Adams A (1999) Worm Breeder's Gazette "Philadelphia's Northeast High School Worm Project experiment on the space shuttle Discovery"

Adams A

[Worm Breeder's Gazette, 1999]

We recently had a chance to do something only a handful of people have ever done: send an experiment up into space. We sent up an 'experimental' group of dauer larvae on the space shuttle Discovery's ten-day mission. ITA of Exton, PA, granted us a very small space on the shuttle. So we decided on the relatively small C. elegans. We figured since John Glenn was going up into space to see the effects on him, we'd do a similar study. We wanted to see if the conditions of space had any effect on the C. elegans normal 18-24 day life span. With every science experiment there is a control group and an experimental group. The control group of about 1000 worms stayed in Philadelphia at Northeast High School the other 1000 worms were blasted off into orbit October 29, 1998.

Podbilewicz B (1996) European C.elegans Meeting "Cell fusions in pharyngeal muscles, hypodermis, sperm, and ADAMs."

Podbilewicz B

[European C.elegans Meeting, 1996]

Adams JRG et al. (2023) Nat Commun "Nanoscale patterning of collagens in C. elegans apical extracellular matrix."

Adams JRG, Ernst AM, Chisholm AD, Jyo EM, Pooranachithra M, Goncharov A, Jin Y, Kramer JM, Zheng SL, Crew JR

[Nat Commun, 2023]

Apical extracellular matrices (aECMs) are complex extracellular compartments that form important interfaces between animals and their environment. In the adult C. elegans cuticle, layers are connected by regularly spaced columnar structures known as struts. Defects in struts result in swelling of the fluid-filled medial cuticle layer ('blistering', Bli). Here we show that three cuticle collagens BLI-1, BLI-2, and BLI-6, play key roles in struts. BLI-1 and BLI-2 are essential for strut formation whereas activating mutations in BLI-6 disrupt strut formation. BLI-1, BLI-2, and BLI-6 precisely colocalize to arrays of puncta in the adult cuticle, corresponding to struts, initially deposited in diffuse stripes adjacent to cuticle furrows. They eventually exhibit tube-like morphology, with the basal ends of BLI-containing struts contact regularly spaced holes in the cuticle. Genetic interaction studies indicate that BLI strut patterning involves interactions with other cuticle components. Our results reveal strut formation as a tractable example of precise aECM patterning at the nanoscale.

Adams, Kevin et al. (2015) International Worm Meeting "Developing a system for cell-specific isolation of extrachromosomal transgene arrays."

Johnson, Steven, Adams, Kevin, Kempton, Colton

[International Worm Meeting, 2015]

We are seeking to understand how chromatin structure is involved in regulating gene expression. In the lab we have transgenic C. elegans that harbor a transgene composed of a minimal unc-54 enhancer coupled with the myo-2 promoter driving gfp expression [1]. This combination of genetic elements results in not only the expected GFP in the pharynx due to myo-2 pharyngeal expression, but also gfp expression in the body wall muscle cells of the worm, due to the minimal unc-54 enhancer [1]. These worms serve as a genetic model for studying transgene silencing through generational time (see Kempton et al poster) and as a surrogate for studying silencing of gene therapy vectors.To confirm that the genetic silencing we see in this model system is due to chromatin remodeling and nucleosome positioning, we are currently focusing our efforts on developing a method to extract extrachromosomal transgene arrays by building arrays that can be isolated from all native chromatin in a tissue-specific manner using a lacO/LacI system. Briefly, we integrate a multiple-copy lacO-harboring plasmid [2] and a cell-specific LacI-expressing plasmid with our transgene of interest. By immunoprecipitation of LacI bound to our extrachromosomal arrays, we should be able to isolate our chromatin of interest and assay nucleosome positioning and chromatin architecture through biochemical and molecular techniques. The first step in this process is building a body wall muscle-specific lacI plasmid as described in this poster.The development of this system will not only facilitate our examination of chromatin structure and gene regulation described here, but will also be applicable to the isolation and biochemical analysis of any extrachromosomal transgenes in other experimental systems.1) Jantsch-Plunger V. and Fire A., 1994 2) Updike D.L. and Mango S.E. 2006.

Adams JM et al. (2002) Curr Opin Cell Biol "Apoptosomes: engines for caspase activation."

Adams JM, Cory S

[Curr Opin Cell Biol, 2002]

Activation of the caspases that initiate apoptosis typically requires cognate scaffold proteins, including CED-4 in Caenorhabditis elegans, Apaf-1 in mammals and Dark in Drosophila. Each scaffold protein oligomerizes procaspases into a complex called the apoptosome, but the regulation and biological roles of the scaffolds differ. Whereas CED-4 is restrained by the Bcl-2 homologue CED-9, Apaf-1 is inhibited by its WD40 repeat region, until it is activated by cytochrome c, derived from damaged mitochondria. Although Dark also has a WD40 region, its activation does not seem to involve cytochrome c. CED-4 is essential for apoptosis in the worm and Dark for many apoptotic responses in the fly, but the Apaf-1/caspase-9 system probably amplifies rather than initiates the

Adams, Jennifer et al. (2019) International Worm Meeting "Patterning of the extracellular matrix: formation of cuticle struts by BLI collagens."

Zheng, Sherry, Chisholm, Andrew, Goncharov, Alexandr, Adams, Jennifer

[International Worm Meeting, 2019]

The C. elegans cuticle is a complex extracellular matrix, composed primarily of collagen proteins as well as many non-collagenous proteins and lipids. The adult cuticle consists of multiple layers, including an electron-lucent medial layer about 200 nm thick containing 'struts' oriented orthogonally to the cuticle plane that connect the outer (cortical) and inner (basal) layers. Struts appear as electron-dense columns in a roughly hexagonal array with a lateral spacing of approximately 300 nm, suggesting a mechanism that distributes struts evenly. Strut patterning is also closely connected with that of the underlying epidermal cytoskeleton. We are interested in struts as an example of a highly ordered extracellular matrix, and have set about dissection of strut biogenesis. A classical set of mutants display cuticle blistering (Bli) phenotypes; ultrastructural analysis supports the hypothesis that these reflect disruption of strut formation and separation of cortical and basal cuticle layers. Indeed, prior work by Jim Kramer's lab (personal communication) identified bli-1 and bli-2 as encoding cuticle collagens, and bli-6 was identified as a collagen by the Hodgkin lab. We have undertaken a comprehensive molecular genetic analysis of bli-1, bli-2, and bli-6. Loss of function in either bli-1 or bli-2 results in similar Bli phenotypes, whereas only gain of function mutations in bli-6 cause blisters. bli-1 encodes the largest C. elegans cuticle collagen, whereas bli-2 and bli-6 are more typical collagens. We generated GFP knock-ins to visualize these BLI proteins. BLI-1 and BLI-2 localize to cuticle puncta likely corresponding to struts, consistent with earlier findings from the Kramer lab on BLI-1, whereas BLI-6::GFP appears to localize to cortical and basal layers of the cuticle. We are performing molecular epistasis analysis to explore the order of assembly of the BLI collagens. We are also examining genetic interactions that affect the Bli phenotype, and are investigating additional bli mutants to identify more factors involved in strut biogenesis.

Coates D et al. (2000) European Worm Meeting "The ADAMs family of C. elegans: what will the new members do?"

Coates D, Daulby J, Hooper NM, Hope IA

[European Worm Meeting, 2000]

ADAMs are a family of integral membrane glycoproteins containing a disintegrin and a metalloprotease domain. The physiological roles of the majority of ADAMs have yet to be elucidated, however some mammalian ADAMs are known to be involved in many diverse processes including sperm migration, sperm-egg binding and fusion, myoblast fusion, the processing of adhesion molecules, cytokines, cytokine receptors and extracellular protein domains, and in neural development. In C. elegans ADAMs are thought to be involved in cell fusion events in sperm and in epithelial cells (ADM-1), in early embryonic development (ADM-2) and in vulval development (SUP-17). In addition to these membrane anchored proteins C. elegans also has soluble ADAM-like proteases, for example GON-1, which plays an essential role in gonadal morphogenesis. We have identified four novel ADAM-like sequences in C. eleganswhich encode a TNFa converting enzyme (TACE) homologue and three soluble ADAM-like proteinases, and our aim is to determine the precise functions of these proteins. Initially we will examine their cellular location with reporter gene constructs and assess the importance of these proteinases by generating gene knockout mutants. We are also interested in finding out what the substrates of these ADAMs are and will biochemically characterise the recombinant proteins. The data we will attain will be related to the ADAM homologues found in humans.

Adam Antebi (2006) WormBook "Nuclear hormone receptors in C. elegans."

Adam Antebi

[WormBook, 2006]

Nuclear receptors (NRs) are transcription factors typically regulated by lipophilic hormones, which coordinate metazoan metabolism, development and homeostasis. C. elegans has undergone a remarkable expansion of the family, harboring 284 of these receptors in its genome. Approximately 20 of them have been analyzed genetically, most of which correspond to conserved homologs in other metazoans. These NRs variously affect broad life history traits such as sex determination, molting, developmental timing, diapause, and life span. They also impact neural development, axon outgrowth and neuronal identity. Finally, they influence lipid and xenobiotic metabolism. The study of C. elegans NRs holds great promise for dissecting nuclear receptor signaling pathways in vivo in the context of complex endocrine networks.

Adams PE et al. (2024) PeerJ "Identifying transgene insertions in Caenorhabditis elegans genomes with Oxford Nanopore sequencing."

Millwood JD, Thies JL, Fierst JL, Caldwell GA, Adams PE, Caldwell KA, Sutton JM

[PeerJ, 2024]

Genetically modified organisms are commonly used in disease research and agriculture but the precise genomic alterations underlying transgenic mutations are often unknown. The position and characteristics of transgenes, including the number of independent insertions, influences the expression of both transgenic and wild-type sequences. We used long-read, Oxford Nanopore Technologies (ONT) to sequence and assemble two transgenic strains of <i>Caenorhabditis elegans</i> commonly used in the research of neurodegenerative diseases: BY250 (pPdat-1::GFP) and UA44 (GFP and human <i>&#x3b1;</i>-synuclein), a model for Parkinson's research. After scaffolding to the reference, the final assembled sequences were &#x223c;102 Mb with N50s of 17.9 Mb and 18.0&#xa0;Mb, respectively, and L90s of six contiguous sequences, representing chromosome-level assemblies. Each of the assembled sequences contained more than 99.2% of the Nematoda BUSCO genes found in the <i>C. elegans</i> reference and 99.5% of the annotated <i>C. elegans</i> reference protein-coding genes. We identified the locations of the transgene insertions and confirmed that all transgene sequences were inserted in intergenic regions, leaving the organismal gene content intact. The transgenic <i>C. elegans</i> genomes presented here will be a valuable resource for Parkinson's research as well as other neurodegenerative diseases. Our work demonstrates that long-read sequencing is a fast, cost-effective way to assemble genome sequences and characterize mutant lines and strains.

Adams PE et al. (2021) Mol Biol Evol "Slow recovery from inbreeding depression generated by the complex genetic architecture of segregating deleterious mutations."

Crist AB, Young EM, Adams PE, Fierst JL, Willis JH, Phillips PC

[Mol Biol Evol, 2021]

The deleterious effects of inbreeding have been of extreme importance to evolutionary biology, but it has been difficult to characterize the complex interactions between genetic constraints and selection that lead to fitness loss and recovery after inbreeding. Haploid organisms and selfing organisms like the nematode Caenorhabditis elegans are capable of rapid recovery from the fixation of novel deleterious mutation; however, the potential for recovery and genomic consequences of inbreeding in diploid, outcrossing organisms are not well understood. We sought to answer two questions: (1) Can a diploid, outcrossing population recover from inbreeding via standing genetic variation and new mutation? and (2) How does allelic diversity change during recovery? We inbred C. remanei, an outcrossing relative of C. elegans, through brother-sister mating for 30 generations followed by recovery at large population size. Inbreeding reduced fitness but, surprisingly, recovery from inbreeding at large populations sizes generated only very moderate fitness recovery after 300 generations. We found that 65% of ancestral single nucleotide polymorphisms (SNPs) were fixed in the inbred population, far fewer than the theoretical expectation of ~99%. Under recovery, 36 SNPs across 30 genes involved in alimentary, muscular, nervous and reproductive systems changed reproducibly across replicates, indicating that strong selection for fitness recovery does exist. Our results indicate that recovery from inbreeding depression via standing genetic variation and mutation is likely to be constrained by the large number of segregating deleterious variants present in natural populations, limiting the capacity for recovery of small populations.