Yuan J et al. (2020) Nature "Two conserved epigenetic regulators prevent healthy ageing."

Yuan J, Yin JA, Lin DY, Gao G, Chang SY, Cheng X, Chen Z, Liu ZY, Cai SQ, Jiang L, Kang XL, Ye SW, Hao P, Yin SG, Liu XJ, Jiang Q

[Nature, 2020]

It has long been assumed that lifespan and healthspan correlate strongly, yet the two can be clearly dissociated^1-6. Although there has been a global increase in human life expectancy, increasing longevity is rarely accompanied by an extended healthspan^4,7. Thus, understanding the origin of healthy behaviours in old people remains an important and challenging task. Here we report a conserved epigenetic mechanism underlying healthy ageing. Through genome-wide RNA-interference-based screening of genes that regulate behavioural deterioration in ageing Caenorhabditis elegans, we identify 59 genes as potential modulators of the rate of age-related behavioural deterioration. Among these modulators, we found that a neuronal epigenetic reader, BAZ-2, and a neuronal histone 3 lysine 9 methyltransferase, SET-6, accelerate behavioural deterioration in C. elegans by reducing mitochondrial function, repressing the expression of nuclear-encoded mitochondrial proteins. This mechanism is conserved in cultured mouse neurons and human cells. Examination of human databases^8,9 shows that expression of the human orthologues of these C. elegans regulators, BAZ2B and EHMT1, in the frontal cortex increases with age and correlates positively with the progression of Alzheimer's disease. Furthermore, ablation of Baz2b, the mouse orthologue of BAZ-2, attenuates age-dependent body-weight gain and prevents cognitive decline in ageing mice. Thus our genome-wide RNA-interference screen in C. elegans has unravelled conserved epigenetic negative regulators of ageing, suggesting possible ways to achieve healthy ageing.

Yuan J et al. (2014) Proc Natl Acad Sci U S A "Gait synchronization in Caenorhabditis elegans."

Bau HH, Yuan J, Raizen DM

[Proc Natl Acad Sci U S A, 2014]

Collective motion is observed in swarms of swimmers of various sizes, ranging from self-propelled nanoparticles to fish. The mechanisms that govern interactions among individuals are debated, and vary from one species to another. Although the interactions among relatively large animals, such as fish, are controlled by their nervous systems, the interactions among microorganisms, which lack nervous systems, are controlled through physical and chemical pathways. Little is known, however, regarding the mechanism of collective movements in microscopic organisms with nervous systems. To attempt to remedy this, we studied collective swimming behavior in the nematode Caenorhabditis elegans, a microorganism with a compact nervous system. We evaluated the contributions of hydrodynamic forces, contact forces, and mechanosensory input to the interactions among individuals. We devised an experiment to examine pair interactions as a function of the distance between the animals and observed that gait synchronization occurred only when the animals were in close proximity, independent of genes required for mechanosensation. Our measurements and simulations indicate that steric hindrance is the dominant factor responsible for motion synchronization in C. elegans, and that hydrodynamic interactions and genotype do not play a significant role. We infer that a similar mechanism may apply to other microscopic swimming organisms and self-propelled particles.

Yuan J et al. (2015) Lab Chip "High-throughput, motility-based sorter for microswimmers such as C. elegans."

Yuan J, Zhou J, Raizen DM, Bau HH

[Lab Chip, 2015]

Animal motility varies with genotype, disease, aging, and environmental conditions. In many studies, it is desirable to carry out high throughput motility-based sorting to isolate rare animals for, among other things, forward genetic screens to identify genetic pathways that regulate phenotypes of interest. Many commonly used screening processes are labor-intensive, lack sensitivity, and require extensive investigator training. Here, we describe a sensitive, high throughput, automated, motility-based method for sorting nematodes. Our method is implemented in a simple microfluidic device capable of sorting thousands of animals per hour per module, and is amenable to parallelism. The device successfully enriches for known C. elegans motility mutants. Furthermore, using this device, we isolate low-abundance mutants capable of suppressing the somnogenic effects of the flp-13 gene, which regulates C. elegans sleep. By performing genetic complementation tests, we demonstrate that our motility-based sorting device efficiently isolates mutants for the same gene identified by tedious visual inspection of behavior on an agar surface. Therefore, our motility-based sorter is capable of performing high throughput gene discovery approaches to investigate fundamental biological processes.

Yuan J et al. (2015) J R Soc Interface "A hydrodynamic mechanism for attraction of undulatory microswimmers to surfaces (bordertaxis)."

Yuan J, Raizen DM, Bau HH

[J R Soc Interface, 2015]

Although small nematodes significantly impact human and animal health, agriculture, and ecology, little is known about the role of hydrodynamics in their life cycles. Using the nematode Caenorhabditis elegans as a model undulatory microswimmer, we have observed that animals are attracted to and swim along surfaces. The attraction to surfaces does not require mechanosensory neuron function. In dilute swarms, swimmers aggregate near surfaces. Using resistive force-based theory, symmetry arguments, and direct hydrodynamic simulations, we demonstrate that forces resulting from the interaction between the swimmer-induced flow field and a nearby surface cause a short-range hydrodynamic torque that stirs the swimmers towards the surface. When combined with steric forces, this causes locomotion along the surface. This surface attraction may affect nematode mate and food finding behaviour and, in the case of parasitic nematodes, may facilitate host penetration. Surface attraction must be accounted for when studying animals' responses to various stimuli, and suggests means of controlling undulatory microswimmers.

Yuan J et al. (2015) Proc Natl Acad Sci U S A "Propensity of undulatory swimmers, such as worms, to go against the flow."

Yuan J, Raizen DM, Bau HH

[Proc Natl Acad Sci U S A, 2015]

The ability to orient oneself in response to environmental cues is crucial to the survival and function of diverse organisms. One such orientation behavior is the alignment of aquatic organisms with (negative rheotaxis) or against (positive rheotaxis) fluid current. The questions of whether low-Reynolds-number, undulatory swimmers, such as worms, rheotax and whether rheotaxis is a deliberate or an involuntary response to mechanical forces have been the subject of conflicting reports. To address these questions, we use Caenorhabditis elegans as a model undulatory swimmer and examine, in experiment and theory, the orientation of C. elegans in the presence of flow. We find that when close to a stationary surface the animal aligns itself against the direction of the flow. We elucidate for the first time to our knowledge the mechanisms of rheotaxis in worms and show that rheotaxis can be explained solely by mechanical forces and does not require sensory input or deliberate action. The interaction between the flow field induced by the swimmer and a nearby surface causes the swimmer to tilt toward the surface and the velocity gradient associated with the flow rotates the animal to face upstream. Fluid mechanical computer simulations faithfully mimic the behavior observed in experiments, supporting the notion that rheotaxis behavior can be fully explained by hydrodynamics. Our study highlights the important role of hydrodynamics in the behavior of small undulating swimmers and may assist in developing control strategies to affect the animals' life cycles.

Yuan J et al. (2016) J R Soc Interface "Terrain following and applications: Caenorhabditis elegans swims along the floor using a bump and undulate strategy."

Raizen DM, Yuan J, Ko H, Bau HH

[J R Soc Interface, 2016]

Nematodes such as Caenorhabditis elegans are heavier than water. When submerged in water, they settle to the bottom surface. Observations reveal that the animals do not lie flat on the bottom surface, but remain substantially suspended above the surface through continuous collisions with the surface, while maintaining their swimming gaits. Consequently, the swimming animals follow the bottom surface topography. When the bottom surface is inclined, the animals swim up or down along the incline. As the magnitude of the gravitational force can be easily estimated, this behaviour provides a convenient means to estimate the animal's propulsive thrust. The animals' tendency to follow the surface topography provides a means to control the swimmers' trajectories and direction of motion, which we demonstrate with a saw tooth-like ratchet that biases the animals to swim in a selected direction. The animals can also serve as surface topography probes since their residence time as a function of position provides information on surface features. Finally, we take advantage of surface following to construct a simple motility-based sorter that can sort animals based on genotype and state of health.

Yuan W et al. (2018) J Virol "Orsay delta protein is required for non-lytic viral egress."

Yuan W, Zhou Y, Tao YJ, Zhong W, Fan Y

[J Virol, 2018]

Non-enveloped gastrointestinal viruses such as human rotavirus can exit infected cells from the apical surface without cell lysis. The mechanism of such non-lytic exit is poorly understood. The non-enveloped Orsay virus is an RNA virus infecting the intestine cells of the nematode <i>Caenorhabditis elegans</i> Dye staining results suggested that Orsay exits from the intestine of infected worms in a non-lytic manner. Therefore, the Orsay-<i>C. elegans</i> system provides an excellent <i>in vivo</i> model to study viral exit. The Orsay genome encodes three proteins: RNA-dependent RNA polymerase, capsid protein (CP), and a nonstructural protein delta. delta can also be expressed as a structural CP-delta fusion. We generated an ATG-to-CTG mutant virus that had normal CP-delta fusion but could not produce free delta due to lack of the start codon. This mutant virus showed a viral exit defect without obvious phenotypes in other steps of viral infection, suggesting that delta is involved in viral exit. Ectopically expressed free delta localized near the apical membrane of intestine cells in <i>C. elegans</i> and co-localized with ACT-5, an intestine-specific actin that is a component of the terminal web. Orsay infection rearranged ACT-5 apical localization. Reduction of ACT-5 level via RNAi significantly exacerbated the viral exit defect of the delta mutant virus, suggesting that and ACT-5 functionally interact to promote Orsay exit. Together, these data support a model that the viral delta protein interacts with the actin network at the apical side of host intestine cells to mediate polarized, non-lytic egress of the Orsay virus.<b>Importance</b> An important step of the viral life cycle is how viruses exit from host cells to spread to other cells. Certain non-enveloped viruses can exit cultured cells in non-lytic ways, however, such non-lytic exit has not been demonstrated <i>in vivo</i> In addition, it is not clear how such non-lytic exit is achieved mechanistically <i>in vivo</i> Orsay is a non-enveloped RNA virus that infects the intestine cells of the nematode <i>C. elegans</i> It is currently the only virus known to naturally infect <i>C. elegans</i> Using this <i>in vivo</i> model, we show that the delta protein encoded by Orsay facilitates the non-lytic exit of the virus, possibly by interacting with host actin on the apical side of the worm intestine cells.

Yuan X et al. (2012) J Biol Chem "Topologically conserved residues direct heme transport in HRG-1-related proteins."

Yuan X, Hamza I, Protchenko O, Philpott CC

[J Biol Chem, 2012]

Caenorhabditis elegans and human HRG-1-related proteins are conserved, membrane-bound permeases that bind and translocate heme in metazoan cells via a currently uncharacterized mechanism. Here, we show that cellular import of heme by HRG-1-related proteins from worms and humans requires strategically located amino acids that are topologically conserved across species. We exploit a heme synthesis-defective Saccharomyces cerevisiae mutant to model the heme auxotrophy of C. elegans and demonstrate that, under heme-deplete conditions, the endosomal CeHRG-1 requires both a specific histidine in the predicted second transmembrane domain (TMD2) and the FARKY motif in the C terminus tail for heme transport. By contrast, the plasma membrane CeHRG-4 transports heme by utilizing a histidine in the exoplasmic (E2) loop and the FARKY motif. Optimal activity under heme-limiting conditions, however, requires histidine in the E2 loop of CeHRG-1 and tyrosine in TMD2 of CeHRG-4. An analogous system exists in humans, because mutation of the synonymous histidine in TMD2 of hHRG-1 eliminates heme transport activity, implying an evolutionary conserved heme transport mechanism that predates vertebrate origins. Our results support a model in which heme is translocated across membranes facilitated by conserved amino acids positioned on the exoplasmic, cytoplasmic, and transmembrane regions of HRG-1-related proteins. These findings may provide a framework for understanding the structural basis of heme transport in eukaryotes and human parasites, which rely on host heme for survival.

Yuan Y et al. (2022) J Neural Eng "A Graph Network Model for Neural Connection Prediction and Connection Strength Estimation."

Xiang F, Lai T, Gu X, Li Z, Rong Y, Yuan Y, Zhao P, Niu X, Fang T, Liu J, Wang W, Xin K, Chen Y, Huo H

[J Neural Eng, 2022]

OBJECTIVE: Reconstruction of connectomes at the cellular scale is a prerequisite for understanding the principles of neural circuits. However, due to methodological limits, scientists have reconstructed the connectomes of only a few organisms such as C. elegans, and estimated synaptic strength indirectly according to their size and number. APPROACH: Here, we propose a graph network model to predict synaptic connections and estimate synaptic strength by using the calcium activity data from C. elegans. MAIN RESULTS: The results show that this model can reliably predict synaptic connections in the neural circuits of C. elegans, and estimate their synaptic strength, which is an intricate and comprehensive reflection of multiple factors such as synaptic type and size, neurotransmitter and receptor type, and even activity dependence. In addition, the excitability or inhibition of synapses can be identified by this model. We also found that chemical synaptic strength is almost linearly positively correlated to electrical synaptic strength, and the influence of one neuron on another is non-linearly correlated with the number between them. This reflects the intrinsic interaction between electrical and chemical synapses. SIGNIFICANCE: Our model is expected to provide a more accessible quantitative and data-driven approach for the reconstruction of connectomes in more complex nervous systems, as well as a promising method for accurately estimating synaptic strength.

Yuan Y et al. (2020) J Microbiol "Extracellular products-mediated interspecific interaction between Pseudomonas aeruginosa and Escherichia coli."

Guo Y, Pan W, Lin J, Yuan Y, Li J, Prithiviraj B, Zhao K, Wang X, Chu Y

[J Microbiol, 2020]

The Gram-negative pathogen Pseudomonas aeruginosa adopts several elaborate strategies to colonize a wide range of natural or clinical niches and to overcome the neighboring bacterial competitors in polymicrobial communities. However, the relationship and interaction mechanism of P. aeruginosa with other bacterial pathogens remains largely unexplored. Here we explore the interaction dynamics of P. aeruginosa and Escherichia coli, which frequently coinfect the lungs of immunocompromised hosts, by using a series of on-plate proximity assays and RNA-sequencing. We show that the extracellular products of P. aeruginosa can inhibit the growth of neighboring E. coli and induce a large-scale of transcriptional reprogramming of E. coli, especially in terms of cellular respiration-related primary metabolisms and membrane components. In contrast, the presence of E. coli has no significant effect on the growth of P. aeruginosa in short-term culture, but causes a dysregulated expression of genes positively controlled by the quorum-sensing (QS) system of P. aeruginosa during subsequent pairwise culture. We further demonstrate that the divergent QS-regulation of P. aeruginosa may be related to the function of the transcriptional regulator PqsR, which can be enhanced by E. coli culture supernatant to increase the pyocyanin production by P. aeruginosa in the absence of the central las-QS system. Moreover, the extracellular products of E. coli promote the proliferation and lethality of P. aeruginosa in infecting the Caenorhabditis elegans model. The current study provides a general characterization of the extracellular products-mediated interactions between P. aeruginosa and E. coli, and may facilitate the understanding of polymicrobial infections.