuss about “Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level”\, David Laloum\, and Marc Robinson-Rechavi\, PLoS computational biology 18.9 (2022): e1010399. \nAbstract: \nMany genes have nycthemeral rhythms of expression\, i.e. a 24-hours periodic variation\, at either mRNA or protein level or both\, and most rhythmic genes are tissue-specific. Here\, we investigate and discuss the evolutionary origins of rhythms in gene expression. Our results suggest that rhythmicity of protein expression could have been favored by selection to minimize costs. Trends are consistent in bacteria\, plants and animals\, and are also supported by tissue-specific patterns in mouse. Unlike for protein level\, cost cannot explain rhythm at the RNA level. We suggest that instead it allows to periodically reduce expression noise. Noise control had the strongest support in mouse\, with limited evidence in other species. We have also found that genes under stronger purifying selection are rhythmically expressed at the mRNA level\, and we propose that this is because they are noise sensitive genes. Finally\, the adaptive role of rhythmic expression is supported by rhythmic genes being highly expressed yet tissue-specific. This provides a good evolutionary explanation for the observation that nycthemeral rhythms are often tissue-specific.
URL:https://www.ibs.re.kr/bimag/event/2022-10-21-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Seoul:20221028T140000
DTEND;TZID=Asia/Seoul:20221028T160000
DTSTAMP:20260426T082529
CREATED:20220930T035148Z
LAST-MODIFIED:20221027T083230Z
UID:6646-1666965600-1666972800@www.ibs.re.kr
SUMMARY:Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19
DESCRIPTION:We will discuss about “Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19”\, Cheng\, Jinyu\, et al.\, Briefings in bioinformatics 22.2 (2021): 988-1005. \nAbstract: \nInferring how gene expression in a cell is influenced by cellular microenvironment is of great importance yet challenging. In this study\, we present a single-cell RNA-sequencing data based multilayer network method (scMLnet) that models not only functional intercellular communications but also intracellular gene regulatory networks (https://github.com/SunXQlab/scMLnet). scMLnet was applied to a scRNA-seq dataset of COVID-19 patients to decipher the microenvironmental regulation of expression of SARS-CoV-2 receptor ACE2 that has been reported to be correlated with inflammatory cytokines and COVID-19 severity. The predicted elevation of ACE2 by extracellular cytokines EGF\, IFN-γ or TNF-α were experimentally validated in human lung cells and the related signaling pathway were verified to be significantly activated during SARS-COV-2 infection. Our study provided a new approach to uncover inter-/intra-cellular signaling mechanisms of gene expression and revealed microenvironmental regulators of ACE2 expression\, which may facilitate designing anti-cytokine therapies or targeted therapies for controlling COVID-19 infection. In addition\, we summarized and compared different methods of scRNA-seq based inter-/intra-cellular signaling network inference for facilitating new methodology development and applications.
URL:https://www.ibs.re.kr/bimag/event/2022-10-28-jc/
LOCATION:B378 Seminar room\, IBS\, 55 Expo-ro Yuseong-gu\, Daejeon\, 34126\, Korea\, Republic of
CATEGORIES:Journal Club
ORGANIZER;CN="Jae Kyoung Kim":MAILTO:jaekkim@kaist.ac.kr
END:VEVENT
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