Shoemaker JE et al. (1987) Worm Breeder's Gazette "progress in cloning the age-1 gene."

Johnson TE, Shoemaker JE

[Worm Breeder's Gazette, 1987]

We are attempting to clone age-1 by the congenic strategy of Ruvkun, et al. The age-1 gene confers a phenotype of long life span and low hermaphrodite self fertility (Hsf). The gene cosegregates with fem-15 and thus maps to a region of linkage group II between dpy-10 and unc-4. Deficiency mapping using the Hsf phenotype supports this map location and we are continuing our mapping of the long-life phenotype itself to confirm these locations. Nine congenic strains were constructed by crossing age-1 to Bergerac BO, then backcrossing to the mutant strain nine more times. The object was to incorporate the wild- type Bergerac DNA around age-1 into the Bristol background of the mutant strain. In order to construct these lines, we took advantage of the low fertility of age-1 males and the fact that the Ts and Hsf phenotypes are closely associated with age-1, since constructing these lines by assaying life span at each generation would take about three years. When age-1 males are crossed to Bergerac BO hermaphrodites (the first generation) the progeny males are 100% heterozygous for age-1 and therefore wild type for the male sterility phenotype. When these F1 males are successively backcrossed to sterilized age-1 hermaphrodites, the 50% age-1 males expected in each generation cross poorly compared to the heterozygotes, yielding more progeny of the desired genotype from the backcross than of the undesirable genotype. After the backcrosses, the lines were selfed for five generations at 20 C. Strains were checked at the fifth and tenth backcross for the Ts and Hsf phenotypes, and again after homozygosis, when 50% were Ts+ ( as expected). The final strains were checked for life span and all of the nine that were wild type for Ts and Hsf also demonstrated a wild type life span. We have grown up these congenic strains in mass liquid culture by a modification of the method of Sulston and Brenner, and isolated DNA. Southern blots probed with Tc1 show the appearance of several new Tc1 bands in the congenic lines. We are continuing our molecular analysis of these lines using other restriction enzymes, and are currently constructing recombinants in the dpy-10 o define which Tc1 elements map most closely to the right and the left of age-1.

Shoemaker JE et al. (1987) International C. elegans Meeting "deficiency mapping of the age-1 locus in C elegans."

Friedman DB, Fitzpatrick PA, Johnson TE, Shoemaker JE

[International C. elegans Meeting, 1987]

Zhang Z et al. (2024) Sci Rep "Jujubae Fructus extract prolongs lifespan and improves stress tolerance in Caenorhabditis elegans dependent on DAF-16/SOD-3."

Luo X, Wang T, Liu X, Li F, Zhang Z, You Y, Li J, Wu C, Li B

[Sci Rep, 2024]

Jujubae Fructus, the fruit of Ziziphus jujuba Mill has been used as one of the medicine food homology species for thousands of years in China. Studies have shown that the active ingredients of Jujubae Fructus have a variety of biological effects, but its role in the aging process still lacks knowledge. Here, we investigated the effect of Jujubae Fructus extract (JE) on Caenorhabditis elegans lifespan and its potential mechanism. The lifespan of C. elegans treated with JE was signifificantly increased in a dose-dependent manner. In addition, JE treatment prolonged the reproductive period and increased normal activity during aging in C. elegans. Similarly, JE supplementation also enhanced the resistance to heat and oxidative stress in C. elegans. Furthermore, the mutant worms' lifespan assays demonstrated that JE requires daf-16 to prolong lifespan. DAF-16::GFP analysis of TJ356 showed that JE treatment translocates DAF-16::GFP to nucleus in transgenic worms. By analyzing the downstream of daf-16, we identify that JE may regulate sod3 downstream of daf-16. Mutant worms' lifespan and transgenic reporter gene expression assays revealed that increasing SOD-3 expression was critical for extending longevity in C. elegans with JE therapy. Collectively, these data indicate that JE may have an important role in C. elegans longevity that is dependent on DAF-16 and SOD-3.

Foltz NL et al. (1988) Worm Breeder's Gazette "long life and low fertility: mating effects on life span."

Foltz NL, Johnson TE, Shoemaker JE

[Worm Breeder's Gazette, 1988]

Mutations in the age-1 gene effect substantial (age-1 mutants live 40% longer than N2 at 20 C) extensions in life span (Friedman and Johnson, 1988, Genetics 118:7586). Because age-1 hermaphrodites also have reduced fertility (at 20 C, age-1 hermaphrodites produce about 50 self progeny), we are performing a series of mating experiments to find out if life extension in age-1 mutants directly results from low fertility. We have measured progeny production and life span in virgin and mated TJ412 [age-1;fer-15(b26ts)] hermaphrodites to determine if mean life span is reduced when mean progeny production is increased. Individual hermaphrodites were cultured first on agar to measure fertility, and then from 8 days until death in liquid microtiter wells to measure life span. Mean progeny production was increased five- to ten-fold in age-1 hermaphrodite by wild type (N2) male crosses. All trials showed significantly lower (P values 0.04, 0.002, <0.001) mean life span for age-1 hermaphrodites when mated to N2 males. Life spans for mated groups were 22, 14, and 16 days, respectively, compared to 31, 22, and 28 days for virgin age-1 hermaphrodites. In these experiments, age-1 hermaphrodites mated to N2 males had life spans indistinguishable from N2. Mated and virgin N2 hermaphrodites were compared to determine if mating itself has an effect on life span. N2 by N2 crosses increased total progeny about two-fold, but did not change life span of hermaphrodites in two trials. Mated N2 also showed significantly lowered life span in one trial. In one trial, TJ412 by TJ412 crosses increased total progeny more than three-fold and showed life span reduction (28 days for unmated; 25 days for mated) that was marginally significant (P value 0.05). TJ412 hermaphrodites mated by TJ412 males were significantly (P = 0.01) longer lived than N2 virgins (21 days). We are currently repeating the experiments with TJ412 and N2 males to find out if the apparent influence of male genotype on life span of mated age-1 hermaphrodites is real. We also are mating age-1 hermaphrodites with BA713 which contains fer-15(b26ts), a gene closely linked to age-1 and present in TJ412, to see if this sperm defect interacts with life span. Correlations between life span and total progeny production in T1412 hermaphrodites mated to N2 or TJ412 males tended to be negative, and repeats will firm up this observation.

Noh H et al. (2021) BMC Bioinformatics "DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks."

Noh H, Gunawan R, Shoemaker JE, Hua Z, Chrysinas P

[BMC Bioinformatics, 2021]

BACKGROUND: Knowledge on the molecular targets of diseases and drugs is crucial for elucidating disease pathogenesis and mechanism of action of drugs, and for driving drug discovery and treatment formulation. In this regard, high-throughput gene transcriptional profiling has become a leading technology, generating whole-genome data on the transcriptional alterations caused by diseases or drug compounds. However, identifying direct gene targets, especially in the background of indirect (downstream) effects, based on differential gene expressions is difficult due to the complexity of gene regulatory network governing the gene transcriptional processes. RESULTS: In this work, we developed a network analysis method, called DeltaNeTS+, for inferring direct gene targets of drugs and diseases from gene transcriptional profiles. DeltaNeTS+ uses a gene regulatory network model to identify direct perturbations to the transcription of genes using gene expression data. Importantly, DeltaNeTS+ is able to combine both steady-state and time-course expression profiles, as well as leverage information on the gene network structure. We demonstrated the power of DeltaNeTS+ in predicting gene targets using gene expression data in complex organisms, including Caenorhabditis elegans and human cell lines (T-cell and Calu-3). More specifically, in an application to time-course gene expression profiles of influenza A H1N1 (swine flu) and H5N1 (avian flu) infection, DeltaNeTS+ shed light on the key differences of dynamic cellular perturbations caused by the two influenza strains. CONCLUSION: DeltaNeTS+ is a powerful network analysis tool for inferring gene targets from gene expression profiles. As demonstrated in the case studies, by incorporating available information on gene network structure, DeltaNeTS+ produces accurate predictions of direct gene targets from a small sample size (~10s). Integrating static and dynamic expression data with transcriptional network structure extracted from genomic information, as enabled by DeltaNeTS+, is crucial toward personalized medicine, where treatments can be tailored to individual patients. DeltaNeTS+ can be freely downloaded from http://www.github.com/cabsel/deltanetsplus .

Johnson TE et al. (1990) "Genetic variants and mutations of Caenorhabditis elegans provide tools for dissecting the aging processes."

Fitzpatrick PA, Friedman DB, Shoemaker JE, Johnson TE, Foltz NL

[1990]

Caenorhabditis elegans is a short-lived species that has been widely used in the genetic dissection of development. This species is becoming important in the genetic analysis of aging because strains with mean life spans more than 70% longer than wild type have been identified both through the use of recombinant inbred lines and by the induction of single-gene mutants. Its unique hermaphroditic mode of reproduction leads to a lack of inbreeding depression and simplifies genetic analyses of quantitative traits such as length of life or behavior. Aging in this organism is composed of at least three independent processes: that specifying length of life, that specifying reproductive senescence, and that specifying senescence of the general motor system. These data suggest that aging is not a unitary process but that many different processes or independent components may be involved in various aspects of aging. Most importantly, an apparent single-gene mutation has been mapped to the middle of linkage group II; this mutation lengthens mean and maximum life span 60-110% and also decreases fertility about five-fold.

David S Peal et al. (2001) International C. elegans Meeting "Chemical and Genetic Inhibition of Sulfation in C. elegans"

David S Peal, Laura L Kiessling

[International C. elegans Meeting, 2001]

In order to examine the process of sulfation in C. elegans, sulfation was inhibited chemically using sodium chlorate, and genetically using the process of RNA-mediated interference (RNAi). Sodium chlorate inhibition during early larval stages resulted in a dose-dependant developmental delay. BLAST searches of characterized sulfotransferases against the worm genome resulted in the identification of 4 putative sulfotransferases: C34F6.4 and F08B4.6 (previously identified: [1] and [2]), F40H3.5, and Y34B4A.e. RNAi of the putative N-deacetylase/N-sulfotransferase F08B4.6 resulted in "stacking" of eggs in the gonad, along with eggs laid at the 2- and 4-celled stage. RNAi of the putative hexuronic 2-O sulfotransferase C34F6.4 resulted in a shortened, bulbous gonad. These initial results indicate that sulfation may be important during development of C. elegans. [1] Shworak, NW, Liu, J, Fritze, LMS, Schwartz, JJ, Zhang, L, Logeart, D, Rosenberg, RD. JBC 272: 28008-19 (1997). [2] Kobayashi, M, Sugumaran, G, Liu, J, Shworak, NW, Silbert, JE, Rosenberg, RD. JBC 274: 10474-80 (1999).

Adam W Tearle et al. (2005) International Worm Meeting "Investigating nicotinic acetylcholine receptors in vulval muscles by calcium imaging."

William R Schafer, Adam W Tearle

[International Worm Meeting, 2005]

We are studying the properties of acetylcholine receptors in C. elegans vulval muscles using the genetically expressed calcium indicator cameleon. The worm is dissected using a technique adapted from Richmond and Jorgensen (1999). Animals are glued down in a perfusion chamber, a small incision made on the ventral side opposite the vulva and the viscera removed. This exposes the vulval muscles and allows the direct application of drugs to these muscles at physiological concentrations. Dissected vulval muscles continue to contract and give corresponding calcium transients. Wild type vulval muscles show a large increase in intracellular calcium in response to 500M nicotine or 100M levamisole. Levamisole receptor mutants, unc-29 and lev-1 do not respond to levamisole but show a smaller response to nicotine than wild type. Further experiments will be performed to determine the response to acetylcholine and the effect of different pharmacological blockers of nicotinic receptors. The effects of adaptation to repeated nicotine stimulation, or long term exposure to nicotine, will also be described. Richmond, JE. and Jorgensen, EM., Nat Neurosci. 1999 (9):791-7

Edward Yeh et al. (2003) International Worm Meeting "A screen to identify factors involved in active zone formation."

Mei ZHEN, Edward YEH

[International Worm Meeting, 2003]

The active zone is a specialized presynaptic structure where vesicles containing neurotransmitters fuse with the plasma membrane, releasing the neurotransmitters to the post-synaptic membrane. At the EM level, electron dense active zones are surrounded by clusters of vesicles. A few components of the active zone have been identified such as UNC-10 (Koushika et al., 2001), UNC-13 (Richmond et al., 1999; Aravamudan et al., 1999) and SYD-2 (Zhen and Jin, 1999) but even fewer have been implicated in active zone establishment, differentiation or maintainance.syd-2 encodes a homolog of liprin- and has been shown to be a component of the active zone. Mutations in syd-2 give rise to larger active zones. At a previous meeting, we reported a SYD-2::GFP marker that could be used to visualize active zones in live animals. The SYD-2::GFP protein marker was placed under the promoter of unc-25 which expresses in GABAergic neurons. We have performed a SYD-2::GFP screen to identify a dditional factors involved in the formation of the active zone. An EMS mutagenesis screen was performed looking for mutations affecting the formation of the active zone. Approximately 2500 haploid genomes were screened and we are currently characterizing 5 isolated mutant alleles. hp77 and hp121 represent two loci on chromosome X, hp102 and hp198 represent two loci on chromosome IV and hp129 is on chromosome V. hp121 and hp102 have behavioural unc phenotypes, hp198 are slightly dumpy while hp77 and hp129 do not appear to have any behaviour or physical phenotypes. Initial characterization and phenotypic analysis will be presented on these mutants. It is our hope that the molecular characterization of these mutants will provide information on factors involved in the establishment, differentiation, and maintenance of active zones. Ultimately, this information will provide insight into the genetic pathways used to establish neural synapses in general.References: Aravamudan B, Fergestad T, Davis WS, Rodesch CK, and Broadie K. (1999) Nature Neuroscience. 2:965; Koushika SP, Richmond JE, Hadwiger G, Weimer RM, Jorgensen EM and Nonet M. (2001) Nature Neuroscience. 4:997-1005; Richmond JE, Davis WS and Jorgensen EM. (1999) Nature Neuroscience. 2:959-64; Zhen M and Jin Y. (1999) Nature. 401:371-5

Klosterman S M et al. (2010) Neuronal Development, Synaptic Function and Behavior, Madison, WI "Regulation of tomosyn (TOM-1) trafficking in C. elegans"

Klosterman S M, Richmond J E

[Neuronal Development, Synaptic Function and Behavior, Madison, WI, 2010]

Regulated exocytosis of secretory vesicles is critically dependent on the assembly of SNARE complexes between the plasma membrane SNAREs, synatxin and SNAP-25 and vesicle-associated synaptobrevin, which render vesicles fusion competent. Tomosyn, a syntaxin-binding protein, forms a complex with syntaxin and SNAP-25 in competition with synaptobrevin predicted to limit fusogenic SNARE complex formation (Fujita et al, 1998). Consistent with these data, the highly conserved C. elegans tomosyn homolog, TOM-1, has been shown to negatively regulate both synaptic and dense-core vesicle release (Gracheva et al., 2006; Gracheva et al.,2007). TOM-1 appears to be associated with both synaptic vesicles (Takamori et al., 2006) and dense core vesicles (Gracheva et al., 2007) via an unknown mechanism. Consequently, the synaptic localization of TOM-1 is dependent on the anterograde vesicle kinesin motor (UNC-104) (McEwen et al., 2006). Given the importance of TOM-1 in the regulation of synaptic strength, we are interested in identifying the mechanism responsible for the synaptic localization of this protein. Neither syntaxin nor SNAP-25, the two established tomosyn-interacting proteins appear to be involved in TOM-1 transport to synapses (McEwen et al., 2006). In order to screen for TOM-1 trafficking defective mutants, we have generated an integrated transgene expressing TOM-1::GFP. We have verified that this protein is expressed at synapses and localizes in an UNC-104-dependent manner. We are currently screening known vesicle-associated candidate proteins by RNAi or by crossing the TOM-1::GFP transgene into reference alleles to examine their potential role in the regulation of tomosyn trafficking. Fujita Y, Shirataki H, Sakisaka T, Asakura T, Ohya T, Kotani H, YokoyamaS, Nishioka H, Matsuura Y, Mizoguchi A, Scheller RH, Takai Y (1998) Tomosyn: asyntaxin-1-binding protein that forms a novel complex in the neurotransmitterrelease process. Neuron 20:905-915. Gracheva EO, Burdina AO, Touroutine D, Berthelot-Grosjean M, Parekh H,Richmond JE (2007) Tomosyn negatively regulates CAPS-dependent peptide releaseat Caenorhabditis elegans synapses. J Neurosci 27:10176-10184. Gracheva EO, Burdina AO, Holgado AM, Berthelot-Grosjean M, Ackley BD,Hadwiger G, Nonet ML, Weimer RM, Richmond JE (2006) Tomosyn inhibits synapticvesicle priming in Caenorhabditis elegans. PLoS Biol 4:e261.McEwen JM, Madison JM, Dybbs M, Kaplan JM (2006) Antagonistic regulationof synaptic vesicle priming by Tomosyn and UNC-13. Neuron 51:303-315. Takamori S et al. (2006) Molecular anatomy of a trafficking organelle.Cell 127:831-846.