scholarly journals NemaLife: A structured microfluidic culture device optimized for aging studies in crawling C. elegans

2019 ◽  
Author(s):  
Mizanur Rahman ◽  
Hunter Edwards ◽  
Nikolajs Birze ◽  
Rebecca Gabrilska ◽  
Kendra P. Rumbaugh ◽  
...  
Keyword(s):  
Large Scale ◽  
The Body ◽  
Physiological Data ◽  
Aging Research ◽  
C Elegans ◽  
Age Related ◽  
Technology Platforms ◽  
Aging Studies ◽  
Pharyngeal Pumping ◽  
Culture Maintenance

AbstractCaenorhabditis elegans is a powerful animal model in aging research. Standard longevity assays on agar plates involve the tedious task of picking and transferring animals to prevent younger progeny from contaminating age-synchronized adult populations. Large-scale studies employ progeny-blocking drugs or sterile mutants to avoid progeny contamination, but such manipulations change adult physiology and alter the influence of reproduction on normal aging. Moreover, for some agar growth-based technology platforms, such as automated lifespan machines, reagents such as food or drugs cannot be readily added/removed after initiation of the study. Current microfluidic approaches are well-suited to address these limitations, but in their liquid-based environments animals swim rather than crawl, introducing swim-induced stress in the lifespan analysis. Here we report a simple microfluidic device that we call NemaLife that features: 1) an optimized micropillar arena in which animals can crawl, 2) sieve channels that separate progeny and prevent the loss of adults from the arena during culture maintenance, and 3) ports which allow rapid accessibility to feed the adult-only population and introduce reagents as needed. Culture maintenance and liquid manipulation are performed with simple hand-held syringes to facilitate integration of our technology into general laboratory protocols. Additionally, device geometry and feeding protocols were designed to emulate the body gait, locomotion, and lifespan of animals reared on agar. We validated our approach with longevity analyses of classical aging mutants (daf-2, age-1, eat-2, and daf-16) and animals subjected to RNAi knockdown of age-related genes (age-1 and daf-16). We also showed that healthspan measures such as pharyngeal pumping and tap-induced stimulated reversals can be scored across the lifespan. Overall, the capacity to generate reliable lifespan and physiological data from the NemaLife chip underscores the potential of this device to accelerate healthspan and lifespan investigations in C. elegans.

scholarly journals NemaLife chip: a micropillar-based microfluidic culture device optimized for aging studies in crawling C. elegans

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mizanur Rahman ◽  
Hunter Edwards ◽  
Nikolajs Birze ◽  
Rebecca Gabrilska ◽  
Kendra P. Rumbaugh ◽  
...  
Keyword(s):  
Physiological Stress ◽  
The Body ◽  
Physiological Data ◽  
C Elegans ◽  
Age Related ◽  
Aging Studies ◽  
Standard Plate ◽  
Pharyngeal Pumping ◽  
Culture Maintenance ◽  
Microfluidic Chambers

Abstract In this study, we report a microfluidic device for the whole-life culture of the nematode Caenorhabditis elegans that allows the scoring of animal survival and health measures. This device referred to as the NemaLife chip features: (1) an optimized micropillar arena in which animals can crawl, (2) sieve channels that separate progeny and prevent the loss of adults from the arena during culture maintenance, and (3) ports that allow rapid accessibility for feeding the adult-only population and introducing reagents as needed. The pillar arena geometry was optimized to accommodate the growing body size during culture and emulate the body gait and locomotion of animals reared on agar. Likewise, feeding protocols were optimized to recapitulate longevity outcomes typical of standard plate growth. Key benefits of the NemaLife Chip include eliminating the need to perform repeated manual transfers of adults during survival assays, negating the need for progeny-blocking chemical interventions, and avoiding the swim-induced stress across lifespan in animals reared in liquid. We also show that the culture of animals in pillar-less microfluidic chambers reduces lifespan and introduces physiological stress by increasing the occurrence of age-related vulval integrity disorder. We validated our pillar-based device with longevity analyses of classical aging mutants (daf-2, age-1, eat-2, and daf-16) and animals subjected to RNAi knockdown of age-related genes (age-1 and daf-16). We also showed that healthspan measures such as pharyngeal pumping and tap-induced stimulated reversals can be scored across the lifespan in the NemaLife chip. Overall, the capacity to generate reliable lifespan and physiological data underscores the potential of the NemaLife chip to accelerate healthspan and lifespan investigations in C. elegans.

scholarly journals DISRUPTION OF CPG ISLAND-MEDIATED CHROMATIN ARCHITECTURE AND TRANSCRIPTIONAL HOMEOSTASIS DURING AGING

2019 ◽  
Vol 3 (Supplement_1) ◽  
pp. S208-S208
Author(s):  
Samuel Beck ◽  
Junyeong Lee
Keyword(s):  
Large Scale ◽  
Cpg Island ◽  
Expression Patterns ◽  
Cpg Islands ◽  
Nuclear Lamina ◽  
The Body ◽  
Chromatin Architecture ◽  
Age Related ◽  
Dna Elements ◽  
Computational Analyses

Abstract Aging causes the global disorganization of nuclear chromatin architecture. In a normal young nucleus, silent heterochromatin is associated with the nuclear lamina layer underlying nuclear envelope, thus spatially separated from euchromatin at the nuclear center. Notably, aging causes the disruption of nuclear lamina and the decondensation of associated heterochromatin. However, it is not clearly understood how these changes of chromatin architectures contribute to age-related diseases. Through large-scale computational analyses, we present that CpG islands (CGIs) give important clues to answering this question. CGIs are DNA elements with high Cytosine-phosphate-Guanine dinucleotide frequencies. In human, about 60% of total genes contain CGIs at their promoters (CGI+ genes) and are broadly expressed throughout the body. The other 40% of genes that do not have CGIs (CGI- genes) exhibit tissue-restricted expression patterns. Our results demonstrate that, in normal young nuclei, only CGI- genes can reside within lamina-associated heterochromatin when transcriptionally inactive, while CGI+ genes associate with nuclear central euchromatin even when they are repressed. In parallel, we show that age-associated heterochromatin decondensation can specifically de-repress tissue-specific CGI- genes leading to their uncontrolled expressions. Our results further demonstrate that global misregulation of CGI- genes increases the noise in gene transcription that, in turn, causes the loss of cellular identities during aging. Taken together, our study establishes critical implication of CGI-mediated chromatin architecture in age-associated degenerative changes and loss of tissue homeostasis.

scholarly journals LONGEVITY OVER THE COUNTER: INVESTIGATING THE EFFECTS OF COMMON DIETARY SUPPLEMENTS ON AGING

2019 ◽  
Vol 3 (Supplement_1) ◽  
pp. S102-S103
Author(s):  
Ben Blue ◽  
Elena Vayndorf ◽  
Matt Kaeberlein
Keyword(s):  
Body Wall ◽  
Video Recording ◽  
The Body ◽  
Limiting Factor ◽  
Time Of Death ◽  
Image Capture ◽  
Over The Counter ◽  
C Elegans ◽  
Short Lifespan ◽  
Age Related

Abstract C. elegans has been a workhorse within the field of aging biology for several decades due to its short lifespan, easy culturing, and robust genetic tools. However, the limiting factor in using C. elegans has been that throughput was constrained by the time and effort needed to manually check the worms for signs of life during longitudinal studies. By using the WormBot, a robotic image capture platform, we are able to successfully screen a wide array of compounds for their effects upon C. elegans lifespan. A single WormBot can monitor 144 individual experiments simultaneously and allows for accurate time of death calls. Here we present data generated with the WormBot that includes a screen of compounds from a wide array of natural and synthetic products that are often available as over-the-counter supplements. In order to better examine the effects of these widely-used compounds upon the aging process and an age-associated disease we examined longevity in a wildtype strain of C. elegans as well as an engineered strain that expresses human Aβ protein in the body wall muscle. The age-related pathogenesis of the Aβ-expressing strain is a progressive paralysis that can be halted with treatment of known effectors of Alzheimer’s disease. As such, we screened our battery of compounds with this strain to determine which compounds have a significant affect on delaying Aβ-associated paralysis. Lastly, using the WormBot’s ability to capture video recording, we examine how each compound affects mobility as animals age.

Micro CT-Based Large Scale Finite Element Modeling of Compressive and Torsional Properties of Human Cortical Bone

2007 ◽  
Author(s):  
Yener N. Yeni ◽  
Roger R. Zauel
Keyword(s):  
Cortical Bone ◽  
Bone Tissue ◽  
Large Scale ◽  
Present Note ◽  
Fragility Fractures ◽  
The Body ◽  
Micro Ct ◽  
Tissue Quality ◽  
Age Related ◽  
Torsional Properties

Cortical bone tissue quality is imperative in maintaining the mechanical competence of whole bones, particularly at sites of overuse and age-related fragility fractures where a considerable cortical bone component is present. (Note that cortical bone tissue is more than 80% of the bone in the body [1].)

scholarly journals Cholinergic signalling at the body wall neuromuscular junction couples to distal inhibition of feeding in C. elegans

2021 ◽  
Author(s):  
Patricia G. Izquierdo ◽  
Thibana Thisainathan ◽  
James H. Atkins ◽  
Christian J. Lewis ◽  
John E.H. Tattersall ◽  
...  
Keyword(s):  
Body Wall ◽  
Neuromuscular Junctions ◽  
Model Organism ◽  
Inhibitory Effect ◽  
The Body ◽  
Body Wall Muscle ◽  
Cholinergic Transmission ◽  
Systematic Screening ◽  
C Elegans ◽  
Pharyngeal Pumping

AbstractComplex biological functions within organisms are frequently orchestrated by systemic communication between tissues. In the model organism C. elegans, the pharyngeal and body wall neuromuscular junctions are two discrete structures that control feeding and locomotion, respectively. These distinct tissues are controlled by separate, well-defined neural circuits. Nonetheless, the emergent behaviours, feeding and locomotion, are coordinated to guarantee the efficiency of food intake. We show that pharmacological hyperactivation of cholinergic transmission at the body wall muscle reduces the rate of pumping behaviour. This was evidenced by a systematic screening of the cholinesterase inhibitor aldicarb’s effect on the rate of pharyngeal pumping on food in mutant worms. The screening revealed that the key determinant of the inhibitory effect of aldicarb on pharyngeal pumping is the L-type nicotinic acetylcholine receptor expressed in body wall muscle. This idea was reinforced by the observation that selective hyperstimulation of the body wall muscle L-type receptor by the agonist levamisole inhibited pumping. Overall, our results reveal that body wall cholinergic transmission controls locomotion and simultaneously couples a distal inhibition of feeding.

scholarly journals Some Phenotypic Characteristics of Nematode Caenorhabditis elegans Strains with Defective Functions of the Sestrin (cSesn) gene

2018 ◽  
Vol 11 (2) ◽  
pp. 759-767 ◽  
Author(s):  
A. O. Zeltukhin ◽  
G. V. Ilyinskaya ◽  
A. V. Budanov ◽  
P. M. Chumakov
Keyword(s):  
Caenorhabditis Elegans ◽  
Redox Homeostasis ◽  
Functional Decline ◽  
Extended Period ◽  
Locomotory Activity ◽  
Pumping Rate ◽  
Phenotypic Differences ◽  
C Elegans ◽  
Age Related ◽  
Pharyngeal Pumping

In mammals a small family of genes called Sestrins play important roles in the maintenance of metabolic and redox homeostasis, suggesting that the genes may positively affect the lifespan and counteract the age-related functional decline. The nematode genome contains a single cSesn gene that makes the Caenorhabditis elegans an excellent model for studying functions of the sestrin family. We describe phenotypic differences of worms that have compromised expression of cSesn gene. By comparing three different cSesn-deficient modes with the wild-type C. elegans strain we show that the abrogation of cSesn expression results in an increased body size, an extended period of body growth, a reduces brood size and number of offspring per a single worm, an accelerated decline in muscular functions revealed as a rapid decrease in the pharyngeal pumping rate and in the overall locomotory activity. The results are consistent with the potential roles of cSesn in counteracting the process of aging in C. elegans.

scholarly journals Aging Atlas: a multi-omics database for aging biology

2020 ◽  
Vol 49 (D1) ◽  
pp. D825-D830 ◽  
Author(s):  
◽  
Guang-Hui Liu ◽  
Yiming Bao ◽  
Jing Qu ◽  
Weiqi Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
High Throughput ◽  
Large Scale ◽  
Wide Spectrum ◽  
Molecular Profile ◽  
Aging Research ◽  
Related Data ◽  
Age Related ◽  
Wide Range

Abstract Organismal aging is driven by interconnected molecular changes encompassing internal and extracellular factors. Combinational analysis of high-throughput ‘multi-omics’ datasets (gathering information from genomics, epigenomics, transcriptomics, proteomics, metabolomics and pharmacogenomics), at either populational or single-cell levels, can provide a multi-dimensional, integrated profile of the heterogeneous aging process with unprecedented throughput and detail. These new strategies allow for the exploration of the molecular profile and regulatory status of gene expression during aging, and in turn, facilitate the development of new aging interventions. With a continually growing volume of valuable aging-related data, it is necessary to establish an open and integrated database to support a wide spectrum of aging research. The Aging Atlas database aims to provide a wide range of life science researchers with valuable resources that allow access to a large-scale of gene expression and regulation datasets created by various high-throughput omics technologies. The current implementation includes five modules: transcriptomics (RNA-seq), single-cell transcriptomics (scRNA-seq), epigenomics (ChIP-seq), proteomics (protein–protein interaction), and pharmacogenomics (geroprotective compounds). Aging Atlas provides user-friendly functionalities to explore age-related changes in gene expression, as well as raw data download services. Aging Atlas is freely available at https://bigd.big.ac.cn/aging/index.

scholarly journals Complex Transmission Patterns and Age-Related Dynamics of a Selfish mtDNA Deletion

2019 ◽  
Vol 59 (4) ◽  
pp. 983-993 ◽  
Author(s):  
Jennifer A Sullins ◽  
Anna L Coleman-Hulbert ◽  
Alexandra Gallegos ◽  
Dana K Howe ◽  
Dee R Denver ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Large Scale ◽  
C Elegans ◽  
Mtdna Mutations ◽  
Age Related ◽  
Selfish Element ◽  
Mtdna Deletion ◽  
Natural Isolates ◽  
Compensatory Mutations ◽  
Short Time

Abstract Despite wide-ranging implications of selfish mitochondrial DNA (mtDNA) elements for human disease and topics in evolutionary biology (e.g., speciation), the forces controlling their formation, age-related accumulation, and offspring transmission remain largely unknown. Selfish mtDNA poses a significant challenge to genome integrity, mitochondrial function, and organismal fitness. For instance, numerous human diseases are associated with mtDNA mutations; however, few genetic systems can simultaneously represent pathogenic mitochondrial genome evolution and inheritance. The nematode Caenorhabditis briggsae is one such system. Natural C. briggsae isolates harbor varying levels of a large-scale deletion affecting the mitochondrial nduo-5 gene, termed nad5Δ. A subset of these isolates contains putative compensatory mutations that may reduce the risk of deletion formation. We studied the dynamics of nad5Δ heteroplasmy levels during animal development and transmission from mothers to offspring in genetically diverse C. briggsae natural isolates. Results support previous work demonstrating that nad5Δ is a selfish element and that heteroplasmy levels of this deletion can be quite plastic, exhibiting high degrees of inter-family variability and divergence between generations. The latter is consistent with a mitochondrial bottleneck effect, and contrasts with previous findings from a laboratory-derived model uaDf5 mtDNA deletion in C. elegans. However, we also found evidence for among-isolate differences in the ability to limit nad5Δ accumulation, the pattern of which suggested that forces other than the compensatory mutations are important in protecting individuals and populations from rampant mtDNA deletion expansion over short time scales.

scholarly journals High-throughput imaging of Caenorhabditis elegans aging using collective activity monitoring

2021 ◽  
Author(s):  
Anthony D Fouad ◽  
Matthew A Churgin ◽  
Julia Hayden ◽  
Joyce Xu ◽  
Jeong-Inn Park ◽  
...  
Keyword(s):  
Large Scale ◽  
Imaging System ◽  
Activity Monitoring ◽  
Automated System ◽  
Aging Research ◽  
C Elegans ◽  
Collective Activity ◽  
Large Numbers ◽  
Natural Isolates ◽  
Rate Of Decline

The genetic manipulability and short lifespan of C. elegans make it an important model for aging research. Widely applied methods for measurements of worm aging based on manual observation are labor intensive and low-throughput. Here, we describe the Worm Collective Activity Monitoring Platform (WormCamp), a system for assaying aging in C. elegans by monitoring activity of populations of worms in standard 24-well plates. We show that metrics based on the rate of decline in collective activity can be used to estimate the average lifespan and locomotor healthspan in the population. Using the WormCamp, we assay a panel of highly divergent natural isolates of C. elegans and show that both lifespan and locomotor healthspan display substantial heritability. To facilitate analysis of large numbers of worms, we developed a robotic imaging system capable of simultaneous automated monitoring of activity, lifespan, and locomotor healthspan in up to 2,304 populations containing a total of ~90,000 animals. We applied the automated system to conduct a large-scale RNA interference screen for genes that affect lifespan and locomotor healthspan. The WormCamp system is complementary to other current automated methods for assessing C. elegans aging and is well suited for efficiently screening large numbers of conditions.

scholarly journals A robotic system for high-throughput automated lifespan and phenotyping analysis in C. elegans

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 886-886
Author(s):  
Elena Vayndorf ◽  
Jason Pitt ◽  
Judy Wu ◽  
Emily Chang ◽  
Richard Nguyen ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Nematode Species ◽  
Robotic System ◽  
Model Organisms ◽  
Biological Aging ◽  
Digital Cameras ◽  
C Elegans ◽  
Age Related ◽  
3D Printers

Abstract A goal of gerontology-related research is to develop therapies to improve the healthy period of life by understanding and targeting the molecular hallmarks of biological aging. Much progress has been made toward understanding the genetic and biochemical nature of these hallmarks through studies using simple invertebrate model organisms, such as the nematode Caenorhabditis elegans. Over the past decade, the identification of potential genetic and pharmacological modifiers of lifespan and age-related pathologies in C. elegans and other model organisms has yielded fruitful leads for follow-up investigation. However, such studies are typically time- consuming and labor-intensive. The goal of our work is to automate tasks that require frequent, repeated observations and hours of manual labor to collect and analyze lifespan, motility, and other behavioral data in C. elegans and other nematode models. The advent of affordable high-quality digital cameras, robotics systems, and 3D printers, as well as the decreasing financial and computational costs of image storage and processing, have allowed us to automate data capture and analysis on a large scale. To this end, our group recently developed a tool, we call the WormBot, consisting of an unbiased, high-throughput, automated robotic system and corresponding software, to perform genetic and pharmacological quantification of lifespan and health measures in C. elegans and related nematode species. We will report updates recently made to this system, including significant improvements to hardware, and present screening results from proteasome stimulator drugs known to reduce the accumulation of proteotoxic proteins linked to neurodegenerative diseases and aging.

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