Detecting gene expression in Caenorhabditis elegans DOI Creative Commons
John A. Calarco, Seth R. Taylor, David M. Miller

et al.

Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 18, 2024

Abstract Reliable methods for detecting and analyzing gene expression are necessary tools understanding development investigating biological responses to genetic environmental perturbation. With its fully sequenced genome, invariant cell lineage, transparent body, wiring diagram, detailed anatomy, wide array of tools, Caenorhabditis elegans is an exceptionally useful model organism linking cellular phenotypes. The new techniques in recent years has greatly expanded our ability detect at high resolution. Here, we provide overview C. elegans, including transcripts proteins situ, bulk RNA sequencing whole worms specific tissues cells, single-cell sequencing, high-throughput proteomics. We discuss important considerations choosing among these publicly available online resources data.

Language: Английский

Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution DOI
Tzu‐Chiao Lu, Maria Brbić, Ye-Jin Park

et al.

Science, Journal Year: 2023, Volume and Issue: 380(6650)

Published: June 15, 2023

Aging is characterized by a decline in tissue function, but the underlying changes at cellular resolution across organism remain unclear. Here, we present Fly Cell Atlas, single-nucleus transcriptomic map of whole aging

Language: Английский

Citations

65
Mechanisms of astrocyte aging in reactivity and disease DOI Creative Commons
Holly K. Gildea, Shane A. Liddelow

Molecular Neurodegeneration, Journal Year: 2025, Volume and Issue: 20(1)

Published: Feb. 21, 2025

Normal aging alters brain functions and phenotypes. However, it is not well understood how astrocytes are impacted by aging, nor they contribute to neuronal dysfunction disease risk as organisms age. Here, we examine the transcriptional, cell biology, functional differences in across normal aging. Astrocytes at baseline heterogenous, responsive their environments, critical regulators of microenvironments function. With increasing age, adopt different immune-related senescence-associated states, which relate organelle loss homeostasis maintenance, both autonomously non-cell autonomously. These perturbed states increasingly associated with age-related onset neurodegeneration, suggesting that astrocyte a compelling target for future manipulation prevention disease.

Language: Английский

Citations

1
The neuron-specific IIS/FOXO transcriptome in aged animals reveals regulatory mechanisms of cognitive aging DOI Creative Commons
Yifei Weng, Shiyi Zhou, Katherine Morillo

et al.

eLife, Journal Year: 2024, Volume and Issue: 13

Published: April 8, 2024

Cognitive decline is a significant health concern in our aging society. Here, we used the model organism C. elegans to investigate impact of IIS/FOXO pathway on age-related cognitive decline. The daf-2 Insulin/IGF-1 receptor mutant exhibits extension learning and memory span with age compared wild-type worms, an effect that dependent DAF-16 transcription factor. To identify possible mechanisms by which mutants maintain while worms lose neuronal function, carried out neuron-specific transcriptomic analysis aged animals. We observed downregulation genes upregulation transcriptional regulation neurons. By contrast, exhibit distinct alterations response aging, including stress specific insulin signaling genes. tested roles significantly transcriptionally-changed regulating functions, identifying novel regulators memory. In addition other mechanistic insights, comparison vs young transcriptome revealed new set potentially neuroprotective upregulated; instead simply mimicking state, may enhance resilience accumulation harm take more active approach combat aging. These findings suggest potential mechanism for function offer insights into therapeutic targets

Language: Английский

Citations

6
A panoramic view of cell population dynamics in mammalian aging DOI
Zehao Zhang, Chloe Schaefer,

Weirong Jiang

et al.

Science, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 28, 2024

To elucidate aging-associated cellular population dynamics, we present PanSci , a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, sexes, and genotypes. This comprehensive dataset reveals more than 3,000 unique states 200 cell populations. Our panoramic analysis uncovered organ-, lineage-, sex-specific shifts of dynamics during lifespan progression. Moreover, identify both systematic organ-specific alterations in immune populations associated with aging. We further explored the regulatory roles system on aging pinpointed specific age-related expansions that are lymphocyte dependent. “cell-omics” strategy enhances comprehension lays groundwork for exploring complex networks diseases.

Language: Английский

Citations

5
Considering Caenorhabditis elegans Aging on a Temporal and Tissue Scale: The Case of Insulin/IGF-1 Signaling DOI Creative Commons
Paola Fabrizio,

Allan Alcolei,

Florence Solari

et al.

Cells, Journal Year: 2024, Volume and Issue: 13(3), P. 288 - 288

Published: Feb. 5, 2024

The aging process is inherently complex, involving multiple mechanisms that interact at different biological scales. nematode

Language: Английский

Citations

4
Chromatin and epigenetics in aging biology DOI
Eric Lieberman Greer, Siu Sylvia Lee, Veena Prahlad

et al.

Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: April 9, 2025

Abstract This book chapter will focus on modifications to chromatin itself, how are regulated, and these deciphered by the cell impact aging. In this chapter, we review change with age, examine chromatin-modifying enzymes have been shown regulate aging healthspan, discuss some of epigenetic changes triggered they can lifespan individual its naïve descendants, speculate future directions for field.

Language: Английский

Citations

0
Bridge-Like Lipid Transfer Proteins (BLTPs) in C. elegans: From Genetics to Structures and Functions DOI Creative Commons
Taruna Pandey, Jianxiu Zhang, Bingying Wang

et al.

Contact, Journal Year: 2023, Volume and Issue: 6

Published: Jan. 1, 2023

In eukaryotic cells, lipid transfer can occur at membrane contact sites (MCS) to facilitate the exchange of various lipids between two adjacent cellular organelle membranes. Lipid proteins (LTPs), including shuttle LTP or bridge-like (BLTP), transport MCS and are critical for diverse processes, metabolism, trafficking, cell signaling. BLTPs (BLTP1-5, ATG2 VPS13 family proteins) contain lipid-accommodating hydrophobic repeating β-groove (RBG) domains that allow bulk through MCS. Compared with vesicular LTP, have been only recently identified. Their functions regulatory mechanisms currently being unraveled in model organisms by approaches. this review, we summarize genetics, structural features, biological BLTP genetically tractable organism C. elegans. We discuss our recent studies findings on elegans LPD-3, a prototypical megaprotein ortholog BLTP1, identified evolutionarily conserved multicellular human cells. also highlight areas future research using complementary systems Given emerging links several diseases, Parkinson's disease Alkuraya-Kučinskas syndrome, discovering roles their regulation action should contribute new advances basic biology potential therapeutic development related disorders.

Language: Английский

Citations

3
The landscape of cellular clearance systems across human tissues and cell types is shaped by tissue-specific proteome needs DOI Creative Commons

Ekaterina Vinogradov,

Lior Ravkaie, Bar Edri

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 26, 2024

ABSTRACT Protein clearance is fundamental to proteome health. In eukaryotes, it carried by two highly conserved proteolytic systems, the ubiquitin-proteasome system (UPS) and autophagy-lysosome pathway (ALP). Despite their pivotal role, basal organization of human protein systems across tissues cell types remains uncharacterized. Here, we interrogated this using diverse omics datasets. Relative other protein-coding genes, UPS ALP genes were more widely expressed, encoded housekeeping proteins, essential for growth, in accordance with roles. Most nevertheless differentially expressed tissues, tissue-specific upregulation was associated functions, phenotypes, disease susceptibility. The small subset that stably growth than suggesting acts as a core. Lastly, compared branches proteostasis network. folding closely coordinated yet both less synthesis. Taken together, propose network organized hierarchically tailored needs. This could contribute illuminate tissue-selective phenotypes.

Language: Английский

Citations

0
Cross-Tissue Coordination between SLC Nucleoside Transporters Regulates Reproduction inCaenorhabditis elegans DOI Creative Commons
Youchen Guan, Yong Yu, Shihong Max Gao

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 16, 2024

Abstract Metabolism is fundamental to organism physiology and pathology. From the intricate network of metabolic reactions, diverse chemical molecules, collectively termed as metabolites, are produced. In multicellular organisms, metabolite communication between different tissues vital for maintaining homeostasis adaptation. However, molecular mechanisms mediating these communications remain poorly understood. Here, we focus on nucleosides nucleotides, essential metabolites involved in multiple cellular processes, report pivotal role SLC29A family transporters nucleoside coordination soma germline. Through genetic analysis, discovered that two Caenorhabditis elegans homologs transporters, Equilibrative Nucleoside Transporter ENT-1 ENT-2, act germline intestine, respectively, regulate reproduction. Their knockdown synergistically results sterility. Further single-cell transcriptomic targeted metabolomic profiling revealed ENT double specifically affects genes purine biosynthesis pathway reduces ratio guanosine adenosine levels. Importantly, supplementation into body cavity/pseudocoelom through microinjection rescued sterility caused by knockdown, whereas had no effect. Together, studies support a rate limiting factor control reproduction, uncover previously unknown nucleoside/nucleotide reproductive success, highlight significance SLC-mediated cell-nonautonomous regulating physiology. Author Summary life, involving complex reactions requires well-organized system maintain efficiency. This includes optimal allocation resources dynamic exchange products various compartments within an organism. Solute carriers (SLCs) largest across animal kingdom. our research, investigated how specific SLC collaborate move key tissues. We identified which transporting guanosine, nucleoside, successful reproduction nematode . ENT-2 acts gut export surrounding cavity, while functions import from cavity. When both disrupted, animals experience significant defects. Our study underscores importance coordinated activity health. A breakdown this can result imbalances physiological dysfunction.

Language: Английский

Citations

0
Unraveling aging from transcriptomics DOI
Yuanfang Huang, Sheng Zhu, Shuai Yao

et al.

Trends in Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 1, 2024

Language: Английский

Citations

0