Functional imaging and quantification of multineuronal olfactory responses in C. elegans

Science Advances, Год журнала: 2023, Номер 9(9)

Опубликована: Март 1, 2023

Many animals perceive odorant molecules by collecting information from ensembles of olfactory neurons, where each neuron uses receptors that are tuned to recognize certain with different binding affinity. Olfactory systems able, in principle, detect and discriminate diverse odorants using combinatorial coding strategies. We have combined microfluidics multineuronal imaging study the ensemble-level representations at sensory periphery nematode Caenorhabditis elegans . The collective activity C. chemosensory neurons reveals high-dimensional across a broad space molecules. reveal tuning properties dose-response curves odorants. describe unique contribution an code for volatile show natural stimuli, set pheromones, also encoded ensemble. integrated contains sufficient robustly encode intensity identity chemical stimuli.

Язык: Английский

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Dissecting the genetic landscape of GPCR signaling through phenotypic profiling in C. elegans

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Дек. 18, 2023

Abstract G protein-coupled receptors (GPCRs) mediate responses to various extracellular and intracellular cues. However, the large number of GPCR genes their substantial functional redundancy make it challenging systematically dissect functions in vivo. Here, we employ a CRISPR/Cas9-based approach, disrupting 1654 GPCR-encoding 284 strains mutating 152 neuropeptide-encoding 38 C. elegans . These two mutant libraries enable effective deorphanization chemoreceptors, characterization for neuropeptides cellular processes. Mutating set closely related GPCRs single strain permits assignment with redundancy. Our analyses identify neuropeptide that interacts three hypoxia-evoked locomotory responses, unveil collection regulators pathogen-induced immune define volatile food-related odorants. results establish our as valuable resources community expedite studies signaling multiple contexts.

Язык: Английский

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Single-nucleus proteomics identifies regulators of protein transport

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 18, 2024

The physiological response of a cell to stimulation depends on its proteome configuration. Therefore, the abundance variation regulatory proteins across unstimulated single cells can be associatively linked with their stimulation. Here we developed an approach that leverages this association individual and nuclei systematically identify potential regulators biological processes, followed by targeted validation. Specifically, applied nucleocytoplasmic protein transport in macrophages stimulated lipopolysaccharide (LPS). To end, quantified proteomes 3,412 nuclei, sampling dynamic LPS treatment, linking functional variability proteomic variability. Minutes after stimulation, correlated strongly known regulators, thus revealing impact natural cellular response. We found simple biophysical constraints, such as quantity nuclear pores, partially explain LPS-induced transport. Among many newly identified associated response, selected 16 for validation knockdown. knockdown phenotypes confirmed inferences derived from demonstrating (sub-)single-cell proteomics infer regulation. expect generalize broad applications enhance interpretability single-cell omics data.

Язык: Английский

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Exploring functional protein covariation across single cells using nPOP

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2021, Номер unknown

Опубликована: Апрель 26, 2021

Many biological processes, such as the cell division cycle, are reflected in protein covariation across single cells. This can be quantified and interpreted by single-cell mass-spectrometry (MS) with sufficiently high throughput accuracy. Towards this goal, we developed nPOP, a method that uses piezo acoustic dispensing to isolate individual cells 300 picoliter volumes performs all subsequent sample preparation steps small droplets on fluorocarbon-coated slide. design enabled simultaneous of thousands cells, including lysing, digesting, labeling 8-20 nl. Protein analysis identified cell-cycle dynamics were similar types differed between types, even within sub-populations melanoma defined markers for drug-resistance priming. The expressing these accumulated G1 phase displayed distinct glycogen, had lower abundance glycolytic enzymes. non-primed exhibited gradients covariation, suggesting transition states. These results validated different MS methods. Together, they demonstrate may reveal functionally concerted differences closely related

Язык: Английский

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Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Март 18, 2022

Major aims of single-cell proteomics include increasing the consistency, sensitivity, and depth protein quantification, especially for proteins modifications biological interest. To simultaneously advance all these aims, we developed prioritized Single Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands peptides across single cells (thus data completeness) while analyzing identifiable at full duty-cycle, thus proteome depth. These strategies increased completeness, coverage over 2-fold. The gains enabled quantifying variation in untreated lipopolysaccharide-treated primary macrophages. Within each condition, covaried within functional sets, including phagosome maturation proton transport. This covariation a treatment condition was similar conditions coupled to phenotypic variability endocytic activity. also proteolytic products, suggesting gradient cathepsin activities condition. is freely available widely applicable, interest without sacrificing coverage. Support at: scp.slavovlab.net/pSCoPE Abstract Figure

Язык: Английский

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Developmental history modulates adult olfactory behavioral preferences via regulation of chemoreceptor expression in Caenorhabditis elegans

Genetics, Год журнала: 2022, Номер 222(3)

Опубликована: Сен. 12, 2022

Abstract Developmental experiences play critical roles in shaping adult physiology and behavior. We others previously showed that Caenorhabditiselegans which transiently experienced dauer arrest during development (postdauer) exhibit distinct gene expression profiles as compared to control adults bypassed the stage. In particular, patterns of subsets chemoreceptor genes are markedly altered postdauer adults. Whether levels drive behavioral plasticity is unknown. Here, we show enhanced attraction a panel food-related attractive volatile odorants including bacterially produced chemical diacetyl. Diacetyl-evoked responses AWA olfactory neuron pair increased both larvae adults, find these correlated with upregulation diacetyl receptor ODR-10 likely via transcriptional posttranscriptional mechanisms. odr-10 part mediated by DAF-16 FOXO transcription factor. Via profiling sorted populations neurons from animals, further subset additional regulated similarly animals. Our results suggest developmental may be encoded at level regulation, provide simple mechanism C. elegans able precisely modulate its preferences function current past experiences.

Язык: Английский

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Olfactory receptor neurons generate multiple response motifs, increasing coding space dimensionality

eLife, Год журнала: 2023, Номер 12

Опубликована: Янв. 31, 2023

Odorants binding to olfactory receptor neurons (ORNs) trigger bursts of action potentials, providing the brain with its only experience environment. Our recordings made in vivo from locust ORNs showed that odor-elicited firing patterns comprise four distinct response motifs, each defined by a reliable temporal profile. Different odorants could elicit different motifs given ORN, property we term motif switching. Further, undergoes own form sensory adaptation when activated repeated plume-like odor pulses. A computational model constrained our revealed organizing responses into multiple provides substantial benefits for classifying odors and processing complex plumes: contributes uniquely encode plume’s composition structure. Multiple switching further improve classification expanding coding dimensionality. demonstrated these features provide navigation, including determining distance an source.

Язык: Английский

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Plant diversity darkspots for global collection priorities

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Сен. 15, 2023

Summary More than 15% of all vascular plant species may remain scientifically undescribed, and many the >340,000 described have no or few geographic records documenting their distribution. Identifying understanding taxonomic knowledge shortfalls is key to prioritising future collection conservation efforts. Using extensive data for 343,523 time-to-event analyses, we conducted multiple tests related shortfalls, identified 32 global diversity darkspots (regions predicted lack most information about distribution). We defined priority regions according several socio-economic environmental scenarios. Most are found within biodiversity hotspots, except New Guinea. identify Guinea, Philippines, Borneo, Myanmar, India, Turkey, Colombia, Ecuador, Peru, as priorities under conditions considered. Our study provides a framework accelerate documentation implementation actions. As digitisation world’s herbaria progresses, soon be identifiable at finer scales.

Язык: Английский

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Threat Expectation Does Not Improve Perceptual Discrimination despite Causing Heightened Priority Processing in the Frontoparietal Network

Journal of Neuroscience, Год журнала: 2024, Номер 44(15), С. e1219232023 - e1219232023

Опубликована: Фев. 23, 2024

Threat cues have been widely shown to elicit increased sensory and attentional neural processing. However, whether this enhanced recruitment leads measurable behavioral improvements in perception is still question. Here, we adjudicate between two opposing theories: that threat do or not enhance perceptual sensitivity. We created stimuli by pairing one direction of motion a random dot kinematogram with an aversive sound. While the MRI scanner, 46 subjects (both men women) completed cued (threat/safe/neutral) decision-making task where they indicated perceived each moving stimulus. found strong evidence did increase sensitivity compared safe neutral cues. This lack improvement ability occurred despite cue resulting widespread increases frontoparietal BOLD activity, as well connectivity right insula network. These results call into question intuitive claim expectation automatically enhances our highlight role network prioritizing processing threat-related environmental

Язык: Английский

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A deep learning pipeline for time-lapse camera monitoring of floral environments and insect populations

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 15, 2024

Abstract Arthropods, including insects, represent the most diverse group and contribute significantly to animal biomass. Automatic monitoring of insects other arthropods enables quick efficient observation management ecologically economically important targets such as pollinators, natural enemies, disease vectors, agricultural pests. The integration cameras computer vision facilitates innovative approaches for agriculture, ecology, entomology, evolution, biodiversity. However, studying their interactions with flowers vegetation in environments remains challenging, even automated camera monitoring. This paper presents a comprehensive methodology monitor abundance diversity wild quantify floral cover key resource. We apply methods across more than 10 million images recorded over two years using 48 insect traps placed three main habitat types. arthropods, visits, on specific mix Sedum plant species white, yellow red/pink colored flowers. proposed deep-learning pipeline estimates flower detects classifies arthropod taxa from time-lapse recordings. serves only an estimate correlate activity flowering plants. Color semantic segmentation DeepLabv3 are combined percent different colors. Arthropod detection incorporates motion-informed enhanced object You-Only-Look-Once (YOLO), followed by filtering stationary objects minimize double counting non-moving animals erroneous background detections. approach has been demonstrated decrease incidence false positives, since occur less 3% captured images. final step involves grouping into 19 taxonomic classes. Seven state-of-the-art models were trained validated, achieving F 1-scores ranging 0.81 0.89 classification arthropods. Among these, selected model, EfficientNetB4, achieved 80% average precision randomly samples when applied complete pipeline, which includes detection, filtering, collected 2021. As expected during beginning end season, reduced correlates noticeable drop method offers cost-effective

Язык: Английский

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