Charest DL et al. (1990) Mol Gen Genet "Genetic and fine structure analysis of unc-26(IV) and adjacent regions in Caenorhabditis elegans."

Charest DL, Green ME, Clark DV, Baillie DL

[Mol Gen Genet, 1990]

The genetic organization of unc-26(IV) and adjacent regions was studied in Caenorhabditis elegans. We constructed a fine structure genetic map of unc-26(IV), a gene that affects locomotion and pharyngeal muscle movement but not muscle structure. Eleven alleles were positioned relative to each other recombinationally and were classified according to phenotypic severity. The unc-26 gene spans at least 0.026 map units, which is exceptionally large for a C. elegans gene. All but one allele, e205, are amorphic alleles. Interestingly, e205 is hypomorphic but also suppressible by the amber suppressor sup-7. Nineteen lethal mutations in the unc-26 region were isolated and characterized. The unc-26 region is subdivided into four zones by five deficiency breakpoints. These mutations fall into 15 complementation groups. The stages of development affected by these mutations were determined.

Okumura E et al. (2013) J Exp Biol "Negative gravitactic behavior of Caenorhabditis japonica dauer larvae."

Yoshiga T, Tanaka R, Okumura E

[J Exp Biol, 2013]

Gravity on Earth is a constant stimulus and many organisms are able to perceive and respond to it. However, there is no clear evidence that nematodes respond to gravity. In this study, we demonstrated negative gravitaxis in a nematode using dauer larvae (DL) of Caenorhabditis japonica, which form an association with their carrier insect Parastrachia japonensis. Caenorhabditis japonica DL demonstrating nictation, a typical host-finding behavior, had a negative gravitactic behavior, whereas non-nictating C. japonica and C. elegans DL did not. The negative gravitactic index of nictating DL collected from younger nematode cultures was higher than that from older cultures. After a 24 h incubation in M9 buffer, nictating DL did not alter their negative gravitactic behavior, but a longer incubation resulted in less pronounced negative gravitaxis. These results are indicative of negative gravitaxis in nictating C. japonica DL, which is maintained once initiated, seems to be affected by the age of DL and does not appear to be a simple passive mechanism.

Tanaka R et al. (2012) Exp Gerontol "Low survivorship of dauer larva in the nematode Caenorhabditis japonica, a potential comparative system for a model organism, C. elegans."

Kanzaki N, Yoshiga T, Okumura E, Tanaka R

[Exp Gerontol, 2012]

The nematode dauer larva (DL) is a non-aging diapause stage. The DL of the model nematode Caenorhabditis elegans has been studied as a model system for aging and longevity. However, information on DL in other nematode species is limited. In this study, the survivorship, storage, energy consumption, and oxidative stress tolerance of Caenorhabditis japonica DL were examined. C. japonica is a close relative of C. elegans, but has species-specific phoretic associations with the shield bug Parastrachia japonensis. Also, its DL has a much longer lifespan than C. elegans in a biological setting. However, when C. japonica DLs were detached from their phoretic host, they did not survive more than 10 days while more than 80% of C. elegans survived under the same conditions. Also, C. japonica DL showed more active movement (swimming) and lower tolerance to oxidative stress than C. elegans DL. Because the concentration of triacylglycerol (TAG), the energy source of nematodes, did not decrease significantly during the experiment, exhaustion of the energy reservoir did not cause the low survivorship of C. japonica. Instead, low tolerance to oxidizing stress and increased production of reactive oxygen species in C. japonica were the main causes of the reduced survivorship. The fact that C. japonica DL cannot survive away from its insect host indicates that its longevity is increased by unknown factors derived from the host. Despite these significant differences between C. japonica and C. elegans, these two species are phylogenetically closely related (they are derived from a common ancestor). Therefore, C. japonica could be a good comparative system for C. elegans, and further physiological and molecular analyses of C. japonica DL may provide important information about the internal and external factors affecting the longevity of nematodes in general.

Rothstein M (1968) Comparative Biochemistry and Physiology "Nematode biochemistry - IX. Lack of sterol biosynthesis in free-living nematodes."

Rothstein M

[Comparative Biochemistry and Physiology, 1968]

1. Under axenic conditions, the free-living nematodes, Caenorhabditis briggsae, Turbatrix aceti and Panagrellus redivivus, are unable to synthesize cholesterol from acetate-2-C14 or DL-mevalonate-2-C14. 2. No evidence could be found that sterols other than cholesterol are synthesized by any of the organisms.

Saini V et al. (2014) Drug Deliv "Humoral and cell-mediated immune responses elicited by poly (DL-lactide) adjuvanted filarial antigen molecules."

Saini V, Murthy PK, Verma AK, Kushwaha V, Joseph SK, Kohli D

[Drug Deliv, 2014]

CONTEXT: In our recent studies, Brugia malayi molecules have shown interesting immune-stimulating and immune-suppressive properties. Among these, F6 a pro-inflammatory (54-68 kDa) SDS-PAGE resolved fraction of the parasite when administered with Freund's complete/incomplete adjuvant in animals, elicited both Th1 and Th2 type immune responses and protects the host from filarial parasite. OBJECTIVE: The present study was aimed at developing biodegradable microspheres for filarial antigenic protein molecules and to investigate the immunoadjuvanticity of microspheres (Ms)-loaded F6 molecules. MATERIALS AND METHODS: Poly-lactide microspheres (DL-PLA-Ms) were prepared using double emulsification and solvent evaporation method; and studied their size, shape, antigen adsorption efficiency, in-process stability, and antigen release profiles. F6 and B. malayi adult worm (BmA: 17 to 180 kDa) protein molecules adsorbed on the Ms were administered in a single shot into Swiss mice, subcutaneously, and investigated their immunoadjuvant effect and compared with one/two doses-schedule of plain F6/BmA. RESULTS: Immunization with F6/BmA-loaded DL-PLA-Ms resulted in upregulation of cellular proliferation, IFN- , TNF- and NO release from host's cells stimulated with F6/BmA or LPS/Con A, IgG, IgG1 and IgG2a levels. These responses were well comparable with the responses produced by two doses of plain BmA/F6. DISCUSSION AND CONCLUSION: In conclusion, a single dose of DL-PLA-Ms-F6 induced predominantly Th1 immune responses and well comparable with two doses of plain F6. This is the first ever report on potential of DL-PLA-Ms as adjuvant for filarial immunogen.

Vertiz, Johnny et al. (2021) MicroPubl Biol

Vertiz, Johnny, Hong, Ray, Carstensen, Heather

[MicroPubl Biol, 2021]

Reproductive adults and developmentally arrested larvae often occupy different ecological niches and thus are expected to respond differently to environmental stimuli. To understand the genes that coordinate dauer development and olfactory behavior, we examined adult and dauer C. elegans in wild-type and dauer constitutive mutants (Daf-c). We found all dauers showed decreased attraction to all three odorants tested compared to adults, with daf-7 dauer larva (DL) exhibiting a concentration-dependent preference shift towards isoamyl alcohol, suggesting that the TGF- pathway is involved in both dauer regulation and dauer-specific odortaxis.

Moosa S et al. (2021) BioData Min "DASSI: differential architecture search for splice identification from DNA sequences."

Moosa S, Amira PA, Boughorbel DS

[BioData Min, 2021]

BACKGROUND: The data explosion caused by unprecedented advancements in the field of genomics is constantly challenging the conventional methods used in the interpretation of the human genome. The demand for robust algorithms over the recent years has brought huge success in the field of Deep Learning (DL) in solving many difficult tasks in image, speech and natural language processing by automating the manual process of architecture design. This has been fueled through the development of new DL architectures. Yet genomics possesses unique challenges that requires customization and development of new DL models. METHODS: We proposed a new model, DASSI, by adapting a differential architecture search method and applying it to the Splice Site (SS) recognition task on DNA sequences to discover new high-performance convolutional architectures in an automated manner. We evaluated the discovered model against state-of-the-art tools to classify true and false SS in Homo sapiens (Human), Arabidopsis thaliana (Plant), Caenorhabditis elegans (Worm) and Drosophila melanogaster (Fly). RESULTS: Our experimental evaluation demonstrated that the discovered architecture outperformed baseline models and fixed architectures and showed competitive results against state-of-the-art models used in classification of splice sites. The proposed model - DASSI has a compact architecture and showed very good results on a transfer learning task. The benchmarking experiments of execution time and precision on architecture search and evaluation process showed better performance on recently available GPUs making it feasible to adopt architecture search based methods on large datasets. CONCLUSIONS: We proposed the use of differential architecture search method (DASSI) to perform SS classification on raw DNA sequences, and discovered new neural network models with low number of tunable parameters and competitive performance compared with manually engineered architectures. We have extensively benchmarked DASSI model with other state-of-the-art models and assessed its computational efficiency. The results have shown a high potential of using automated architecture search mechanism for solving various problems in the field of genomics.

Lu NC et al. (1977) Nematologica "The requirement of sterol and various sterol precursors in free-living nematodes."

Lu NC, Newton C, Stokstad ELR

[Nematologica, 1977]

The quantitative sterol requirements were studied in C. briggsae, C. elegans (Be), C. elegans (Br), and T. aceti. It was shown that all four nematodes had similar minimal sterol requirements (0.1-2.0 ug/ml) and toxicity appeared in T. aceti at 50 ug/ml. Cholesterol and five precursors were tested for population growth. We found that acetic acid, DL-mevalonic acid lactone, and farnesol did not support population growth; while squalene, lanosterol, and cholesterol supported significant population growth in all four nematodes. Our results suggest that the major metabolic block in the pathway of sterol biosynthesis occurs between the step of farnesol and squalene.

Liu Y et al. (2017) PLoS One "NtrC-dependent control of exopolysaccharide synthesis and motility in Burkholderia cenocepacia H111."

Lardi M, Eberl L, Pedrioli A, Pessi G, Liu Y

[PLoS One, 2017]

Burkholderia cenocepacia is a versatile opportunistic pathogen that survives in a wide variety of environments, which can be limited in nutrients such as nitrogen. We have previously shown that the sigma factor 54 is involved in the control of nitrogen assimilation and virulence in B. cenocepacia H111. In this work, we investigated the role of the 54 enhancer binding protein NtrC in response to nitrogen limitation and in the pathogenicity of H111. Of 95 alternative nitrogen sources tested the ntrC showed defects in the utilisation of nitrate, urea, L-citrulline, acetamide, DL-lactamide, allantoin and parabanic acid. RNA-Seq and phenotypic analyses of an ntrC mutant strain showed that NtrC positively regulates two important phenotypic traits: exopolysaccharide (EPS) production and motility. However, the ntrC mutant was not attenuated in C. elegans virulence.

Migunova VD et al. (2005) Pedobiologia (Jena) "Determinants of trophic modes of the nematophagous fungus Arthrobotrys oligospora interacting with bacteriovous nematode Caenorhabditis elegans."

Migunova VD, Byzov BA

[Pedobiologia (Jena), 2005]

The determinants of saprotrophic or predatory modes of the nematophagous fungus Arthrobotrys oligospora were investigated in soil microcosms and on solid nutrient media. A sterilized soil amended with 1% w/w alfalfa meat (C:N = 32) and inocutated with conidia of A. oligospora, showed lower mycelium biomass and higher specific rate of conidia production in the presence of the bacterivorous nematode Caenorhabditis elegans than in its absence. As few as 10 nematodes g-1 soil. were sufficient to enhance spore formation by the vegetative mycelium. Given that the fungus was not limited by available carbon and nitrogen, this indicates that nematodes provide essential. growth factors regulating the development of A. oligospora. Carbon mineralisation by A. oligospora, measured as the rate of CO2 production, was found to be 25-35% tower in the presence of 20-60 C. elegans g(-1) soil compared to soil without nematodes. This showed that A. oligospora had tower saprotrophic activity in the predaceous phase. Trap formation and nematophagous activity of A. oligospora were observed only where conidia were inoculated on nutrient poor medium (water agar), on tow-nitrogen medium (Yeast Carbon Base agar) or on medium containing no amino-acids or vitamins (Czapek-Dox agar). A. oligospora did not form trapping structures when grown on nutrient-rich media containing three amino-acids (L-histidine monohydrocloride, DL-methionine and DL-tryptophan) and vitamins (biotin, calcium pantothenate, folic acid, inositol, niacin, p-aminobenzoic acid, pyridoxine hydrochloride, riboflavine, thiamine hydrochloride). It is concluded that predaceous behaviour of A. oligospora can be regulated either by nitrogen sources or by physiologically active compounds (amino-acids or vitamins) present in nematodes.