Li K et al. (2018) Environ Pollut "Assessing the influence of the genetically modified factor on mixture toxicological interactions in Caenorhabditis elegans: Comparison between wild type and a SOD type."

Liu SS, Li K, Feng L, Xu YQ

[Environ Pollut, 2018]

How to evaluate the ecological risk of transgenic technology is a focus of scientists because of the safety concerns raised by genetically modified (GM) organisms. Nevertheless, most studies are based on individual chemicals and always analyze the GM organism as a type of toxicant. In this study, we changed the approach and used GM organisms as the test objects with normal chemical exposure. Three types of chemicals (two substituted phenols, 4-chlorophenol and 4-nitrophenol; two ionic liquids, 1-butylpyridinium chloride and 1-butylpyridinium bromide; two pesticides, dichlorvos and glyphosate) were used to construct a six-component mixture system. The lethality to wild-type (N2) and sod-3::GFP (SOD-3) Caenorhabditis elegans was determined when they were exposed to the same mixture system after 12 and 24h. The results showed that the pEC50 values of all of the single chemicals on SOD-3 were greater than those on N2 at 24h. The toxicities of the single chemicals and nine mixture rays on the two strains increased with time. Notably, we discovered a significant difference between the two strains; time-dependent synergism occurred in mixtures on N2, but time-dependent antagonism occurred in mixtures on SOD-3. Finally, the strength of the synergism or antagonism turned to additive action on the two strains as the exposure time increased. These findings illustrated that the GM factor of the nematode influenced the mixture toxicological interaction at some exposure times. Compared with N2, SOD-3 were more sensitive to stress or toxic reactions. Therefore, the influence of the GM factor on mixture toxicological interactions in environmental risk assessment must be considered.

Gronenborn AM et al. (1990) Biochemistry "Sequential resonance assignment and secondary structure determination of the Ascaris trypsin inhibitor, a member of a novel class of proteinase inhibitors."

Peanasky RJ, Nilges M, Clore GM, Gronenborn AM

[Biochemistry, 1990]

The solution conformation of the Ascaris trypsin inhibitor, a member of a novel class of proteinase inhibitors, has been investigated by nuclear magnetic resonance spectroscopy. Complete sequence-specific assignments of the 1H NMR spectrum have been obtained by using a number of two-dimensional techniques for identifying through-bond and through-space (less than 5-A) connectivities. Elements of regular secondary structure have been identified on the basis of a qualitative interpretation of the nuclear Overhauser enhancement, coupling constant, and amide exchange data. These are two beta-sheet regions. One double-stranded antiparallel beta-sheet comprises residues 11-14 (strand 1) and 37-39 (strand 2). The other triple-stranded sheet is formed by two antiparallel strands comprising residues 45-49 (strand 4) and 53-57 (strand 5) connected by a turn (residues 50-52), and a small strand consisting of residues 20-22 (strand 3) that is parallel to strand 4.

Soderlund CA et al. (1990) Worm Breeder's Gazette "gm Sequence Analysis System Update"

Soderlund CA, Fields CA, Shanmugam P

[Worm Breeder's Gazette, 1990]

A number of improvements have been made in the gm automated DNA sequence analysis system: (1) The ratio of AT-containing to CG-containing dinucleotides has been added as a test for introns. This works better than AT frequency alone in C. elegans.(2) A branch site consensus sequence or an enhanced dinucleotide ratio can be required as an additional test on introns. (3) Predicted amino-acid sequence files are generated in a format appropriate for input to the Dana-Farber motif-identification program plsearch. (4) A graphic interface based on X-windows, version 11 is available as an option. (5) The complete analysis algorithm is significantly faster than the previous version. (6) A greedy model evaluation algorithm is available as an option. This algorithm generates the longest, non-overlapping models that cover a sequence and is much faster than the complete analysis algorithm. The program has been tested on Sun3, Sun4 and VAX machines running Unix (Ultrix on the VAX). Results for a series of tests run on a Sun 4/60 are shown in the table. [See Figure 1] gm can be run remotely on our machine, using the Internet. To do this, telnet to haywire.nmsu.edu, and logon as gm_guest with password gmuser. Read the README file for information on running gm. We are also distributing gm as C source code to nonprofit laboratories, either via anonymous ftp to haywire.nmsu.edu, or on tape. If you would like to receive gm on tape, send a 1/4' cartridge or 1/2' reel tape to: Chris Fields, Box 30001/3CRL, New Mexico State University, Las Cruces, New Mexico 88003-0001, USA; Telephone (505) 646-2848.

Dougherty EC et al. (1959) Ann N Y Acad Sci "Axenic cultivation of Caenorhabditis briggsae (Nematoda: Rhabditidae) with unsupplemented and supplemented chemically defined media."

Nicholas WL, Yarwood EA, Mollett JA, Hansen EL, Dougherty EC

[Ann N Y Acad Sci, 1959]

A detailed summary of methods for axenic cultivation of Caenorhabditis briggsae is given. Results of axenic culture on chemically defined basal media (GM and GS) and on these media supplemented with undefined preparations of horse liver and chick embryos are reported in detail, with a review of the formulation of the GM and GS designs and of the chronology of changes made therein. The best growth so far realized with C. briggsae in axenic culture is suboptimal as compared with growth in the presence of bacteria, and maturation takes longer (4 to 5 days instead of about 3 days at 20C). Suitable media of the GM design give good axenic growth with relatively low levels of complex supplements-Liver Protein Fraction C (LPF-C) and chick embryo extract (CEE), both of which presumably include a protein-linked requirement, Factor Rb. With GM-16 plus CEE or certain GSs plus CEE, requirements have been variously demonstrated for 6 B-vitamins: folic acid, niacinamide, pantothenic acid, pyridoxine, riboflavin, and thiamine; one of these-folic acid-had already been shown to be required. Only niacinamide is also demonstrated as a requirement in the presence of low levels of LPF-C. In the presence of CEE we have tested the essentiality of the other 5 vitamins only by omitting them singly from vitamin mixes added at increased (5 to 50 times GS) levels to media of GM or GS type. Preliminary evidence is given that the ten "rat-essential" amino acids are required. Improvement of nutritional balance with respect to amino acid levels and to relative levels of amino acids in relation to vitamins or salts is discussed as an explanation of differential growth on different media. Possibly the variations of DM-GS so far tested contain unnecessarily high amino acid levels. The definition of nutritional requirements for C. briggsae still presents many

Braddock DT et al. (2002) Nature "Structure and dynamics of KH domains from FBP bound to single-stranded DNA."

Baber JL, Clore GM, Levens D, Louis JM, Braddock DT

[Nature, 2002]

Gene regulation can be tightly controlled by recognition of DNA deformations that are induced by stress generated during transcription. The KH domains of the FUSE-binding protein (FBP), a regulator of c-myc expression, bind in vivo and in vitro to the single-stranded far-upstream element (FUSE), 1,500 base pairs upstream from the c-myc promoter. FBP bound to FUSE acts through TFIIH at the promoter. Here we report the solution structure of a complex between the KH3 and KH4 domains of FBP and a 29-base single-stranded DNA from FUSE. The KH domains recognize two sites, 9-10 bases in length, separated by 5 bases, with KH4 bound to the 5' site and KH3 to the 3' site. The central portion of each site comprises a tetrad of sequence 5'd-ATTC for KH4 and 5'd-TTTT for KH3. Dynamics measurements show that the two KH domains bind as articulated modules to single-stranded DNA, providing a flexible framework with which to recognize transient, moving targets.

Rahman, Maisha et al. (2021) International Worm Meeting "Specific N-glycans fine-tune somatosensory dendrite patterning"

Diaz-Balzac, Carlos, Rahman, Maisha, Bulow, Hannes

[International Worm Meeting, 2021]

Dendrites are essential for the transmission and processing of stimuli through the nervous system, and their development requires the precise orchestration of many proteins. For example, the C. elegans PVD somatosensory neurons require a conserved cell-adhesion 'menorin' complex - comprised of skin-derived MNR-1/Menorin and SAX-7/L1CAM, muscle secreted LECT-2/Chondromodulin II, and the transmembrane receptor, DMA-1/LRR-TM, in PVD - for their stereotyped arborization. We found that a key enzyme in the N-glycosylation pathway, AMAN-2/Golgi alpha-mannosidase II, plays a role in fine-tuning PVD dendrite patterning. aman-2/GM-II encodes an evolutionarily conserved enzyme required for the formation of complex and paucimannose N-glycans. Mutations in aman-2/GM-II result in dendritic trees with reduced complexity, and enhance the severity of dendrite defects in hypomorphic alleles of members of the menorin complex. AMAN-2/GM-II requires enzymatic activity in PVD to form higher order branches, suggesting that N-glycosylation of a menorin complex component in PVD itself may be significant. Consistent with this hypothesis, we find that DMA-1/LRR-TM is glycosylated in vivo with primarily high-mannose/hybrid N-glycans, and that DMA-1/LRR-TM carries larger, abnormal N-glycans in aman-2/GM-II mutants. Importantly, we determined that the presence of abnormal N-glycans, rather than the absence of wildtype N-glycans, is the root cause of the observed defects, and likely leads to altered protein-protein interactions. Lastly, we found that specific N-glycosylation sites in DMA-1/LRR-TM are important for PVD dendrite morphogenesis. Collectively, our findings suggest that specific N-glycan structures fine-tune dendrite patterning, possibly by regulating complex formation of the DMA-1/LRR receptor with other components of the menorin complex.

McIntyre LM et al. (2022) Sci Rep "GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease."

Huertas F, Miller GW, McIntyre LM, Murphy CT, Morse AM, Conesa A, Kaletsky R, Kalia V, Moskalenko O, Mor DE

[Sci Rep, 2022]

Parkinson's disease (PD) is a disabling neurodegenerative disorder in which multiple cell types, including dopaminergic and cholinergic neurons, are affected. The mechanisms of neurodegeneration in PD are not fully understood, limiting the development of therapies directed at disease-relevant molecular targets. C. elegans is a genetically tractable model system that can be used to disentangle disease mechanisms in complex diseases such as PD. Such mechanisms can be studied combining high-throughput molecular profiling technologies such as transcriptomics and metabolomics. However, the integrative analysis of multi-omics data in order to unravel disease mechanisms is a challenging task without advanced bioinformatics training. Galaxy, a widely-used resource for enabling bioinformatics analysis by the broad scientific community, has poor representation of multi-omics integration pipelines. We present the integrative analysis of gene expression and metabolite levels of a C. elegans PD model using GAIT-GM, a new Galaxy tool for multi-omics data analysis. Using GAIT-GM, we discovered an association between branched-chain amino acid metabolism and cholinergic neurons in the C. elegans PD model. An independent follow-up experiment uncovered cholinergic neurodegeneration in the C. elegans model that is consistent with cholinergic cell loss observed in PD. GAIT-GM is an easy to use Galaxy-based tool for generating novel testable hypotheses of disease mechanisms involving gene-metabolite relationships.

Horvitz HR et al. (1981) Worm Breeder's Gazette "octopamine in C elegans."

Horvitz HR, Chalfie M, Evans PD, Trent C

[Worm Breeder's Gazette, 1981]

Octopamine (p-hydroxyphenylethanolamine) seems likely to be a common neurotransmitter in invertebrates. To determine if octopamine is present in C. elegans, extracts were prepared by sonication and assayed biochemically. The assay used involves the transfer by phenylethanolamine N-methyltransferase of a radioactive methyl group from [3H]-methyl-S-adenosyl-L-methionine to octopamine to form [3H]- synephrine (N-methyloctopamine), which is then selectively extracted and subjected to chromatography in a variety of solvents. About 0.1 g of octopamine are present per gm of C. elegans tissue. This level is similar to that of dopamine (Sulston et al., J. Comp. Neurol. 163, 215, 1975); C. elegans hermaphrodites have only eight dopaminergic neurons, suggesting that a similar number of octopaminergic neurons may be present. The level of octopamine varies with both the temperature of growth (0.3 g/gm at 15 C; 0.1 g/gm at 20 C; 0.05 g/gm. at 25 C) and developmental stage (larvae have at least 5-10X less octopamine than adults). Exogenous octopamine (10 mg/ml) depresses egg-laying, suggesting that the adult-specificity of endogenous octopamine may be related to the adult-specific behavior of egg-laying. Octopamine levels have been determined for many behavioral mutants. None were octopamine-deficient, but a number of strains -- CB268 (unc- 41 V), CB204 (unc-33 IV) and CB15 (unc-28 IV) -- appear to overproduce octopamine. We do not know if the abnormalities in coordination and octopamine levels in these strains result from the same mutations. Many neurons have uptake systems that allow them to concentrate their own transmitters as well as closely related compounds. Norepinephrine is structurally similar to octopamine (octopamine lacks the 3-0H of norepinephrine) but, unlike octopamine, can be visualized histochemically by the technique of formaldehyde-induced fluorescence ( FIF). Hoping to reveal octopaminergic cells, we have exposed animals to norepinephrine and examined their FIF. In addition to the known dopaminergic neurons (dopamine is also closely related to norepinephrine), a pair of cells in the tail and, occasionally, a pair of (amphidial?) cells in the head accumulate exogenous norepinephrine.

Chuang P-T et al. (1996) Science "Sex-specific assembly of a dosage compensation complex on the nematode X chromosome."

Lieb JD, Meyer JB, Chuang P-T

[Science, 1996]

In nematodes, flies, and mammals, dosage compensation equalizes X-chromosome gene expression between the sexes through chromosome-wide regulatory mechanisms that function in one sex to adjust the levels of X-linked transcripts. Here, a dosage compensation complex was identified in the nematode Caenorhabditis elegans that reduces transcript levels from the two X chromosomes in hermaphrodites. This complex contains at least four proteins, including products of the dosage compensation genes dpy-26 and dpy-27. Specific localization of the complex to the hermaphrodite X chromosomes is conferred by XX-specific regulatory genes that coordinately control both sex determination and dosage compensation.AD - Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.FAU - Chuang, P TAU - Chuang PTFAU - Lieb, J DAU - Lieb JDFAU - Meyer, B JAU - Meyer BJLA - engID - GM30702/GM/NIGMSID - T32 GM07127/GM/NIGMSPT - Journal ArticleCY - UNITED STATESTA - ScienceJID - 0404511RN - 0 (Carrier Proteins)RN - 0 (DPY-27 protein)RN - 0 (Helminth Proteins)RN - 0 (Nuclear Proteins)RN - 0 (RNA, Helminth)RN - 0 (RNA, Messenger)SB - IM

Turaga PS et al. (2000) Infect Immun "Immunity to onchocerciasis: cells from putatively immune individuals produce enhanced levels of interleukin-5, gamma interferon, and granulocyte-macrophage colony-stimulating factor in response to Onchocerca volvulus larval and male worm antigens."

Lustigman S, Simonek SC, Bennett KE, Tierney TJ, McCarthy MC, Enyong PA, Turaga PS, Moukatte DW

[Infect Immun, 2000]

Antigen-specific interleukin-5 (IL-5), gamma interferon (IFN-gamma), and granulocyte-macrophage colony-stimulating factor (GM-CSF) responses in individuals living in an area of hyperendemicity for onchocerciasis in Cameroon were examined. The responses against antigens prepared from Onchocerca volvulus third-stage larvae (L3), molting L3 (mL3), and crude extract from adult males (M-OvAg) were compared to the responses against antigens from adult female worms and skin microfilariae. Cytokine responses for the putatively immune individuals (PI) and the infected individuals (INF) were compared. A differential cytokine profile of IL-5 (Th2 phenotype) and IFN-gamma (Th1 phenotype) was found in these individuals in response to the antigens. In both the PI and the INF, Th2 responses against all the antigens tested were dominant. However, in the PI group as a whole, there was an enhanced Th2 response against the larval antigens and the adult male and adult female antigens, and a Th1 response in a subgroup of the PI (27 to 54.5%) against L3, mL3, and M-OvAg antigens was present. While the PI produced significantly higher levels of GM-CSF against L3, mL3, and M-OvAg antigens than the INF, there was no difference in the GM-CSF responses of the groups against the other antigens. The present study indicated that, in comparison to the INF, the PI have distinct larva-specific and adult male-specific cytokine responses, thus supporting the premise that immunological studies of the PI would lead to the identification of immune mechanisms and the target genes that play a role in protective immunity.