Biology subjects

Zhou, J.

Publications and source records attributed to Zhou, J..

At least 649 records · Page 36Linked to original sources

bioRxiv2019

Dicer1 is reduced in APPswe/PSEN1dE9 mice and is regulated by Nrf2

The pathogenesis of Alzheimers disease (AD) involves the central roles of oxidative stress. Oxidative stress due to Dicer1 depletion may underline the neurodegeneration in the central nervous system and degeneration of retinal pigment epithelial cells in geographic atrophy form of age-related macular degeneration. We hypothesized that Dicer1 may play roles in AD pathogenesis. Indeed, Dicer1 was reduced in the hippocampus and cortex of APPswe/PSEN1dE9 mice, an AD model. Dicer1 knockdown induced oxidative stress, mitochondrial dysfunction, apoptosis in cultured neurons, and increased secretions of interleukin-1{beta}/-18, indicators of inflammasome activation. Accordingly, Dicer1 was decreased by amyloid peptide and the effect was connected with down-regulation of nuclear factor erythroid 2-related factor 2 (Nrf2). Anti-oxidant response elements (AREs) were identified in the promoter of Dicer1 and Keap1-Nrf2-AREs signaling was demonstrated to regulate Dicer1 expression. Furthermore, overexpression of Dicer1 carried by adenovirus in the cultured neurons rescued neurite deficit induced by amyloid peptide. In consistent with the in vitro results, injection of Dicer1-overexperssion adenovirus in the hippocampus of the AD mice significantly improved spatial learning. Altogether, we unveiled an unexploited roles of Dicer1 in AD and a novel way of Dicer1 regulation. These findings suggest that Dicer1 may be a target in AD therapy.\n\nSignificance StatementDicer1 is a microRNA-processing enzyme, which is central to microRNA maturation. For the first time, we herein reported that Dicer1 was reduced in the hippocampus or the cortex of AD mice before overt amyloid plque deposition and overexpression of Dicer1 in the hippocampus significantly improved spatial learning in AD mice. We also demonstrated that Dicer1 was regulated by Keap1-Nrf2-ARE signaling which is unreported before. These findings advance understandings of AD pathogenesis and suggest that Dicer1 may be a molecular target in AD therapy.

neuroscience↗

bioRxiv2019

Conformational Dynamics of Nonenveloped Circovirus Capsid to the Host Cell Receptor

Circovirus, comprising one capsid protein, is the smallest nonenveloped virus and induces lymphopenia. Circovirus can be used to explore the cell adhesion mechanism of nonenveloped viruses. We developed a single-molecule fluorescence resonance energy transfer (smFRET) assay to directly visualize the capsids conformational feature. The capsid underwent reversible dynamic transformation between three conformations. The cell surface receptor heparan sulfate (HS) altered the dynamic equilibrium of the capsid to the high-FRET state, revealing the HS binding region. Neutralizing antibodies restricted capsid transition to a low-FRET state, masking the HS binding domain. The lack of positively charged amino acids in the HS binding site reduced cell surface affinity and attenuated virus infectivity via conformational changes. These intrinsic characteristics of the capsid suggested that conformational dynamics is critical for the structural changes occurring upon cell surface receptor binding, supporting a dynamics-based mechanism of receptor binding.\n\nImportanceViral proteins were commom working as ligand to interacte with cell surface glycosaminoglycan receptors to achieve the virus attachment, during which the conformational dynamics of the protein ligand are also vital for the binding properties. In this study, PCV2 capsid and heparin sulfate were used to study the protein conformational dynamics of nonenveloped and icosahedral circovirus capsid during triggering to cell surface receptor. we demonstrated the PCV2 capsid could acts as a dynamic machine, spontaneously adopting multiple conformations with reversible interconversion and intrinsic conformational features could be regulated by glycosaminoglycan receptors and neutralizing antibodies. These increased our understanding of the mechanism by which nonenveloped virus attach to cells.

microbiology↗

bioRxiv2019

Engineering oleaginous yeast Yarrowia lipolytica for violacein production: extraction, quantitative measurement and culture optimization

Violacein is a naturally occurring anticancer therapeutic with deep purple color. Yeast fermentation represents an alternative approach to efficiently manufacturing violacein from inexpensive feedstocks. In this work, we optimized the extraction protocol to improve violacein recovery ratio and purity from yeast culture, including the variations of organic solvents, the choice of mechanical shear stress, incubation time and the use of cell wall-degrading enzymes. We also established the quantitative correlation between HPLC and microplate reader method. We demonstrated that both HPLC and microplate reader are technically equivalent to measure violacein from yeast culture. Furthermore, we optimized the yeast cultivation conditions, including carbon/nitrogen ratio and pH conditions. Our results indicated that ethyl acetate is the best extraction solvent with glass beads grinding the cell pellets, the maximum violacein and deoxyviolacein production was 70.04 mg/L and 5.28 mg/L in shake flasks, respectively. Violacein purity reaches 86.92% at C/N ratio of 60, with addition of 10 g/L CaCO3 to control the media pH. Taken together, the development of efficient extraction protocol, quantitative correlation between HPLC and microplate reader, and the optimization of culture conditions set a new stage for engineering violacein production in Y. lipolytica. This information should be valuable for us to build a renewable and scalable violacein production platform from the novel host oleaginous yeast species.

microbiology↗

bioRxiv2019

Minimum epistasis interpolation for sequence-function relationships

Massively parallel phenotyping assays have provided unprecedented insight into how multiple mutations combine to determine biological function. While these assays can measure phenotypes for thousands to millions of genotypes in a single experiment, in practice these measurements are not exhaustive, so that there is a need for techniques to impute values for genotypes whose phenotypes are not directly assayed. Here we present a method based on the idea of inferring the least epistatic possible sequence-function relationship compatible with the data. In particular, we infer the reconstruction in which mutational effects change as little as possible across adjacent genetic backgrounds. Although this method is highly conservative and has no tunable parameters, it also makes no assumptions about the form that genetic interactions take, resulting in predictions that can behave in a very complicated manner where the data require it but which are nearly additive where data is sparse or absent. We apply this method to analyze a fitness landscape for protein G, showing that our technique can provide a substantially less epistatic fit to the landscape than standard methods with little loss in predictive power. Moreover, our analysis reveals that the complex structure of epistasis observed in this dataset can be well-understood in terms of a simple qualitative model consisting of three fitness peaks where the landscape is locally additive in the vicinity of each peak.

bioinformatics↗

bioRxiv2019

A Novel Type 2 Diabetes Locus in sub-Saharan Africans, ZRANB3, is Implicated in Beta Cell Proliferation

Genome analysis of diverse human populations has contributed to the identification of novel genomic loci for diseases of major clinical and public health impact. Here, we report the largest genome-wide analysis of type 2 diabetes (T2D) in sub-Saharan Africans, an understudied ancestral group. We analyzed ~18 million autosomal SNPs in 5,231 individuals from Nigeria, Ghana and Kenya. TCF7L2 rs7903156 was the most significant locus (p=7.288 x 10-13). We identified a novel genome wide significant locus: ZRANB3 (Zinc Finger RANBP2-Type Containing 3, lead SNP chr2:136064024, T allele frequency=0.034, p=2.831x10-9). Knockdown of the zebrafish ortholog resulted in reduction in pancreatic beta cell number in the developing organism, suggesting a potential mechanism for its effect on glucose hemostasis. We also showed transferability in our study of 32 established T2D loci. Our findings provide evidence of a novel candidate T2D locus and advance understanding of the genetics of T2D in non-European ancestry populations.

genetics↗

bioRxiv2019

Bayogenin 3-O-Cellobioside is a novel non-cultivar specific anti-blast metabolite produced in rice in response to Pyricularia oryzae infection

Rice cultivars from japonica and indica lineage possess differential resistance against blast fungus on an account genetic divergence. Whether different rice cultivars also show distinct metabolomic changes in response to P. oryzae, and their role in host resistance, are poorly understood. Here, we examine the responses of six different rice cultivars from japonica and indica lineage challenged with P. oryzae. Both susceptible and resistant rice cultivars expressed several metabolites exclusively during P. oryzae infection, including the saponin Bayogenin 3-O-cellobioside. Bayogenin 3-O-cellobioside level in infected rice directly correlated with their resistant attributes. These findings reveal, for the first time to our knowledge that besides oat, other grass plants including rice produces protective saponins. Our study provides insight into the role of pathogen-mediated metabolomics-reprogramming in host immunity. The correlation between Bayogenin 3-O-Cellobioside levels and blast resistance suggests that engineering saponin expression in cereal crops represents an attractive and sustainable disease control strategy.

biochemistry↗

bioRxiv2019

Century long fertilization reduces stochasticity controlling grassland microbial community succession

Determining the drivers underlying ecological succession is a fundamental goal of ecological research and essential for predicting ecosystem functioning in response to human-induced environmental changes. Although various studies have examined the impacts of nitrogen (N) addition on plant and microbial community diversity, structure and activities, it remains unknown how long-term anthropogenic fertilization affects the ecological succession of microbial functional guilds and its underlying community assembly mechanisms. Here, using archived soils, we examined more than a centurys succession in soil microbial functional communities (from 1870 to 2008) from the Park Grass Experiment at Rothamsted Experimental Station, the longest running ecological experiment in the world. Long-term fertilization was found to significantly alter soil functional community structure and led to increasingly convergent succession of soil microbial communities. Meta-analysis indicated that microbial temporal turnover (w) was highly time scale-dependent, and the w value threshold was estimated as 0.0025 with a threshold time point of approximately 160 years. In addition, the importance of stochastic assembly varied greatly in regulating the succession of different microbial guilds. Fertilization had large to medium effects on reducing ecological stochasticity for microbial guilds involved in carbon (C) fixation and degradation, N fixation and mineralization, and denitrification. This century long-term study elucidated the differing influences of assembly mechanisms on soil microbial functional communities involved in C and N cycling, which could not be derived from taxonomic or phylogenetic approaches.

ecology↗

bioRxiv2019

A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila

Genetic screens are powerful tools for the functional annotation of genomes. In the context of multicellular organisms, interrogation of gene function is greatly facilitated by methods that allow spatial and temporal control of gene abrogation. Here, we describe a large-scale transgenic short guide (sg) RNA library for efficient CRISPR-based disruption of specific target genes in a constitutive or conditional manner. The library consists currently of more than 2600 plasmids and 1600 fly lines with a focus on targeting kinases, phosphatases and transcription factors, each expressing two sgRNAs under control of the Gal4/UAS system. We show that conditional CRISPR mutagenesis is robust across many target genes and can be efficiently employed in various somatic tissues, as well as the germline. In order to prevent artefacts commonly associated with excessive amounts of Cas9 protein, we have developed a series of novel UAS-Cas9 transgenes, which allow fine tuning of Cas9 expression to achieve high gene editing activity without detectable toxicity. Functional assays, as well as direct sequencing of genomic sgRNA target sites, indicates that the vast majority of transgenic sgRNA lines mediate efficient gene disruption. Furthermore, we conducted the so far largest fully transgenic CRISPR screen in any metazoan organism, which further supported the high efficiency and accuracy of our library and revealed many so far uncharacterized genes essential for development.

genetics↗

bioRxiv2019

Identification of NAD-dependent xylitol dehydrogenase from Gluconobacter oxydans WSH-003

Gluconobacter oxydans plays important role in conversion of D-sorbitol to L-sorbose, which is an essential intermediate for industrial-scale production of vitamin C. In the fermentation process, some D-sorbitol could be converted to D-fructose and other byproducts by uncertain dehydrogenases. Genome sequencing has revealed the presence of diverse genes encoding dehydrogenases in G. oxydans. However, the characteristics of most of these dehydrogenases remain unclear. Therefore, analyses of these unknown dehydrogenases could be useful for identifying those related to the production of D-fructose and other byproducts. Accordingly, dehydrogenases in G. oxydans WSH-003, an industrial strain used for vitamin C production, were examined. An NAD-dependent dehydrogenase, which was annotated as xylitol dehydrogenase 2, was identified, codon-optimized, and expressed in Escherichia coli BL21 (DE3) cells. The enzyme exhibited high preference for NAD+ as the cofactor, while no activity with NADP+, FAD, or PQQ was noted. Although this enzyme presented high similarity with NAD-dependent xylitol dehydrogenase, it showed high activity to catalyze D-sorbitol to D-fructose. Unlike the optimum temperature and pH for most of the known NAD-dependent xylitol dehydrogenases (30{degrees}C-40{degrees}C and about 6-8, respectively), those for the identified enzyme were 57{degrees}C and 12, respectively. The Km and Vmax of the identified dehydrogenase towards L-sorbitol were 4.92 M and 196.08 M/min, respectively. Thus, xylitol dehydrogenase 2 can be useful for cofactor NADH regeneration under alkaline conditions or its knockout can improve the conversion ratio of D-sorbitol to L-sorbose.\n\nImportanceProduction of L-sorbose from D-sorbitol by Gluconobacter oxydans is the first step for industrial scale production of L-ascorbic acid. G. oxydans contains a lot of different dehydrogenases, among which only several are responsible for the conversion of D-sorbitol to L-sorbose, while others may responsible for the accumulation of byproducts, thus decreased the yield of L-sorbose on D-sorbitol. Therefore, a new xylitol dehydrogenase has been identified from 44 dehydrogenases of G. oxydans. Optimum temperature and pH of the xylitol dehydrogenase are different to most of the known ones. Knock-out of the dehydrogenase may improve the conversion ratio of D-sorbitol to L-sorbose. Besides, the enzyme exhibits high preference for NAD+ and have potential to be used for cofactor regeneration.

bioengineering↗

bioRxiv2019

Soil and vegetation conditions changes following the different sand dune restoration measures on the Zoige Plateau

Restoration of alpine sand dunes has been increasingly attracting the attention of ecologists due to their difficulty and importance among the mountain-river-forest-farmland-lake-grass system (referred as meta-ecosystem) restoration. Alpine sand dunes are suffered from unstable soil and lack of plants. Efficient restoration measures are vital to guide the sand dune restoration. Whether the engineering materials co-applied with seeding could achieve considerable restoration in such areas? Here, sandbag and wicker as environmental friendly materials combined with Elymus nutans seeding were implemented on the Zoige Plateau sand dune, comparing with the control treatment that only seeding. We assessed the topsoil conditions by sampled the surface soil and measured the water capacity and nutrients. We also utilized interspecific relationship and population niche to analyse the plant community structure variances among different restoration measures. Results showed that the soil conditions got clearly improved in sandbag area than that in wicker area when compared with that in control area. The community in control area was the least structured, while the species showed the closest related in sandbag area. In addition, average population niche overlap showed a control (0.26) < wicker (0.32) < sandbag (0.39) ranking. Thus, we suggested that sandbag or wicker co-applied with indigenous grass seeding is a practical and quick restoration approach in alpine sand dunes, and the sandbag may surpasses the wicker. Moreover, soil amending measures including nutrient improvement, and microbial fertilizer addition may further accelerate sand dune restoration.

ecology↗

bioRxiv2019

Optimizing oleaginous yeast cell factories for flavonoids and hydroxylated flavonoids biosynthesis

Plants possess myriads of secondary metabolites with a broad spectrum of health-promoting benefits. Up to date, plant extraction is still the primary route to produce high-value natural products, which inherently suffers from economics and scalability issues. Heterologous production in microbial host is considered as a feasible approach to overcoming these limitations. Flavonoid and its hydroxylated derivatives represent a diversified family of bioactive compounds, most prominently known as antioxidant and anti-aging agents. Oleaginous yeast is rich in hydrophobic lipid bodies and spatially-organized organelles, which provides the ideal environment for the regioselectivity and stereoselectivity of many plant-specific enzymes. In this report, we validated that Y. lipolytica is a superior platform for heterologous production of high-value flavonoids and hydroxylated flavonoids. By modular construction and characterization, we determined the rate-limiting steps for efficient flavonoids biosynthesis in Y. lipolytica. We evaluated various precursor pathways and unleashed the metabolic potential of Y. lipolytica to produce flavonoids, including the supply of acetyl-CoA, malonyl-CoA and chorismate. Coupled with the optimized chalcone synthase module and the hydroxylation module, our engineered strain produced 252.4 mg/L naringenin, 134.2 mg/L eriodictyol and 110.5 mg/L taxifolin from glucose. Collectively, these findings demonstrate our ability to harness oleaginous yeast as microbial workhorse to expand natures biosynthetic potential, enabling us to bridge the gap between drug discovery and natural product manufacturing.

synthetic biology↗

bioRxiv2019

Niche differentiation is spatially and temporally regulated in the rhizosphere

The rhizosphere is a hotspot for microbial C transformations, and the origin of root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter. However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. Using Avena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial function in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Population transcripts were binned with a unique reference database generated from soil isolate and single amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition gene expression, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were high in the combined rhizosphere-detritusphere--suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling.

ecology↗

bioRxiv2019

Intronic heterochromatin prevents cryptic transcription initiation in Arabidopsis

Intronic transposable elements (TEs) comprise a large proportion in eukaryotic genomes, but how they regulate the host genes remains to be explored. Our forward genetic screen disclosed the plant specific RNA polymerases IV and V in suppressing intronic TE-mediated cryptic transcription initiation of a chimeric transcripts at FLC (FLCTE). Initiation of FLCTE transcription is blocked by the locally formed intronic heterochromatin, which is directly associated with RNA Pol V to inhibit the entry of RNA Pol II and the occupancy of H3K4 methylation. Genome-wide Pol II Ser5p native elongation transcription sequencing revealed that this is a common mechanism among intronic heterochromatin-containing genes. This study sheds light on deeply understanding the function of intronic heterochromatin on host genes expression in eukaryotic genome.

plant biology↗

bioRxiv2019

Deficient stereopsis in the normal population revisited: why current clinical stereo tests may not be adequate

Significance statementApplied applications for occupational screening, clinical tests should assess sensitivity to the sign as well as the magnitude of disparity.\n\nPurposeTo determine why the high incidence of stereo anomaly found using laboratory tests with polarity-based increment judgements (i.e., depth sign) is not reflected in clinical measurements that involve single-polarity incremental judgements (i.e., depth magnitude).\n\nMethodsAn iPod-based measurement that involved the detection of an oriented shape defined by a single polarity-depth increment within a random dot display was used. A staircase procedure was used to gather sufficient trials to derive a meaningful measure of variance for the measurement of stereopsis over a large disparity range. Forty-five adults with normal binocular vision (20 - 65 years old) and normal or corrected-to-normal (0 logMAR or better) monocular vision participated in this study.\n\nResultsObservers stereo acuities ranged between 10 and 100 arc seconds, and were normally distributed on a log scale (p = 0.90, 2-tailed Shapiro-Wilk test). The present results using a single polarity depth increment task (i.e., depth magnitude) show a similar distribution to those using a similar task using the Randot preschool stereo test on individuals between the ages of 19-35 using either the 4-book test (n = 33) or the 3-book test (n = 40), but very different results when the iPod test involved a polarity-based increment judgement (i.e., depth sign).\n\nConclusionsThe present clinical stereo tests are based on magnitude judgements and are unable to detect the high percentage of stereo anomalous individuals in the normal population revealed using depth sign judgements.

neuroscience↗

bioRxiv2019

A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans to Conserve Energy to Support Growth from Extracellular Electron Transfer

Conservation of energy to support growth solely from extracellular electron transfer was demonstrated for the first time in a methanogen. Methanosarcina acetivorans grew with methanol as the sole electron donor and the extracellular electron acceptor anthraquione-2,6-disulfonate (AQDS) as the sole electron acceptor when methane production was inhibited with bromoethanesulfonate. Transcriptomics revealed that transcripts for the gene for the transmembrane, multi-heme, c-type cytochrome MmcA were 4-fold higher in AQDS-respiring cells versus methanogenic cells. A strain in which the gene for MmcA was deleted failed to grow via AQDS reduction whereas strains in which other cytochrome genes were deleted grew as well as the wild-type strain. The MmcA-deficient strain grew with the conversion of methanol or acetate to methane, suggesting that MmcA has a specialized role as a conduit for extracellular electron transfer. Enhanced expression of genes for methanol conversion to methyl-coenzyme M and components of the Rnf complex suggested that methanol is oxidized to carbon dioxide in AQDS-respiring cells through a pathway that is similar to methyl-coenezyme M oxidation in methanogenic cells. However, during AQDS respiration the Rnf complex and reduced methanophenazine probably transfer electrons to MmcA, which functions as the terminal reductase for AQDS reduction. Extracellular electron transfer may enable survival of methanogens in dynamic environments in which oxidized humic substances and Fe(III) oxides are intermittently available. The availability of tools for genetic manipulation of M. acetivorans makes it an excellent model microbe for evaluating c-type cytochrome-dependent extracellular electron transfer in Archaea.\n\nImportanceExtracellular electron exchange in Methanosarcina species and closely related Archaea plays an important role in the global carbon cycle and can enhance the speed and stability of anaerobic digestion, an important bioenergy strategy. The potential importance of c-type cytochromes for extracellular electron transfer to syntrophic bacterial partners and/or Fe(III) minerals in some Archaea has been suspected for some time, but the studies with Methanosarcina acetivorans reported here provide the first genetic evidence supporting this hypothesis. The results suggest parallels with Gram-negative bacteria, such as Shewanella and Geobacter species, in which outer-surface c-type cytochromes are an essential component for electrical communication with the extracellular environment. M. acetivorans offers an unprecedented opportunity to study mechanisms for energy conservation from the anaerobic oxidation of one-carbon organic compounds coupled to extracellular electron transfer in Archaea with implications not only for methanogens, but possibly also for anaerobic methane oxidation.

microbiology↗

bioRxiv2019

Clades of huge phage from across Earth’s ecosystems

Phage typically have small genomes and depend on their bacterial hosts for replication. DNA sequenced from many diverse ecosystems revealed hundreds of huge phage genomes, between 200 kbp and 716 kbp in length. Thirty-four genomes were manually curated to completion, including the largest phage genomes yet reported. Expanded genetic repertoires include diverse and new CRISPR-Cas systems, tRNAs, tRNA synthetases, tRNA modification enzymes, translation initiation and elongation factors, and ribosomal proteins. Phage CRISPR-Cas systems have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phage may repurpose bacterial CRISPR-Cas systems to eliminate competing phage. We phylogenetically define major clades of huge phage from human and other animal microbiomes, oceans, lakes, sediments, soils and the built environment. We conclude that their large gene inventories reflect a conserved biological strategy, observed over a broad bacterial host range and across Earths ecosystems.

microbiology↗

bioRxiv2019

Streamlined low-input transcriptomics through EASY-RNAseq

High-throughput sequencing for transcriptome profiling is an increasingly accessible and important tool for biological research. However, accurate profiling of small cell populations remains challenging due to issues with gene detection sensitivity and experimental complexity. Here we describe a streamlined RNAseq protocol (EASY RNAseq) for sensitive transcriptome assessment starting from low amount of input materials. EASY RNAseq is technically robust enough for sequencing small pools of homogenous and heterogeneous cells, recovering higher numbers of genes and with a more even expression distribution pattern than other commonly used methods. Application of EASY RNAseq to single human embryos at the 8-cell stage was able to achieve detection of 70% protein-coding genes. This workflow may thus serve as a useful tool for sensitive interrogation of rare cell populations.

genomics↗

bioRxiv2019

Satiety, Thermosensation and Mechanosensation Regulate a Spontaneous C. elegans Sleep State

One remarkable feature of the nervous system is its ability to rapidly and spontaneously switch between activity states. In the extreme example of sleep, animals arrest locomotion, reduce their sensitivity to sensory stimuli, and dramatically alter their neural activity. Small organisms are useful models to better understand these sudden changes in neural states because we can simultaneously observe whole-brain activity, monitor behavior and precisely regulate the external environment. Here, we show a spontaneous sleep-like behavior in C. elegans that is associated with a distinct global-brain state and regulated by both the animals internal physiological state and input from multiple sensory circuits. Specifically, we found that when confined in microfluidic chambers, adult worms spontaneously transition between periods of normal activity and short quiescent bouts, with behavioral state transitions occurring every few minutes. This quiescent state, which we call Sleep, meets the behavioral requirements of C. elegans sleep, is dependent on known sleep-promoting neurons ALA and RIS, and is associated with a global down-regulation of neural activity. Consistent with prior studies of C. elegans sleep, we found that Sleep is regulated by satiety and temperature. In addition, we show for the first time that quiescence can be either driven or suppressed by thermosensory input, and that animal restraint induces quiescence through mechanosensory pathways. Together, these results establish a rich model system for studying how neural and behavioral state transitions are influenced by multiple physiological and environmental conditions. Significance StatementUnique brain states govern animal behaviors like sleep and wakefulness; however, how the brain regulates these dramatic state transitions is not well understood. Brain activity can be influenced by a complex interaction between sensory circuits that monitor the external environment, neural circuits that control behavior, and internal chemical signaling. Here, we describe a platform to study behavioral states in a context that allows us to record whole-brain activity while controlling the environment and monitoring animal behavior. Specifically, we identify a pattern of sleep bouts in the roundworm C. elegans that occur when they are confined to microscopic fluidic chambers. This behavior platform provides a powerful system to study how neural circuits interact with chemical signaling to drive brain state transitions.

neuroscience↗