Witvliet D et al. (2021) Nature "Connectomes across development reveal principles of brain maturation."

Witvliet D, Chisholm AD, Holmyard D, Berger DR, Shavit N, Wu Y, Meirovitch Y, Liu Y, Lichtman JW, Samuel ADT, Mulcahy B, Zhen M, Mitchell JK, Koh WX, Schalek RL, Parvathala R

[Nature, 2021]

An animal's nervous system changes as its body grows from birth to adulthood and its behaviours mature^1-8. The form and extent of circuit remodelling across the connectome is unknown^3,9-15. Here we used serial-section electron microscopy to reconstruct the full brain of eight isogenic Caenorhabditis elegans individuals across postnatal stages to investigate how it changes with age. The overall geometry of the brain is preserved from birth to adulthood, but substantial changes in chemical synaptic connectivity emerge on this consistent scaffold. Comparing connectomes between individuals reveals substantial differences in connectivity that make each brain partly unique. Comparing connectomes across maturation reveals consistent wiring changes between different neurons. These changes alter the strength of existing connections and create new connections. Collective changes in the network alter information processing. During development, the central decision-making circuitry is maintained, whereas sensory and motor pathways substantially remodel. With age, the brain becomes progressively more feedforward and discernibly modular. Thus developmental connectomics reveals principles that underlie brain maturation.

Witvliet, D. et al. (2017) International Worm Meeting "The C. elegans connectome consist of invariant, stochastic, and developmentally regulated synapses."

Berger, D.R., Wang, J., Cook, S.J., Holmyard, D., Lichtman, J.W., Neubauer, M., Laskova, V., Zhen, M., Emmons, S.W., Mulcahy, B., Samuel, A.D.T., Kersen, D., Chisholm, A.D., Schalek, R.L., Koh, W.X., Qian, J., Hall, D.H., Mitchell, J.K., Chang, M., Witvliet, D.

[International Worm Meeting, 2017]

When animals are born, neuronal networks are already in place to integrate sensory cues and effect appropriate behavioral or homeostatic responses. During the course of postnatal development, synapses and circuits undergo refinement and remodeling, updating or adapting sensorimotor behaviors. Rules for developmental remodeling are poorly characterized, because a circuit-level analyses at multiple time points, in multiple animals are missing. We use an isogenic C. elegans N2 population to examine how the neural circuit changes during development. At birth, C. elegans has 218 neurons (excluding CAN); 82 new neurons are incorporated into the nervous system before the end of larval development. These include sensory, motor, and interneurons that are located throughout the body, suggesting a system-wide modification of the juvenile circuit during post-embryonic development. Using serial-section electron microscopy, we mapped the synaptic connectivity in the head and tail ganglia for five animals, from hatching to late larval development. These datasets allow us to separate the connectome into core connections, synapses that are present throughout the lifetime, transient connections, synapses that are present only during early or late development, and variable connections, synapses that are not conserved between animals. We propose that the core connections may drive hard-wired behaviors, and developmentally regulated connections exert stage-specific roles, while variable connections may confer individual variability and/or be stochastic in nature. Our current data analyses lead to two notions: First, developmentally regulated connections are enriched for synapses between sensory neurons, and with neuromodulatory neurons, while connections between interneurons are remarkably stable. This implies that for C. elegans, core circuits for decision-making are already established at birth, but their modulation and multi-sensory integration are refined or shaped during development. Second, variable connections, comprising about half of the connection edges in the published adult dataset, are prominent. Stochastic or experience dependent variability in connections may contribute to variability of behaviors set by hard-wired core connections.

Witvliet, D. et al. (2019) International Worm Meeting "Structural plasticity of the C. elegans connectome across development and between individuals."

Neubauer, M., Witvliet, D., Mitchell, J.K., Maeng, S., Meirovitch, Y., Chisholm, A.D., Wang, M.D., Shavit, N., Wang, Z., Ho, C.Y., Samuel, A.D.T., Lichtman, J.W., Koh, W.X., Schalek, R.L., Rehaluk, C., Mulcahy, B., Holmyard, D., Berger, D.R., Zhen, M., Cook, S.J.

[International Worm Meeting, 2019]

Nervous system development is widely thought to be optimized for precise wiring and efficient networks. Maintaining plasticity, however, is necessary for animals to adapt, learn, and evolve. This is especially evident during postembryonic development when newly born neurons are integrated into functioning neurocircuits. Rules for circuit plasticity and variability during and after development are poorly because circuit-level analyses across multiple animals and developmental time points are missing. Using electron microscopy, we mapped the connectome of the central nervous system for eight isogenic C. elegans animals spanning from birth to adulthood. These datasets reveal a highly dynamic circuit architecture, with a five-fold increase in synapse number across postembryonic development. Synapses are built and removed for multiple reasons: (1) to strengthen a remarkably stable core circuitry for decision-making, (2) to fine-tune multi-sensory integration and motor responses by building new unique cell-cell connections, (3) to streamline circuit computations, and (4) to fill connectivity gaps as a result of evolutionary pressures to hatch before initial wiring is complete. This remodeling is driven independently of the contact area between neurons and instead is dependent on neuron class and centrality. Remodeling is overrepresented between connections from sensory neurons to motor and interneurons, while connections between interneurons are remarkably stable. Well-connected, central neurons (typically interneurons), are more heavily regulated than other neurons, but surprisingly this regulation does not originate from other central neurons. Thus, the driving force for synaptic growth is not uniform, and may depend on neuron identity, suggesting an underpinning by genetic or functional identity. Together, our findings show that even in one of the most deterministic animals, nervous system wiring retains a high degree of plasticity. The connectome should be separated into core connections, that are present throughout life, developmentally changing connections, that depend on the stage of development, and variable connections, that are not conserved among individuals. Core connections are the strongest class of connections, but they make up less than half of all connections. The prevalence of wiring plasticity implicates relevance to nervous system adaptation and variability. Our data will be available on nemanode.org before the end of the summer.

Sakoguchi H et al. (2016) Biosci Biotechnol Biochem "Screening of biologically active monosaccharides: growth inhibitory effects of d-allose, d-talose, and l-idose against the nematode Caenorhabditis elegans."

Izumori K, Yoshihara A, Sakoguchi H, Sato M

[Biosci Biotechnol Biochem, 2016]

We compared the growth inhibitory effects of all aldohexose stereoisomers against the model animal Caenorhabditis elegans. Among the tested compounds, the rare sugars d-allose (d-All), d-talose (d-Tal), and l-idose (l-Ido) showed considerable growth inhibition under both monoxenic and axenic culture conditions. 6-Deoxy-d-All had no effect on growth, which suggests that C6-phosphorylation by hexokinase is essential for inhibition by d-All.

Sakoguchi H et al. (2016) Bioorg Med Chem Lett "Growth inhibitory effect of d-arabinose against the nematode Caenorhabditis elegans: Discovery of a novel bioactive monosaccharide."

Shintani T, Izumori K, Sato M, Sakoguchi H, Okuma K, Yoshihara A

[Bioorg Med Chem Lett, 2016]

Biological activities of unusual monosaccharides (rare sugars) have largely remained unstudied until recently. We compared the growth inhibitory effects of aldohexose stereoisomers against the animal model Caenorhabditis elegans cultured in monoxenic conditions with Escherichia coli as food. Among these stereoisomers, the rare sugar d-arabinose (d-Ara) showed particularly strong growth inhibition. The IC50 value for d-Ara was estimated to be 7.5mM, which surpassed that of the potent glycolytic inhibitor 2-deoxy-d-glucose (19.5mM) used as a positive control. The inhibitory effect of d-Ara was also observed in animals cultured in axenic conditions using a chemically defined medium; this excluded the possible influence of E. coli. To our knowledge, this is the first report of biological activity of d-Ara. The d-Ara-induced inhibition was recovered by adding either d-ribose or d-fructose, but not d-glucose. These findings suggest that the inhibition could be induced by multiple mechanisms, for example, disturbance of d-ribose and d-fructose metabolism.

Yoshihara A et al. (2019) Bioorg Med Chem Lett "Growth inhibition by 1-deoxy-d-allulose, a novel bioactive deoxy sugar, screened using Caenorhabditis elegans assay."

Sakoguchi H, Fleet GWJ, Izumori K, Shintani T, Sato M, Yoshihara A

[Bioorg Med Chem Lett, 2019]

The biological activities of deoxy sugars (deoxy monosaccharides) have remained largely unstudied until recently. We compared the growth inhibition by all 1-deoxyketohexoses using the animal model Caenorhabditis elegans. Among the eight stereoisomers, 1-deoxy-d-allulose (1d-d-Alu) showed particularly strong growth inhibition. The 50% inhibition of growth (GI₅₀) concentration by 1d-d-Alu was estimated to be 5.4mM, which is approximately 10 times lower than that of d-allulose (52.7mM), and even lower than that of the potent glycolytic inhibitor, 2-deoxy-d-glucose (19.5mM), implying that 1d-d-Alu has a strong growth inhibition. In contrast, 5-deoxy- and 6-deoxy-d-allulose showed no growth inhibition of C. elegans. The inhibition by 1d-d-Alu was alleviated by the addition of d-ribose or d-fructose. Our findings suggest that 1d-d-Alu-mediated growth inhibition could be induced by the imbalance in d-ribose metabolism. To our knowledge, this is the first report of biological activity of 1d-d-Alu which may be considered as an antimetabolite drug candidate.

Katane M et al. (2020) Biochim Biophys Acta Proteins Proteom "Biochemical characterization of d-aspartate oxidase from Caenorhabditis elegans: Its potential use in the determination of free D-glutamate in biological samples."

Katane M, Sekine M, Nakayama K, Homma H, Kuwabara H, Saitoh Y, Miyamoto T

[Biochim Biophys Acta Proteins Proteom, 2020]

d-Aspartate oxidase (DDO) is a flavin adenine dinucleotide (FAD)-containing flavoprotein that stereospecifically acts on acidic D-amino acids (i.e., free d-aspartate and D-glutamate). Mammalian DDO, which exhibits higher activity toward d-aspartate than D-glutamate, is presumed to regulate levels of d-aspartate in the body and is not thought to degrade D-glutamate in vivo. By contrast, three DDO isoforms are present in the nematode Caenorhabditis elegans, DDO-1, DDO-2, and DDO-3, all of which exhibit substantial activity toward D-glutamate as well as d-aspartate. In this study, we optimized the Escherichia coli culture conditions for production of recombinant C. elegans DDO-1, purified the protein, and showed that it is a flavoprotein with a noncovalently but tightly attached FAD. Furthermore, C. elegans DDO-1, but not mammalian (rat) DDO, efficiently and selectively degraded D-glutamate in addition to d-aspartate, even in the presence of various other amino acids. Thus, C. elegans DDO-1 might be a useful tool for determining these acidic D-amino acids in biological samples.

Shintani T et al. (2019) J Appl Glycosci (1999) "D-Allose, a Stereoisomer of D-Glucose, Extends the Lifespan of Caenorhabditis elegans via Sirtuin and Insulin Signaling."

Izumori K, Sakoguchi H, Yoshihara A, Shintani T, Sato M

[J Appl Glycosci (1999), 2019]

D-Allose (D-All), C-3 epimer of D-glucose, is a rare sugar known to suppress reactive oxygen species generation and prevent hypertension. We previously reported that D-allulose, a structural isomer of D-All, prolongs the lifespan of the nematode Caenorhabditis elegans. Thus, D-All was predicted to affect longevity. In this study, we provide the first empirical evidence that D-All extends the lifespan of C. elegans. Lifespan assays revealed that a lifespan extension was induced by 28 mM D-All. In particular, a lifespan extension of 23.8 % was achieved (p< 0.0001). We further revealed that the effects of D-All on lifespan were dependent on the insulin gene daf-16 and the longevity gene sir-2.1, indicating a distinct mechanism from those of other hexoses, such as D-allulose, with previously reported antiaging effects.

Sato M et al. (2008) J Nat Med "Potential anthelmintic: D-psicose inhibits motility, growth and reproductive maturity of L1 larvae of Caenorhabditis elegans."

Izumori K, Yamasaki T, Kurose H, Sato M

[J Nat Med, 2008]

No anthelmintic sugars have yet been identified. Eight ketohexose stereoisomers (D- and L-forms of psicose, fructose, tagatose and sorbose), along with D-galactose and D-glucose, were examined for potency against L1 stage Caenorhabditis elegans fed Escherichia coli. Of the sugars, D-psicose specifically inhibited the motility, growth and reproductive maturity of the L1 stage. D-Psicose probably interferes with the nematode nutrition. The present results suggest that D-psicose, one of the rare sugars, is a potential anthelmintic.

Yasuaki Saitoh et al. (2010) East Asia Worm Meeting "Study on physiological functions of D-amino acid degradative enzymes in nematode Caenorhabditis elegans"

Yousuke Seida, Kazuhiro Maeda, Tomonori Kawata, Masumi Katane, Hiroyuki Kobuna, Takao Inoue, Yasuaki Saitoh, Hiroyuki Arai, Yasuhito Nakagawa, Masae Sekine, Taro Sakamoto, Hiroshi Homma, Takemitsu Furuchi

[East Asia Worm Meeting, 2010]

Among free D-amino acids existing in living organisms, D-serine (D-Ser) and D-aspartate (D-Asp) are the most actively studied. D-Ser has been proposed as a neuromodulator that regulates L-glutamate-mediated activation of the N-methyl-D-Asp (NMDA) receptor by acting as a co-agonist. On the other hand, several lines of evidence suggest that D-Asp plays important roles in regulating developmental processes, hormone secretion and steroidogenesis. D-Amino acid oxidase (DAO) and D-Asp oxidase (DDO) are known as stereospecific degradative enzymes that catalyze the oxidative deamination of D-amino acids. DAO displays broad substrate specificity and acts on several neutral and basic D-amino acids, while DDO is highly specific for acidic D-amino acids. DAO and DDO are presumed to regulate endogenous D-Ser and D-Asp levels, respectively, as well as mediate the elimination of accumulated exogenous D-amino acids in various organs. Previously, we demonstrated that nematode Caenorhabditis elegans, a multicellular model animal has at least one active DAO gene and three active DDO genes, while it had been thought that most organisms bear only one copy of each DAO and DDO gene. In addition, our previous study revealed that the spatiotemporal distributions of these enzymes in the body of C. elegans are different from one another. In this study, to elucidate the physiological roles of the C. elegans DAO and DDOs, we characterized several phenotypes of four C. elegans mutants in which each gene is partially deleted and inactivated. We also determined free D-amino acid contents in several worm samples using high-performance liquid chromatography (HPLC) techniques. We will report the phenotypes of the C. elegans mutants in comparison with those of wild-type C. elegans, as well as alterations in D-amino acid levels within the body.