Zhang L et al. (2019) Anal Chem "Interaction-Transferable Graphene-Isolated Superstable AuCo Nanocrystal-Enabled Direct Cyanide Capture."

Xu Y, Liao Y, Li Z, Li S, Zheng Z, Tan W, Chen Z, Zhang J, Liu Z, Yi H, Zhang L

[Anal Chem, 2019]

Noble metals with strong plasmons have been widely used as enhancement substrates for molecule identification. However, cyanide, a toxic and important signaling molecule with a corrosive nature to noble metals, makes direct recognition challenging. Herein a novel superstable magnetic graphene-isolated AuCo nanocrystal (MACG) has been designed. Such graphene isolation enables superior stability without corrosion. Moreover, unexpectedly, although graphene isolated direct contact between Au and cyanide, their interaction was transferable and remained, which gifted MACGs direct cyanide capture capability with no specific ligands needed. Density functional theory calculations and natural bond orbital analysis indicated that the graphene isolation only slightly affected the charge transfer and that a relatively strong interaction was maintained between Au and cyanide. MACGs were utilized for efficient cyanide capture and clearance in various hydrologic environments and sensitive in vivo cyanide capture in C. elegans infected with P. aeruginosa, a pathogen with cyanide as the biomarker, indicating promise for various applications.

Sorensen, Erika B. et al. (2017) International Worm Meeting "ChIP-Seq reveals miRNA61-250 and deps-1 as Notch target genes in germline stem cells."

Kimble, Judith, Noble, Dan C., Porter, Doug F., Sorensen, Erika B., Sorokin, Elena P., Doenier, Emma, Lee, ChangHwan, Groth, Amy C.

[International Worm Meeting, 2017]

Notch signaling activates transcription of target genes and thereby regulates stem cells and differentiation broadly during animal development. The nematode C. elegans employs Notch signaling to maintain germline stem cells (GSCs) (1). Previous work identified two Notch targets with a candidate gene approach (2). Here we used chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) to identify GSC Notch targets on a genomic scale. ChIPs of the LAG-1/CSL DNA binding protein identified 384 significant peaks, of which 8 were also identified in parallel ChIPs of the GLP-1/Notch receptor. Two of these 8 common peaks belonged to the targets already known. In addition, we found peaks in the promoters of RNA regulators. One peak was in the promoter of mir-61 and mir-250, termed collectively mir61-250 (3). In situ hybridization demonstrates that these miRNAs are transcribed in GSCs and that their transcription is Notch-dependent. To ask if mir61-250 affects GSC maintenance, we used CRISPR-Cas9 (4,5) to delete the mir61-250 promoter. The resultant mir61-250 promoter deletion abolishes transcription of the miRNAs and therefore provides a loss-of-function mutant. Yet no GSC defect was seen. One explanation is that mir61-250 is functionally redundant with other genes. We are currently determining if miRNA overexpression or the presence of a miRNA sponge affects GSCs (6). Another ChIP peak was in the promoter of deps-1, a protein localized to the P-granule (7). Single molecule fluorescence in situ hybridization (smFISH) demonstrates that deps-1 expression in GSCs is Notch-dependent. We are exploring how these newly identified Notch target genes function as RNA regulators to control GSC maintenance. (1) Kimble and Crittenden. (2007) Annu Rev Cell Dev Biol, 23: 405; (2) Kershner et al. (2014) PNAS,111(10): 3739; (3) Martinez et al. (2008) Genome Res 18: 2005; (4) Arribere et al. (2014) Genetics 198(3): 837; (5) Paix et al. (2014) Genetics 198(4): 1347; (6) Ebert and Sharp (2010) RNA, 16: 2043; (7) Spike et al. (2007) Dev, 135: 983.

Carta L (1998) East Coast Worm Meeting "TOXICITY OF 4 SERRATIA MARCESCENS BACTERIAL STRAINS TOWARD C. ELGANS N2, PGP-3 AND OTHER NEMATODES IS INVERSELY RELATED TO PIGMENT"

Carta L

[East Coast Worm Meeting, 1998]

We are testing a number of biocontrol bacteria (eg. Burkholderia, Pseudomonas and Stenotrophomonas) for toxicity to bacterial feeding nematodes including C. elegans N2 and pgp-3. Serratia marcescens in particular had a measurable effect on number of eggs over 24 hours and relative motility in microtiter wells. Serratia marcescens strains with increasing amounts of red pigmentation (BF1-5@ (albino), D1, N4-5, NIMA) were tested for relative motility to C. elegans N2, pgp3, Oscheius myriophila DF5020, Panagrellus redivivus PS 1163, Mesorhabditis sp. PS1170 and Zeldia punctata PS 1153. Toxicity directly increases with decreasing amount of pigment in Caenorhabditis, Oscheius and Panagrellus. The order of relative toxicity is reversed for the 2 highly pigmented strains and the 2 least pigmented strains (2143 vs. 1234) in Mesorhabditis and Zeldia. These nematodes are phylogenetically distant from C. elegans. Bacterial strains were provided by Phyllis Martin and Dan Roberts, USDA.

Sela N et al. (2008) Biol Direct "Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans."

Ast G, Makalowski W, Sela N, Pupko T, Stern A

[Biol Direct, 2008]

ABSTRACT: Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR) sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM) that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5'' splice site of this open reading frame may have reactivated the transduplicated RRM motif. Reviewers: This article was reviewed by Dan Graur and William Martin. For the full reviews, please go to the Reviewers'' Reports section.

Zhao Y et al. (2007) BMC Genomics "Poly-G/poly-C tracts in the genomes of Caenorhabditis."

Zhao Y, O'Neil NJ, Rose AM

[BMC Genomics, 2007]

ABSTRACT: BACKGROUND: In the genome of Caenorhabditis elegans, homopolymeric poly-G/poly-C tracts (G/C tracts) exist at high frequency and are maintained by the activity of the DOG-1 protein. The frequency and distribution of G/C tracts in the genomes of C. elegans and the related nematode, C. briggsae were analyzed to investigate possible biological roles for G/C tracts. RESULTS: In C. elegans, G/C tracts are distributed along every chromosome in a non-random pattern. Most G/C tracts are within introns or are close to genes. Analysis of SAGE data showed that G/C tracts correlate with the levels of regional gene expression in C. elegans. G/C tracts are over-represented and dispersed across all chromosomes in another Caenorhabditis species, C. briggase. However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans. Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants. CONCLUSIONS: The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.

Bhagwati P Gupta et al. (2002) West Coast Worm Meeting "Genetic analysis of the vulval mutants in C. briggsae"

Shahla Gharib, Bhagwati P Gupta, Paul W Sternberg, Jennifer X Li

[West Coast Worm Meeting, 2002]

To understand the evolution of developmental mechanisms, we are doing a comparative analysis of vulval patterning in C. elegans and C. briggsae. C. briggsae is closely related to C. elegans and has identical looking vulval morphology. However, recent studies have indicated subtle differences in the underlying mechanisms of development. The recent completion of C. briggsae genome sequence by the C. elegans Sequencing Consortium is extremely valuable in identifying the conserved genes between C. elegans and C. briggsae.

Antika TR et al. (2023) J Biol Chem "Sequence-specific targeting of C. elegans C-Ala to the D-loop of tRNAAla."

Horng JC, Hsu HL, Nazilah KR, Wang CC, Wang TL, Wang SC, Antika TR, Chuang TH, Chrestella DJ, Wang SW, Tseng YK, Pan HC

[J Biol Chem, 2023]

Alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout its biology. Nevertheless, its C-terminal domain (C-Ala) is highly diverged and has been shown to play a role in either tRNA or DNA binding. Interestingly, we discovered that Caenorhabditis elegans cytoplasmic C-Ala (Ce-C-Ala_c) robustly binds both ligands. How Ce-C-Ala_c targets its cognate tRNA and whether a similar feature is conserved in its mitochondrial counterpart remain elusive. We show that the N- and C-terminal subdomains of Ce-C-Ala_c are responsible for DNA and tRNA binding, respectively. Ce-C-Ala_c specifically recognized the conserved invariant base G¹⁸ in the D-loop of tRNA^Ala through a highly conserved lysine residue, K934. Despite bearing little resemblance to other C-Ala domains, C. elegans mitochondrial C-Ala (Ce-C-Ala_m) robustly bound both tRNA^Ala and DNA and maintained targeting specificity for the D-loop of its cognate tRNA. This study uncovers the underlying mechanism of how C. elegans C-Ala specifically targets the D-loop of tRNA^Ala.

Blumenthal TE et al. (1994) Worm Breeder's Gazette "C. elegans U2AF 65."

Zorio DAR, Lea K, Blumenthal TE

[Worm Breeder's Gazette, 1994]

C. elegans U2AF65

Noble, M. et al. (2017) International Worm Meeting "The Nucleosome Remodelling Factor subunit pyp-1 negatively regulates the heat shock response upon aging in Caenorhabditis elegans ."

Guisbert, E, Bowie, L, Deonarine, A., Westerheide, S, Lugano, D., Noble, M.

[International Worm Meeting, 2017]

Title: The Nucleosome Remodelling Factor subunit pyp-1 negatively regulates the heat shock response upon aging in Caenorhabditis elegans Mark Noble, Andrew Deonarine, Doreen Lugano, Lori-Ann Bowie and Sandy D. Westerheide The heat shock response is a conserved eukaryotic stress response known to regulate protein homeostasis (proteostasis) and it is regulated by the transcription factor hsf-1. Previous studies have shown tremendous effects of the HSR on life span, health span, and disease models of neurodegenerative diseases such as Alzheimer's, Parkinson and Huntington's disease. In C. elegans, proteostasis has been shown to decline with the onset of adulthood in parallel to the decline of the HSR. Therefore, understanding the molecular mechanisms and regulation of this response is vital in revealing its effects on various stresses. Recent studies have shown a link between chromatin remodelers and regulation of the heat shock response. Thus, utilizing RNAi genetic screen, we were able a uncover pyp-1, a pyrophosphatase and subunit of the Nucleosome-remodeling factor (NURF) which showed tremendous effects on the HSR. From a different screen, pyp-1 was also found to be a negative regulator of the heat shock response in C. elegans. We hypothesize that the age-dependent decrease in HSR induction may be due to repressive chromatin changes conferred by chromatin remodeling complexes. As a result, we identified pyp-1 as a novel negative regulator of the heat shock response and proteostasis upon aging in C.elegans.

Oomura, S. et al. (2019) International Worm Meeting "Early embryogenesis of C. inopinata, a sibling species of C.elegans."

Matsumura, Y., Haruta, N., Hoshi, Y., Sugimoto, A., Oomura, S.

[International Worm Meeting, 2019]

C. inopinata is a newly discovered sibling species of C. elegans. Despite their phylogenetic closeness, they have many differences in morphology and ecology. For example, while C. elegans is hermaphroditic, C. inopinata is gonochoristic; C. inopinata is nearly twice as long as C. elegans. A comparative analysis of C. elegans and C. inopinata enables us to study how genomic changes cause these phenotypic differences. In this study, we focused on early embryogenesis of C. inopinata. First, by the microparticle bombardment method we made a C. inopinata line that express GFP::histone in whole body, and compared the early embryogenesis with C. elegans by DIC and fluorescent live imaging. We found that the position of pronuclei and polar bodies were different between these two species. In C. elegans, the female and male pronuclei first become visible in anterior and posterior sides, respectively, then they meet at the center of embryo. On the other hand, the initial position of pronuclei were more closely located in C. inopinata. Also, the polar bodies usually appear in the anterior side of embryo in C. elegans, but they appeared at random positions in C. inopinata. Therefore, we infer that C. inopinata may have a different polarity formation mechanism from that in C. elegans. We are also analyzing temperature dependency of embryogenesis in C. inopinata, whose optimal temperature is ~7 degree higher than that in C. elegans.