Arey RN et al. (2018) Neuron "Activation of Gq Signaling Enhances Memory Consolidation and Slows Cognitive Decline."

Arey RN, Kauffman A, Kaletsky R, Murphy CT, Stein GM

[Neuron, 2018]

Perhaps the most devastating decline with age is theloss of memory. Therefore, identifying mechanisms to restore memory function with age is critical. Using C.elegans associative learning and memory assays, we identified a gain-of-function G_q signaling pathway mutant that forms a long-term (cAMP response element binding protein [CREB]-dependent) memory following one conditioned stimulus-unconditioned stimulus (CS-US) pairing, which usually requires seven CS-US pairings. Increased CREB activity in AIM interneurons reduces the threshold for memory consolidation through transcription of a set of previously identified "long-term memory" genes. Enhanced G_q signaling in the AWC sensory neuron is both necessary and sufficient for improved memory and increased AIM CREB activity, and activation of G_q specifically inaged animals rescues the ability to form memory. Activation of G_q in AWC sensory neurons non-cell autonomously induces consolidation after one CS-US pairing, enabling both cognitive function maintenance with age and restoration of memory function in animals with impaired memory performance without decreased longevity.

Reis-Rodrigues P et al. (2012) Aging Cell "Proteomic analysis of age-dependent changes in protein solubility identifies genes that modulate lifespan."

Gaman EA, Hughes RE, Czerwieniec G, Vantipalli M, Peters TW, Evani US, Lithgow GJ, Reis-Rodrigues P, Mooney SD, Alavez S, Gibson BW

[Aging Cell, 2012]

While it is generally recognized that misfolding of specific proteins can cause late-onset disease, the contribution of protein aggregation to the normal aging process is less well understood. To address this issue, a mass spectrometry-based proteomic analysis was performed to identify proteins that adopt sodium dodecyl sulfate (SDS)-insoluble conformations during aging in Caenorhabditis elegans. SDS-insoluble proteins extracted from young and aged C.elegans were chemically labeled by isobaric tagging for relative and absolute quantification (iTRAQ) and identified by liquid chromatography and mass spectrometry. Two hundred and three proteins were identified as being significantly enriched in an SDS-insoluble fraction in aged nematodes and were largely absent from a similar protein fraction in young nematodes. The SDS-insoluble fraction in aged animals contains a diverse range of proteins including a large number of ribosomal proteins. Gene ontology analysis revealed highly significant enrichments for energy production and translation functions. Expression of genes encoding insoluble proteins observed in aged nematodes was knocked down using RNAi, and effects on lifespan were measured. 41% of genes tested were shown to extend lifespan after RNAi treatment, compared with 18% in a control group of genes. These data indicate that genes encoding proteins that become insoluble with age are enriched for modifiers of lifespan. This demonstrates that proteomic approaches can be used to identify genes that modify lifespan. Finally, these observations indicate that the accumulation of insoluble proteins with diverse functions may be a general feature of aging.

Zlotkowski K et al. (2013) Chembiochem "Small-molecule-mediated axonal branching in Caenorhabditis elegans."

Siegel D, Pierce-Shimomura J, Zlotkowski K

[Chembiochem, 2013]

An in vivo system for monitoring small-molecule-mediated neuronal branching has been developed by using C. elegans. Growth-promoting compounds can be detected by visual inspection of GFPlabeled cholinergic neurons, as axonal branching occurs following treatment with neurotrophic agents. Investigation of the structure-activity relationship of the neurotrophic natural product clovanemagnolol (1) led us to a comparable chemically edited derivative.

Kumar N et al. (2019) Methods Mol Biol "Using ChIP-Based Approaches to Characterize FOXO Recruitment to its Target Promoters."

Mukhopadhyay A, Kumar N

[Methods Mol Biol, 2019]

Chromatin immunoprecipitation (ChIP) coupled to quantitative real-time PCR (ChIP-qPCR) or Next-Generation Sequencing (ChIP-seq) enables us to study the dynamics of chromatin recruitment of transcription factors (TFs). The popular model system Caenorhabditis elegans has provided us with fundamental understanding of the role of Insulin/IGF-1-like signaling (IIS) in metabolism and aging. The FOXO TF DAF-16 is the major output of the pathway that regulates most of the phenotypes associated with the IIS pathway. Here, we describe a ChIP protocol to study FOXO recruitment dynamics in whole C. elegans extracts. We discuss detailed practical procedures, including optimization, growth, harvesting, formaldehyde fixation, sonication of worms, TF immunoprecipitation for further downstream processing using qPCR as well as NGS for the analysis of FOXO-bound DNA.

Wiuf C et al. (2006) Proc Natl Acad Sci U S A "A likelihood approach to analysis of network data."

Hagberg O, Stumpf MP, Wiuf C, Brameier M

[Proc Natl Acad Sci U S A, 2006]

Biological, sociological, and technological network data are often analyzed by using simple summary statistics, such as the observed degree distribution, and nonparametric bootstrap procedures to provide an adequate null distribution for testing hypotheses about the network. In this article we present a full-likelihood approach that allows us to estimate parameters for general models of network growth that can be expressed in terms of recursion relations. To handle larger networks we have developed an importance sampling scheme that allows us to approximate the likelihood and draw inference about the network and how it has been generated, estimate the parameters in the model, and perform parametric bootstrap analysis of network data. We illustrate the power of this approach by estimating growth parameters for the Caenorhabditis elegans protein interaction network.

Beaudoin F et al. (2000) Biochem Soc Trans "Production of C20 polyunsaturated fatty acids (PUFAs) by pathway engineering: identification of a PUFA elongase component from Caenorhabditis elegans."

Sayanova O, Napier JA, Beaudoin F, Lewis MJ, Michaelson LV, Shewry PR

[Biochem Soc Trans, 2000]

Using a combination of database-mining and functional characterization, we have identified a component of the polyunsaturated fatty acid (PUFA) elongase. Co-expression of this elongating activity with fatty acid desaturases has allowed us to heterologously reconstitute the PUFA biosynthetic pathway. Both these enzymes (desaturases and elongase components) have undergone gene-duplication events which provide a paradigm for the diverged nature of PUFA biosynthetic activities.

Gregory WF et al. (2003) Comp Funct Genomics "Caenorhabditis elegans-applications to nematode genomics."

Gregory WF, Parkinson J

[Comp Funct Genomics, 2003]

The complete genome sequence of the free-living nematode Caenorhabditis elegans was published 4 years ago. Since then, we have seen great strides in technologies that seek to exploit this data. Here we describe the application of some of these techniques and other advances that are helping us to understand about not only the biology of this important model organism but also the entire phylum Nematoda.

Hong RL et al. (2006) Bioessays "Pristionchus pacificus: a well-rounded nematode."

Sommer RJ, Hong RL

[Bioessays, 2006]

Nematodes pervade Earth''s biosphere and occupy innumerable ecological niches. The role of Caenorhabditis elegans as a model for developmental processes has encouraged us to cultivate a second nematode, Pristionchus pacificus, as a comparative counterpoint to address questions in development, behavior and ecology in nematode evolution. We hope that this endeavor, now more than a decade underway, will allow us to project findings onto other comparative models for biological processes. To this end, our laboratory has made an extensive genetic map and mutant screens to understand changes in developmental programs. Recently, we have been capitalizing on the whole genome sequence of P. pacificus to describe more thoroughly the molecular basis for these changes, as well as to better integrate our molecular knowledge with the biodiversity of Pristionchus species. BioEssays 28: 651-659, 2006. (c) 2006 Wiley Periodicals, Inc.

James SA et al. (2016) Sci Rep "XANES: In vivo imaging of metal-protein coordination environments."

de Jonge MD, Jenkins NL, James SA, McColl G, Hare DJ, Bush AI

[Sci Rep, 2016]

We have developed an X-ray absorption near edge structure spectroscopy method using fluorescence detection for visualizing in vivo coordination environments of metals in biological specimens. This approach, which we term fluorescence imaging XANES (XANES), allows us to spatially depict metal-protein associations in a native, hydrated state whilst avoiding intrinsic chemical damage from radiation. This method was validated using iron-challenged Caenorhabditis elegans to observe marked alterations in redox environment.

McGuire SH et al. (2017) J Biol Phys "Gibbs free energy as a measure of complexity correlates with time within C. elegans embryonic development."

McGuire SH, Rietman EA, Tuszynski JA, Siegelmann H

[J Biol Phys, 2017]

We investigate free energy behavior in the nematode Caenorhabditis elegans during embryonic development. Our approach utilizes publicly available gene expression data, which gives us a picture of developmental changes in protein concentration and, resultantly, chemical potential and free energy. Our results indicate a clear global relationship between Gibbs free energy and time spent in development and provide thermodynamic indicators of the large-scale biological events of cell division and differentiation.