DuPlissis, A. J.T. et al. (2019) International Worm Meeting "Neural signal extraction from high dimensional calcium imaging using spatiotemporal neural networks."

DuPlissis, A. J.T., Ben-Yakar, A., Mondal, S., Kato, S.

[International Worm Meeting, 2019]

While many scientific and industrial imaging applications have enjoyed significant automation of feature detection via machine learning algorithms, high dimensional (3D and 4D) imaging systems have yet to experience such a revolution. One such challenge is whole brain calcium imaging of C. elegans. To extract biologically relevant data from volumetric video microscopy, each neuron in a volume must be segmented and subsequently tracked through time. The amount of data collected in an imaging session prohibits manual performance of this task. Current automated segmentation and tracking solutions first dissociate the temporal and spatial domains, leading to two issues: 1) the inability to optimize volumetric segmentation jointly with temporal coherence, and 2) the requirement to perform neuron tracking and segmentation separately. Many of these approaches further dissociate the spatial domain by treating axial slices as independent measurements, leading to further loss of potential computational efficiency. Here, we propose a novel machine learning approach for neuron segmentation and low-level tracking that addresses these issues. Our solution is a four-dimensional convolutional neural network that learns to discriminate background from foreground in a pixel-wise manner and also learns the underlying distribution of the ground truth via an adversarial discriminator network. With processing speeds on a desktop computer exceeding two volumes per second, this system can allow near-real time data extraction when fed data directly from an imaging system. Our approach should be translatable to any fluorescent imaging environment. We demonstrate the successful use of this system on various whole brain recording setups.

Watson N et al. (2020) Front Opt "Planar Laser Activated Neuronal Scanning (PLANS) System for in vivo Flow Cytometry."

Ben-Yakar A, Mondal S, DuPlissis A, Kim KH, Watson N

[Front Opt, 2020]

We present a light-sheet flow cytometer for screening of C. elegans. A machine learning approach is utilized to enable real-time analysis of protein aggregation models.

Mondal, S. et al. (2019) International Worm Meeting "A whole-animal confocal imaging platform shows oscillating motor neuron activities in the basal motor neuron circuit."

Ben-Yakar, A., Zimmer, M., Kato, S., Mondal, S., Martin, C., Hegarty, E., ZHAO, P., Duplissis, A., Kim, K.H.

[International Worm Meeting, 2019]

One of the many complex behaviors is the locomotion of living creatures that are controlled by a well-coordinated neural network and the neuromuscular junctions. It has been difficult to probe and understand this complex behavior in the larger animals. The simplicity of the invertebrate neuronal system has helped to identify system-level information to understand the biological process underlying how complex neuronal networks operate. In order to study latent motor neuron activities, we capture all the motor neurons present in the ventral cord of a larval 4 stage C. elegans. The animal is immobilized inside a meander-shaped microfluidic channel to mimic its natural body posture during crawling. A custom-designed confocal system with a flexible field of view is used to image the entire animal within 630 × 160 mum2 and using 430 nm optical resolutions. We characterized the basal activities of the entire motor neuron circuit in the anesthetic-free animal to identify oscillatory neuron responses using imaging rate of >5 volumes per second. To autonomously extract each neuron's signal, we denoise each volume via multiscale analysis and identify unique neurons based on a set of pixel-wise statistical and morphological features. An interactive software allows for human input and customizes neuron identification to correct for the errors made during automated analysis before each neural trace is extracted for further analysis. We observed sparse latent signaling patterns in the C. elegans motor activities that can be described well by a low-dimensional space, within some bound of error, to a high degree of precision.

Zhao P et al. (2023) Nat Methods "Femtosecond laser microdissection for isolation of regenerating C. elegans neurons for single-cell RNA sequencing."

Jiang N, Ma KY, Chizari S, Ben-Yakar A, DuPlissis A, Martin C, Mondal S, Messing RO, Maiya R, Zhao P

[Nat Methods, 2023]

Our understanding of nerve regeneration can be enhanced by delineating its underlying molecular activities at single-neuron resolution in model organisms such as Caenorhabditis elegans. Existing cell isolation techniques cannot isolate neurons with specific regeneration phenotypes from C. elegans. We present femtosecond laser microdissection (fs-LM), a single-cell isolation method that dissects specific cells directly from living tissue by leveraging the micrometer-scale precision of fs-laser ablation. We show that fs-LM facilitates sensitive and specific gene expression profiling by single-cell RNA sequencing (scRNA-seq), while mitigating the stress-related transcriptional artifacts induced by tissue dissociation. scRNA-seq of fs-LM isolated regenerating neurons revealed transcriptional programs that are correlated with either successful or failed regeneration in wild-type and dlk-1 (0) animals, respectively. This method also allowed studying heterogeneity displayed by the same type of neuron and found gene modules with expression patterns correlated with axon regrowth rate. Our results establish fs-LM as a spatially resolved single-cell isolation method for phenotype-to-genotype mapping.

Quartey MO et al. (2021) Sci Rep "The A(1-38) peptide is a negative regulator of the A(1-42) peptide implicated in Alzheimer disease progression."

Pennington PR, Heistad RM, Nyarko JNK, Barnes JR, Bolanos MAC, Parsons MP, Knudsen KJ, De Carvalho CE, Leary SC, Mousseau DD, Buttigieg J, Maley JM, Quartey MO

[Sci Rep, 2021]

The pool of -Amyloid (A) length variants detected in preclinical and clinical Alzheimer disease (AD) samples suggests a diversity of roles for A peptides. We examined how a naturally occurring variant, e.g. A(1-38), interacts with the AD-related variant, A(1-42), and the predominant physiological variant, A(1-40). Atomic force microscopy, Thioflavin T fluorescence, circular dichroism, dynamic light scattering, and surface plasmon resonance reveal that A(1-38) interacts differently with A(1-40) and A(1-42) and, in general, A(1-38) interferes with the conversion of A(1-42) to a -sheet-rich aggregate. Functionally, A(1-38) reverses the negative impact of A(1-42) on long-term potentiation in acute hippocampal slices and on membrane conductance in primary neurons, and mitigates an A(1-42) phenotype in Caenorhabditis elegans. A(1-38) also reverses any loss of MTT conversion induced by A(1-40) and A(1-42) in HT-22 hippocampal neurons and APOE 4-positive human fibroblasts, although the combination of A(1-38) and A(1-42) inhibits MTT conversion in APOE 4-negative fibroblasts. A greater ratio of soluble A(1-42)/A(1-38) [and A(1-42)/A(1-40)] in autopsied brain extracts correlates with an earlier age-at-death in males (but not females) with a diagnosis of AD. These results suggest that A(1-38) is capable of physically counteracting, potentially in a sex-dependent manner, the neuropathological effects of the AD-relevant A(1-42).

Danielle Thierry-Mieg et al. (2003) Worm Breeder's Gazette "www.wormgenes.org , a new gene centered database"

Vahan Simonyan, Michel Potdevin, Mark Sienkiewicz, Yuji KOHARA, Jean Thierry-Mieg, Danielle Thierry-Mieg, Tadasu SHIN-I

[Worm Breeder's Gazette, 2003]

Wormgenes is a new resource for C.elegans offering a detailed summary about each gene and a powerful query system.

Tangrodchanapong T et al. (2020) Front Pharmacol "Frondoside A Attenuates Amyloid- Proteotoxicity in Transgenic Caenorhabditis elegans by Suppressing Its Formation."

Tangrodchanapong T, Sobhon P, Meemon K

[Front Pharmacol, 2020]

Oligomeric assembly of Amyloid- (A) is the main toxic species that contribute to early cognitive impairment in Alzheimer's patients. Therefore, drugs that reduce the formation of A oligomers could halt the disease progression. In this study, by using transgenic <i>Caenorhabditis elegans</i> model of Alzheimer's disease, we investigated the effects of frondoside A, a well-known sea cucumber <i>Cucumaria frondosa</i> saponin with anti-cancer activity, on A aggregation and proteotoxicity. The results showed that frondoside A at a low concentration of 1 M significantly delayed the worm paralysis caused by A aggregation as compared with control group. In addition, the number of A plaque deposits in transgenic worm tissues was significantly decreased. Frondoside A was more effective in these activities than ginsenoside-Rg3, a comparable ginseng saponin. Immunoblot analysis revealed that the level of small oligomers as well as various high molecular weights of A species in the transgenic <i>C. elegans</i> were significantly reduced upon treatment with frondoside A, whereas the level of A monomers was not altered. This suggested that frondoside A may primarily reduce the level of small oligomeric forms, the most toxic species of A. Frondoside A also protected the worms from oxidative stress and rescued chemotaxis dysfunction in a transgenic strain whose neurons express A. Taken together, these data suggested that low dose of frondoside A could protect against A-induced toxicity by primarily suppressing the formation of A oligomers. Thus, the molecular mechanism of how frondoside A exerts its anti-A aggregation should be studied and elucidated in the future.

Hodgkin JA (1998) International Journal of Developmental Biology "Seven types of pleiotropy."

Hodgkin JA

[International Journal of Developmental Biology, 1998]

Pleiotropy , a situation in which a single gene influences multiple phenotypic tra its, can arise in a variety of ways. This paper discusses possible underlying mechanisms and proposes a classification of the various phenomena involved.

Tuck S (2011) Curr Biol "Extracellular vesicles: budding regulated by a phosphatidylethanolamine translocase."

Tuck S

[Curr Biol, 2011]

Recent work on a Caenorhabditis elegans transmembrane ATPase reveals a central role for the aminophospholipid phosphatidylethanolamine in the production of a class of extracellular vesicles.

Viney ME et al. (2004) Naturwissenschaften "Is dauer pheromone of Caenorhabditis elegans really a pheromone?"

Viney ME, Franks NR

[Naturwissenschaften, 2004]

Animals respond to signals and cues in their environment. The difference between a signal (e.g. a pheromone) and a cue (e.g. a waste product) is that the information content of a signal is subject to natural selection, whereas that of a cue is not. The model free-living nematode Caenorhabditis elegans forms an alternative developmental morph (the dauer larva) in response to a so-called 'dauer pheromone', produced by all worms. We suggest that the production of 'dauer pheromone' has no fitness advantage for an individual worm and therefore we propose that 'dauer pheromone' is not a signal, but a cue. Thus, it should not be called a pheromone.