Zetka M-C et al. (1993) Worm Breeder's Gazette "Mapping of the rec-1 Mutation"

Rose AM, Zetka M-C

[Worm Breeder's Gazette, 1993]

MAPPING OF THE rec-1 MUTATION Monique-Claire Zetka and Ann M. Rose, Dept. of Medical Genetics, 6174 University Blvd., University of British Columbia, Vancouver, B.C., V6T lZ3.

Haesemeyer M et al. (2019) Neuron "Convergent Temperature Representations in Artificial and Biological Neural Networks."

Haesemeyer M, Schier AF, Engert F

[Neuron, 2019]

Discoveries in biological neural networks (BNNs) shaped artificial neural networks (ANNs) and computational parallels between ANNs and BNNs have recently been discovered. However, it is unclear to what extent discoveries in ANNs can give insight into BNN function. Here, we designed and trained an ANN to perform heat gradient navigation and found striking similarities in computation and heat representation to a known zebrafish BNN. This included shared ON- and OFF-type representations of absolute temperature and rates of change. Importantly, ANN function critically relied on zebrafish-like units. We furthermore used the accessibility of the ANN to discover anew temperature-responsive cell type in the zebrafish cerebellum. Finally, constraining the ANN by the C.elegans motor repertoire retuned sensory representations indicating that our approach generalizes. Together, these results emphasize convergence of ANNs and BNNs on stereotypical representations and that ANNs form a powerful tool to understand their biological counterparts.

Cindy M Voisine et al. (2003) International Worm Meeting "Modifiers of polyglutamine-mediated neurodegeneration in C. elegans"

Anne C Hart, Adriana Jones, Ann Fisher, Cindy M Voisine

[International Worm Meeting, 2003]

At least eight hereditary neurodegenerative disorders, including Huntington's Disease, have been identified in which the disease locus expresses a protein that contains an expanded glutamine tract. We have previously established a model system for studying polyglutamine (polyQ) neurotoxicity in C. elegans (PNAS 96, 179-184, 1999). The N-terminus of the mutant human huntingtin protein, which contains an expanded glutamine tract, is expressed in the well-characterized ASH neurons. Expression of the expanded huntingtin polyglutamine tract leads to age-dependent degeneration of the ASH neurons. To identify genes that normally protect neurons from polyQ-mediated neurodegeneration, we performed an F2 EMS screen for mutations in genes that enhanced polyQ toxicity in ASH neurons. Seven strains were isolated that carried mutations in a previously uncharacterized gene, pqe-1 (polyQ enhancer-1). Differential splicing of pqe-1 results in at least three nuclear localized PQE-1 proteins. PQE-1A and PQE-1B contain a putative exonuclease domain. PQE-1A and PQE-1C contain a large glutamine/proline-rich domain which is essential for pqe-1 function (PNAS 99, 17131-6, 2002). To understand the relationship between polyglutamine toxicity and pqe-1 function, we plan to use a yeast two hybrid screen to identify PQE-1 interacting factors. Currently, we are determining the smallest region of PQE-1 necessary to protect ASH neurons from polyQ insults. Two genetic approaches are underway to identify additional genes that modulate polyQ toxicity. First, we are using RNA interference (RNAi) to systematically target genes that protect neurons from polyQ-mediated neurodegeneration. We are focusing on those genes whose decrease in function results in sterility or reduced viability, since these candidates may have been missed in the original F2 EMS screen described above. To identify genes that are required for poly-Q mediated neurodegeneration, we also performed a genetic screen to isolate mutations that suppress polyQ-mediated ASH neurodegeneration. Identification and characterization of genes isolated from these collective approaches will provide insight into pathogenic mechanisms underlying polyQ-induced neurodegeneration.

Avery L (1995) Worm Breeder's Gazette "Effects of Conus venoms on the pharynx"

Avery L

[Worm Breeder's Gazette, 1995]

Cone snails are predatory snails. They harpoon their prey, which may be small fish, marine worms, or other snails, then inject a paralyzing venom through the hollow harpoon (Olivera et al, Science 249: 257). The venom is a complex mixture of tiny peptide toxins, different in each species. Several of these toxins have been shown to act on cell-surface molecules important for nervous system function such as the N-type Ca++ channel or the voltage-gated Na+ channel (Gray et al, Ann Rev Biochem 57: 665).

Park C et al. (2023) Exp Neurobiol "Caenorhabditis elegans Connectomes of both Sexes as Image Classifiers."

Kim JS, Park C

[Exp Neurobiol, 2023]

Connectome, the complete wiring diagram of the nervous system of an organism, is the biological substrate of the mind. While biological neural networks are crucial to the understanding of neural computation mechanisms, recent artificial neural networks (ANNs) have been developed independently from the study of real neural networks. Computational scientists are searching for various ANN architectures to improve machine learning since the architectures are associated with the accuracy of ANNs. A recent study used the hermaphrodite <i>Caenorhabditis elegans</i> (<i>C. elegans</i>) connectome for image classification tasks, where the edge directions were changed to construct a directed acyclic graph (DAG). In this study, we used the whole-animal connectomes of <i>C. elegans</i> hermaphrodite and male to construct a DAG that preserves the chief information flow in the connectomes and trained them for image classification of MNIST and fashion-MNIST datasets. The connectome-inspired neural networks exhibited over 99.5% and 92.6% of accuracy for MNIST and fashion-MNIST datasets, respectively, which increased from the previous study. Together, we conclude that realistic biological neural networks provide the basis of a plausible ANN architecture. This study suggests that biological networks can provide new inspiration to improve artificial intelligences (AIs).

Nakajima R et al. (2021) Mol Brain "Similarities of developmental gene expression changes in the brain between human and experimental animals: rhesus monkey, mouse, Zebrafish, and Drosophila."

Hagihara H, Nakajima R, Miyakawa T

[Mol Brain, 2021]

Aim: Experimental animals, such as non-human primates (NHPs), mice, Zebrafish, and Drosophila, are frequently employed as models to gain insights into human physiology and pathology. In developmental neuroscience and related research fields, information about the similarities of developmental gene expression patterns between animal models and humans is vital to choose what animal models to employ. Here, we aimed to statistically compare the similarities of developmental changes of gene expression patterns in the brains of humans with those of animal models frequently used in the neuroscience field.Methods: The developmental gene expression datasets that we analyzed consist of the fold-changes and P values of gene expression in the brains of animals of various ages compared with those of the youngest postnatal animals available in the dataset. By employing the running Fisher algorithm in a bioinformatics platform, BaseSpace, we assessed similarities between the developmental changes of gene expression patterns in the human (Homo sapiens) hippocampus with those in the dentate gyrus (DG) of the rhesus monkey (Macaca mulatta), the DG of the mouse (Mus musculus), the whole brain of Zebrafish (Danio rerio), and the whole brain of Drosophila (D. melanogaster).Results: Among all possible comparisons of different ages and animals in developmental changes in gene expression patterns within the datasets, those between rhesus monkeys and mice were highly similar to those of humans with significant overlap P-value as assessed by the running Fisher algorithm. There was the highest degree of gene expression similarity between 40-59-year-old humans and 6-12-year-old rhesus monkeys (overlap P-value = 2.1 10- 72). The gene expression similarity between 20-39-year-old humans and 29-day-old mice was also significant (overlap P = 1.1 10- 44). Moreover, there was a similarity in developmental changes of gene expression patterns between 1-2-year-old Zebrafish and 40-59-year-old humans (Overlap P-value = 1.4 10- 6). The overlap P-value of developmental gene expression patterns between Drosophila and humans failed to reach significance (30 days Drosophila and 6-11-year-old humans; overlap P-value = 0.0614).Conclusions: These results indicate that the developmental gene expression changes in the brains of the rhesus monkey, mouse, and Zebrafish recapitulate, to a certain degree, those in humans. Our findings support the idea that these animal models are a valid tool for investigating the development of the brain in neurophysiological and neuropsychiatric studies.

Tiffany Roby et al. (2002) Mid-west Worm Meeting "Defining Regulatory Regions In Nematode Muscle Genes By Computational And Transgenic Studies."

Gary Stormo, Lawrence Schriefer, Robert Waterston, Tiffany Roby, Michelle Hresko, Debraj GuhaThakurta

[Mid-west Worm Meeting, 2002]

We have initiated experiments designed to understand the regulatory regions of C. elegans genes using known muscle genes of C. elegans as a model(1). Our primary approach is to use a combination of computational methods to identify potential muscle specific regulatory elements from the known set of C. elegans muscle genes. Local multiple sequence alignment methods like Consensus(1), Ann-Spec(2), and Co-Bind(3) are being used to identify these potential regulatory elements. Using the above method we have already identified several potential regulatory elements that show high degree of specificity for the muscle genes. The regulatory elements that these computational methods predict can then be used to screen the C. elegansgenome for new genes that are expressed in muscle cells.

Stewart HI et al. (1996) West Coast Worm Meeting "Rescue of New Essential Genes on LGIII(left), in the Nematode Caenorhabditis elegans."

Stewart HI, Franz NW, Barbazuk BW, Baillie DL, Ha TT

[West Coast Worm Meeting, 1996]

We utilized trangenic strains containing cosmids, sequenced by the sequencing consortium, to rescue the lethal phenotype of several essential genes (See presentation by Diana Janke et al, this session). The rescued genes are positioned on LGIII(left) balanced by the duplication sDp3(see poster; Stewart et al, this session). A set of overlapping deficiencies was utilized to define areas within which to focus our rescue attempts). PCR analysis was utilized to further define the end points of these deficiencies, facilitating our analysis ( see poster ; Norm Franz et al, this session). We concentrated our analysis on areas to the right of dpy-17, in the interval between dpy-17 to dpy-19. Lethals mapping to sDf125 that were not rescued by sDp8 are presented in a poster by Nigel O'Niel et al, this session. We have rescued several essential genes. Our rescues will facilitate the functional analysis of these new genes. These rescues have also helped us to align and correlate the physical and genetic maps. Our estimates are that there will be more than two essential genes per cosmid. A total of 202 recessive lethal mutations have been generated, using EMS as a mutagen. We intend to make molecular assignments of all of these elements, through our cosmid rescue experiments. As we have estimated that there is only a 28% saturation of the area for essential genes, we will be generating more recessive lethal genes, to facilitate this analysis. This work has been funded by grants from the National Institute of Health (N.I.H.), U. S.A. to Ann Rose; D. Riddle and David Baillie and Canadian Genome and Advanced Technologies (C.G.A.T.), Canada to Ann Rose and David Baillie.

Hurd DD (2008) CBE Life Sci Educ "A microcosm of the biomedical research experience for upper-level undergraduates."

Hurd DD

[CBE Life Sci Educ, 2008]

The skill set required of biomedical researchers continues to grow and evolve as biology matures as a natural science. Science necessitates creative yet critical thinking, persuasive communication skills, purposeful use of time, and adeptness at the laboratory bench. Teaching these skills can be effectively accomplished in an inquiry-based, active-learning environment at a primarily undergraduate institution. Cell Biology Techniques, an upper-level cell biology laboratory course at St. John Fisher College, features two independent projects that take advantage of the biology of the nematode Caenorhabditis elegans, a premier yet simple model organism. First, students perform a miniature epigenetic screen for novel phenotypes using RNA interference. The results of this screen combined with literature research direct students toward a singe gene that they attempt to subclone in the second project. The biology of the chosen gene/protein also becomes an individualized focal point with respect to the content of the laboratory. Progress toward course goals is evaluated using written, oral, and group-produced assignments, including a concept map. Pre- and postassessment indicates a significant increase in the understanding of broad concepts in cell biological research.

Papp A (1992) Worm Breeder's Gazette "Results of Worm Plate Survey"

Papp A

[Worm Breeder's Gazette, 1992]

After tabulating the results of the Worm Plate Survey. we have come up with some interesting results. Most notably. the high variability in prices that labs are paying for their plates, even for the exact same plates from the same supplier, and the fact that most plates are marked up considerably over the actual cost. The replies can be separated into 4 categories: Labs that get plates from Fisher ($29-$58). but wish they had non-vented plates Labs that get non-vented plates via Applied Scientific (~$38) Labs that get plates from Falcon (vented) or Nunc (non-vented) and pay much more Most labs' plates were "slipable" or "semi-stackable", but all labs wanted plates that stack well for easy manual pouring, seeding, carrying, and using. Everyone wanted plates with shallow lids such that the bottoms can be lifted out of the tops for inverted use. Some labs expressed an interest in plates slightly smaller than "60 mm". That number is in quotes because all of the companies' plates have bottoms smaller than 60 mm (e.g. Fisher -54 x 14 mm). We have negotiated with the plastic companies that really make the plates for Fisher, Applied Scientific, etc. (that actually just resell them to you). I have come to the conclusion that we can provide you with better worm plates, the same worm plates cheaper, or in most cases better worm plates cheaper. This is true for every lab. The bottom line is that we can get you top quality non-vented "60 mm" plates (like Applied Scientific's, except fully stackable) for about $29 per 500 case INCLUDING shipping depending on your usage and how many cases you can receive at one time. Several labs have found the non-vented plates last longer without drying out or getting contaminated, compared with normal vented plates, so you should save that way, too. We offer full service shipping (e.g. standing orders and same-day telephone orders, free. Similarly low prices are available on 100 mm and 150 mm plates that exceed industry standards for flatness (reducing media usage) and clarity. The 100 mm are about $27 per 500 case plus shipping; The 150 mm dishes (good for DNA & RNA preps and library platings, with more than 2.25x the surface area of 100 mm dishes) are made thicker and deeper than industry standards and are about $21.50 per 100 case plus shipping. The shipping charge is very low for labs, or groups of labs in one city, that can take delivery of many cases in a single shipment. You can even suggest that your stockroom order plates from us. Call us for an exact price quote depending on your usage and how many cases you can receive at one time. In any case, we'll work things out to save you money. In the future, we can offer inexpensive 35 mm dishes if the community at large can order about 2000 cases per year, so let me know about your needs for other sizes. The response was very mixed about pre-poured plates. We may set that up later, but for now we can help the most by saving you lots on empty petri dishes (and later, maybe media .supplies). We are happy to send out free samples so you can examine the dishes. If we haven't contacted you yet, just give us a call. Respondents: 38 (including 5 anonymous) "Winners": Horvitz = 550, Meyer = 400, Thomas = 400, Greenwald = 300 200-299 cases 8 labs 100-199 cases 7 labs 4-99 cases 19 labs Highest price per case: US = 118.75, Canada = $117 (non-vented) Lowest price per case: US = $29, Canada = $25 (vented) Farthest away response: Malta! No responses from MRC or anyone else in Europe or Asia. It is possible that we can save money and/or provide better plates for these labs, including, shipping, too. Let us know.