Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans.

We develop a data harmonization approach for C. elegans volumetric microscopy data, still or video, consisting of a standardized format, data pre-processing techniques, and a set of human-in-the-loop machine learning based analysis software tools. We unify a diverse collection of 118 whole-brain neural activity imaging datasets from 5 labs, storing these and accompanying tools in an online repository called WormID ( wormid.org ). We use this repository to generate a statistical atlas that, for the first time, enables accurate automated cellular identification that generalizes across labs, approaching human performance in some cases. We mine this repository to identify factors that influence the developmental positioning of neurons. To facilitate communal use of this repository, we created open-source software, code, web-based tools, and tutorials to explore and curate datasets for contribution to the scientific community. This repository provides a growing resource for experimentalists, theorists, and toolmakers to investigate neuroanatomical organization and neural activity across diverse experimental paradigms, develop and benchmark algorithms for automated neuron detection, segmentation, cell identification, tracking, and activity extraction, and inform models of neurobiological development and function.

Microfluidic approach to correlate C. elegans neuronal functional aging and underlying changes of gene expression in mechanosensation.

The aging process has broad physiological impacts, including a significant decline in sensory function, which threatens both physical health and quality of life. One ideal model to study aging, neuronal function, and gene expression is the nematode Caenorhabditis elegans, which has a short lifespan and relatively simple, thoroughly mapped nervous system and genome. Previous works have identified that mechanosensory neuronal structure changes with age, but importantly, the actual age-related changes in the function and health of neurons, as well as the underlying genetic mechanisms responsible for these declines, are not fully understood. While advanced techniques such as single-cell RNA-sequencing have been developed to quantify gene expression, it is difficult to relate this information to functional changes in aging due to a lack of tools available. To address these limitations, we present a platform capable of measuring both physiological function and its associated gene expression throughout the aging process in individuals. Using our pipeline, we investigate the age-related changes in function of the mechanosensing ALM neuron in C. elegans, as well as some relevant gene expression patterns (mec-4 and mec-10). Using a series of devices for animals of different ages, we examined subtle changes in neuronal function and found that while the magnitude of neuronal response to a large stimulus declines with age, sensory capability does not significantly decline with age; further, gene expression is well maintained throughout aging. Additionally, we examine PVD, a harsh-touch mechanosensory neuron, and find that it exhibits a similar age-related decline in magnitude of neuronal response. Together, our data demonstrate that our strategy is useful for identifying genetic factors involved in the decline in neuronal health. We envision that this framework could be applied to other systems as a useful tool for discovering new biology.

Effect of three unsaturated fatty acids on the protein oxidation and structure of myofibrillar proteins from rainbow trout (Oncorhynchus mykiss).

In this study, the impact of three unsaturated fatty acids (Oleic acid: OA, Eicosapentaenoic acid: EPA, Docosahexaenoic acid: DHA) on the oxidation and structure of rainbow trout myofibrillar protein (MP) was explored. The findings revealed a notable increase in carbonyl content (P < 0.05) and a significant decrease in total sulfhydryl content (P < 0.05) of MP with the concentration increase of the three unsaturated fatty acids. Endogenous fluorescence spectroscopy and surface hydrophobicity analyses showed that unsaturated fatty acids can cause unfolding and exposure of hydrophobic groups in MP. In addition, SDS-PAGE showed that disulfide bonds were associated with MP cross-linking and aggregate size induced by unsaturated fatty acids. Overall, three unsaturated fatty acid treatments facilitated the oxidation of myofibrillar proteins, and the extent of protein oxidation was closely associated with the concentration of unsaturated fatty acids.

Regulation of quorum sensing activities by the stringent response gene rsh in sphingomonads is species-specific and culture condition dependent.

Stringent response and quorum sensing (QS) are two essential mechanisms that control bacterial global metabolism for better survival. Sphingomonads are a clade of bacteria that survive successfully in diverse ecosystems. In silico survey indicated that 36 out of 79 investigated sphingomonads strains contained more than one luxI homolog, the gene responsible for the biosynthesis of QS signal acyl homoserine lactones (AHLs). Investigation of the regulatory effects of the stringent response gene rsh on QS related bioactivities were carried out using rsh mutants of Sphingobium japonicum UT26 and Sphingobium sp. SYK-6, both had three luxI homologs. Results indicated that deletion of rsh upregulated the overall production of AHLs and extracellular polymeric substances (EPS) in both UT26 and SYK-6 in rich medium, but affected expressions of these luxI/luxR homologs in different ways. In the poor medium (1% LB), rsh mutant of SYK-6 significantly lost AHLs production in broth cultivation but not in biofilm cultivation. The regulatory effects of rsh on QS activities were growth phase dependent in UT26 and culture condition dependent in SYK-6. Our results demonstrated the negative regulatory effect of rsh on QS activities in sphingomonads, which were very different from the positive effect found in sphingomonads containing only one luxI/R circuit. This study extends the current knowledge on the intricate networks between stringent response and QS system in sphingomonads, which would help to understand their survival advantage.

Non-Invasive Label-free Analysis Pipeline for In Situ Characterization of Differentiation in 3D Brain Organoid Models.

Brain organoids provide a unique opportunity to model organ development in a system similar to human organogenesis in vivo. Brain organoids thus hold great promise for drug screening and disease modeling. Conventional approaches to organoid characterization predominantly rely on molecular analysis methods, which are expensive, time-consuming, labor-intensive, and involve the destruction of the valuable 3D architecture of the organoids. This reliance on end-point assays makes it challenging to assess cellular and subcellular events occurring during organoid development in their 3D context. As a result, the long developmental processes are not monitored nor assessed. The ability to perform non-invasive assays is critical for longitudinally assessing features of organoid development during culture. In this paper, we demonstrate a label-free high-content imaging approach for observing changes in organoid morphology and structural changes occurring at the cellular and subcellular level. Enabled by microfluidic-based culture of 3D cell systems and a novel 3D quantitative phase imaging method, we demonstrate the ability to perform non-destructive high-resolution imaging of the organoid. The highlighted results demonstrated in this paper provide a new approach to performing live, non-destructive monitoring of organoid systems during culture.

Reconstructable Carbon Monolayer-MoS2 Intercalated Heterostructure Enabled by Atomic Layers-Confined Topotactic Transformation for Ultrafast Lithium Storage.

The intercalation structure of two-dimensional materials with expanded interlayer distance can facilitate mass transport, which is promising in fast-charging lithium-ion batteries (LIBs). However, the designed intercalation structures will be pulverized and destroyed under tough working conditions, causing overall performance deterioration of the batteries. Here, we present that an intercalated heterostructure made of the typical layered material of MoS2 intercalated by N-doped graphene-like carbon monolayer (MoS2/g-CM) through a polymer intercalation strategy exhibits a unique behavior of reversible reconstructability as an LIB anode during cycling. A mechanism of "carbon monolayers-confined topotactic transformation" is proposed, which is evidenced by substantial in/ex situ characterizations. The intercalated heterostructure of MoS2/g-CM featuring a reconstructable property and efficient interlayer electron/ion transport exhibits an unprecedented rate capability up to 50 A g-1 and outstanding long cyclability. Moreover, the proposed strategy based on g-CM intercalation has been extended to the MoSe2 system, also realizing reconstructability of the intercalated heterostructure and improved LIB performance, demonstrating its versatility and great potential in applications.

Microfluidic Localized Hydrogel Polymerization Enables Simultaneous Recording of Neural Activity and Behavior in C. elegans.

Monitoring an animal's brain activity during motion provides a means to interpret the brain activity in the context of movement. However, it is challenging to obtain information about the animal's movement during neural imaging in the popular model organism C. elegans due to its small size. Here, we present a microfluidic tool to immobilize only the head region of C. elegans for simultaneous recording of neuronal activity and tail movement. We combine hydrogel photopolymerization and microfluidics to realize controlled head immobilization in a semi-continuous fashion. To optimize the immobilization process, we characterize the hydrogel polymerization under different experimental conditions, including under the effect of fluid flow. We show that the Damköhler number specifically defined for our reactive transport phenomena can predict the success of such photopolymerized hydrogels used for sample immobilization. In addition to simultaneous recording of neural activity and behavior in C. elegans, we demonstrate our method's capability to temporarily reconfigure fluid flow and deliver chemical stimuli to the animal's nose to examine the animal's responses. We envision this approach to be useful for similar recordings for other small motile organisms, as well as scenarios where microfluidics and polymerization are used to control flow and rection.

Traditional herbal medicine: Therapeutic potential in acute gouty arthritis.

ETHNOPHARMACOLOGICAL RELEVANCE: Acute gouty arthritis (AGA) is characterized by a rapid inflammatory reaction caused by the build-up of monosodium urate (MSU) crystals in the tissues surrounding the joints. This condition often associated with hyperuricemia (HUA), is distinguished by its symptoms of intense pain, active inflammation, and swelling of the joints. Traditional approaches in AGA management often fall short of desired outcomes in clinical settings. However, recent ethnopharmacological investigations have been focusing on the potential of Traditional Herbal Medicine (THM) in various forms, exploring their therapeutic impact and targets in AGA treatment. AIM OF THE REVIEW: This review briefly summarizes the current potential pharmacological mechanisms of THMs - including active ingredients, extracts, and prescriptions -in the treatment of AGA, and discusses the relevant potential mechanisms and molecular targets in depth. The objective of this study is to offer extensive information and a reference point for the exploration of targeted AGA treatment using THMs. MATERIALS AND METHODS: This review obtained scientific publications focused on in vitro and in vivo studies of anti-AGA THMs conducted between 2013 and 2023. The literature was collected from various journals and electronic databases, including PubMed, Elsevier, ScienceDirect, Web of Science, and Google Scholar. The retrieval and analysis of relevant articles were guided by keywords such as "acute gouty arthritis and Chinese herbal medicine," "acute gouty arthritis herbal prescription," "acute gouty arthritis and immune cells," "acute gouty arthritis and inflammation," "acute gouty arthritis and NOD-like receptor thermoprotein domain associated protein 3 (NLRP3)," "acute gouty arthritis and miRNA," and "acute gouty arthritis and oxidative stress." RESULTS: We found that AGA has a large number of therapeutic targets, highlighting the effectiveness the potential of THMs in AGA treatment through in vitro and in vivo studies. THMs and their active ingredients can mitigate AGA symptoms through a variety of therapeutic targets, such as influencing macrophage polarization, neutrophils, T cells, natural killer (NK) cells, and addressing factors like inflammation, NLRP3 inflammasome, signaling pathways, oxidative stress, and miRNA multi-target interactions. The anti-AGA properties of THMs, including their active components and prescriptions, were systematically summarized and categorized based on their respective therapeutic targets. CONCLUSION: phenolic, flavonoid, terpenoid and alkaloid compounds in THMs are considered the key ingredients to improve AGA. THMs and their active ingredients achieve enhanced efficacy through interactions with multiple targets, of which NLRP3 is a main therapeutic target. Nonetheless, given the intricate composition of traditional Chinese medicine (TCM), additional research is required to unravel the underlying mechanisms and molecular targets through which THMs alleviate AGA.

Multimodal deep learning-based diagnostic model for BPPV.

BACKGROUND: Benign paroxysmal positional vertigo (BPPV) is a prevalent form of vertigo that necessitates a skilled physician to diagnose by observing the nystagmus and vertigo resulting from specific changes in the patient's position. In this study, we aim to explore the integration of eye movement video and position information for BPPV diagnosis and apply artificial intelligence (AI) methods to improve the accuracy of BPPV diagnosis. METHODS: We collected eye movement video and diagnostic data from 518 patients with BPPV who visited the hospital for examination from January to March 2021 and developed a BPPV dataset. Based on the characteristics of the dataset, we propose a multimodal deep learning diagnostic model, which combines a video understanding model, self-encoder, and cross-attention mechanism structure. RESULT: Our validation test on the test set showed that the average accuracy of the model reached 81.7%, demonstrating the effectiveness of the proposed multimodal deep learning method for BPPV diagnosis. Furthermore, our study highlights the significance of combining head position information and eye movement information in BPPV diagnosis. We also found that postural and eye movement information plays a critical role in the diagnosis of BPPV, as demonstrated by exploring the necessity of postural information for the diagnostic model and the contribution of cross-attention mechanisms to the fusion of postural and oculomotor information. Our results underscore the potential of AI-based methods for improving the accuracy of BPPV diagnosis and the importance of considering both postural and oculomotor information in BPPV diagnosis.

Dynamic temperature control in microfluidics for in vivo imaging of cold-sensing in C. elegans.

The ability to perceive temperature is crucial for most animals. It enables them to maintain their body temperature and swiftly react to noxiously cold or hot objects. Caenorhabditis elegans is a powerful genetic model for the study of thermosensation as its simple nervous system is well characterized and its transparent body is suited for in vivo functional imaging of neurons. The behavior triggered by experience-dependent thermosensation has been well studied in C. elegans under temperature-gradient environments. However, how C. elegans senses temperature via its nervous system is not well understood due to the limitations of currently available technologies. One major bottleneck is the difficulty in creating fast temperature changes, especially cold stimuli. Here, we developed a microfluidic-based platform that allowed the in vivo functional imaging of C. elegans responding to well-controlled temporally varying temperature stimulation by rapidly switching fluid streams at different temperatures. We used computational models to enable rational design and optimization of experimental conditions. We validated the design and utility of our system with studies of the functional role of thermosensory neurons. We showed that the responses of PVD polymodal nociceptor neurons observed in previous studies can be recapitulated. Further, we highlighted how this platform may be used to dissect neuronal circuits with an example of activity recording in PVC interneurons. Both of these neuron types show sensitization phenotypes. We envision that both the engineered system and the findings in this work will spur further studies of molecular and cellular mechanisms underlying cold-sensing through the nervous system.

Toolkits for detailed and high-throughput interrogation of synapses in C. elegans.

Visualizing synaptic connectivity has traditionally relied on time-consuming electron microscopy-based imaging approaches. To scale the analysis of synaptic connectivity, fluorescent protein-based techniques have been established, ranging from the labeling of specific pre- or post-synaptic components of chemical or electrical synapses to transsynaptic proximity labeling technology such as GRASP and iBLINC. In this paper, we describe WormPsyQi, a generalizable image analysis pipeline that automatically quantifies synaptically localized fluorescent signals in a high-throughput and robust manner, with reduced human bias. We also present a resource of 30 transgenic strains that label chemical or electrical synapses throughout the nervous system of the nematode Caenorhabditis elegans, using CLA-1, RAB-3, GRASP (chemical synapses), or innexin (electrical synapse) reporters. We show that WormPsyQi captures synaptic structures in spite of substantial heterogeneity in neurite morphology, fluorescence signal, and imaging parameters. We use these toolkits to quantify multiple obvious and subtle features of synapses - such as number, size, intensity, and spatial distribution of synapses - in datasets spanning various regions of the nervous system, developmental stages, and sexes. Although the pipeline is described in the context of synapses, it may be utilized for other 'punctate' signals, such as fluorescently tagged neurotransmitter receptors and cell adhesion molecules, as well as proteins in other subcellular contexts. By overcoming constraints on time, sample size, cell morphology, and phenotypic space, this work represents a powerful resource for further analysis of synapse biology in C. elegans.

Automated cell annotation in multi-cell images using an improved CRF_ID algorithm.

Cell identification is an important yet difficult process in data analysis of biological images. Previously, we developed an automated cell identification method called CRF_ID and demonstrated its high performance in C. elegans whole-brain images (Chaudhary et al, 2021). However, because the method was optimized for whole-brain imaging, comparable performance could not be guaranteed for application in commonly used C. elegans multi-cell images that display a subpopulation of cells. Here, we present an advance CRF_ID 2.0 that expands the generalizability of the method to multi-cell imaging beyond whole-brain imaging. To illustrate the application of the advance, we show the characterization of CRF_ID 2.0 in multi-cell imaging and cell-specific gene expression analysis in C. elegans. This work demonstrates that high accuracy automated cell annotation in multi-cell imaging can expedite cell identification and reduce its subjectivity in C. elegans and potentially other biological images of various origins.

A Ternary (P, Se, S) Covalent Inorganic Framework as a Shuttle Effect-Free Cathode for Li-S Batteries.

Developing new cathode materials to avoid shuttle effect of Li-S batteries at source is crucial for practical high-energy applications, which, however, remains a great challenge. Herein, a new class of sulfur-containing ternary covalent inorganic framework (CIF), P4 Se6 S40 , is explored, by simply comelting powders of P, S, and Se. The P4 Se6 S40 CIF with open framework enables all active sites available during electrochemical reactions, giving a high capacity delivery. Moreover, introducing Se atoms can improve intrinsic electronic conductivity of S chains yet without remarkably compromising the capacity because Se is also electrochemical active to lithium storage. More importantly, Se atoms in S-Se chains can serve as a heteroatom barrier to block the bonding of S atoms around, effectively avoiding the formation of long-chain polysulfides during cycling. Besides, stable Li3 PS4 with a tetrahedral configuration formed after lithiation works as not only a good ionic conductor to promote Li ion diffusion, but a three-dimensional spatial barrier and chemical anchor to suppress the dissolution and diffusion of lithium polysulfides (LiPS), further inhibiting the shuttle effect. Consequently, the P4 Se6 S40 cathode delivers high capacity and excellent capacity retention with even a high loading of 10.5 mg cm-2 which far surpasses the requirement for commercial applications.

Mechanical intelligence simplifies control in terrestrial limbless locomotion.

Limbless locomotors, from microscopic worms to macroscopic snakes, traverse complex, heterogeneous natural environments typically using undulatory body wave propagation. Theoretical and robophysical models typically emphasize body kinematics and active neural/electronic control. However, we contend that because such approaches often neglect the role of passive, mechanically controlled processes (those involving "mechanical intelligence"), they fail to reproduce the performance of even the simplest organisms. To uncover principles of how mechanical intelligence aids limbless locomotion in heterogeneous terradynamic regimes, here we conduct a comparative study of locomotion in a model of heterogeneous terrain (lattices of rigid posts). We used a model biological system, the highly studied nematode worm Caenorhabditis elegans, and a robophysical device whose bilateral actuator morphology models that of limbless organisms across scales. The robot's kinematics quantitatively reproduced the performance of the nematodes with purely open-loop control; mechanical intelligence simplified control of obstacle navigation and exploitation by reducing the need for active sensing and feedback. An active behavior observed in C. elegans, undulatory wave reversal upon head collisions, robustified locomotion via exploitation of the systems' mechanical intelligence. Our study provides insights into how neurally simple limbless organisms like nematodes can leverage mechanical intelligence via appropriately tuned bilateral actuation to locomote in complex environments. These principles likely apply to neurally more sophisticated organisms and also provide a design and control paradigm for limbless robots for applications like search and rescue and planetary exploration.

Combined effect of cortical superficial siderosis and cerebral microbleed on short-term and long-term outcomes after intracerebral haemorrhage.

BACKGROUND AND PURPOSE: Cortical superficial siderosis (cSS) and cerebral microbleed (CMB) have distinct effects on intracerebral haemorrhage (ICH). We aim to investigate the combined effect of cSS and CMB on outcomes after ICH. METHODS: Based on a single-centre stroke registry database, patients with spontaneous ICH who had CT scan within 48 hours after ictus and MRI subsequently were identified. Eligible patients were divided into four groups (cSS-CMB-, cSS-CMB+, cSS+CMB-, cSS+CMB+) according to cSS and CMB on susceptibility-weighted image of MRI. Primary outcomes were haematoma volume on admission and unfavourable outcome defined as modified Rankin Scale scores ≥3 at 3 months. Secondary outcomes were all-cause death, recurrence of stroke and ICH during follow-up (median follow-up 2.0 years, IQR 1.0-3.0 years). RESULTS: A total of 673 patients were identified from 1044 patients with spontaneous ICH. 131 (19.5%) had cSS and 468 (69.5%) had CMB. Patients with cSS+CMB+ had the highest rate of poor outcome at 3 months, as well as all-cause death, recurrent stroke and ICH during follow-up. In cSS- patients, CMB was associated with smaller haematoma (ß -0.13; 95% CI -0.22 to -0.03; p=0.009), but it still increased risks of recurrent ICH (OR 4.6; 95% CI 1.3 to 15.6; p=0.015) and stroke (OR 2.0; 95% CI 1.0 to 4.0; p=0.049). These effects of CMB became unremarkable in the context of cSS+. CONCLUSIONS: Patients with different combinations of cSS and CMB have distinct patterns of short-term and long-term outcomes. Although CMB is related to restrained haematoma, it does not improve long-term outcomes. TRIAL REGISTRATION NUMBER: NCT04803292.

Electrochemical Synthesis and Electrocatalytic Oxygen-Evolution Performance of Two-Dimensional NiCo-BPDC Materials.

Metal-organic frameworks (MOFs) have been widely studied as electrocatalysts, and the research strategy to improve their electrocatalytic oxygen evolution reaction (OER) performance is to modify their structure. In this paper, two-dimensional bimetallic MOFs were constructed to improve electrocatalytic OER performance. Using a mild electrochemical method with Ni and Co as metal sources and 4, 4 '-biphenyl dicarboxylic acid (H2 BPDC) as ligand, two-dimensional NiCo-BPDC was synthesized and then deposited on a carbon cloth electrode. The results show that NiCo-BPDC/CC possessed a low overpotential of 356 mV at a current density of 20 mA cm-2 with a small Tafel slope of 86 mV dec-1 in 1.0 M KOH solution. The two-dimensional NiCo-BPDC exhibits excellent electrocatalytic OER performance because the coordination of Ni and Co in the material and the interaction of the two-dimensional materials provide a large electrochemically active surface area and expose more metal active sites for OER, thus improving the reaction efficiency and indicating NiCo-BPDC as potential OER electrocatalyst.

Electroacupuncture may alleviate diabetic neuropathic pain by inhibiting the microglia P2X4R and neuroinflammation.

Diabetic neuropathic pain (DNP) is a common and destructive complication of diabetes mellitus. The discovery of effective therapeutic methods for DNP is vitally imperative because of the lack of effective treatments. Although 2 Hz electroacupuncture (EA) was a successful approach for relieving DNP, the mechanism underlying the effect of EA on DNP is still poorly understood. Here, we established a rat model of DNP that was induced by streptozotocin (STZ) injection. P2X4R was upregulated in the spinal cord after STZ-injection. The upregulation of P2X4R was mainly expressed on activated microglia. Intrathecal injection of a P2X4R antagonist or microglia inhibitor attenuated STZ-induced nociceptive thermal hyperalgesia and reduced the overexpression of brain-derived neurotrophic factor (BDNF), interleukin-1ß (IL-1ß) and tumor necrosis factor-α (TNF-α) in the spinal cord. We also assessed the effects of EA treatment on the pain hypersensitivities of DNP rats, and further investigated the possible mechanism underlying the analgesic effect of EA. EA relieved the hyperalgesia of DNP. In terms of mechanism, EA reduced the upregulation of P2X4R on activated microglia and decreased BDNF, IL-1ß and TNF-α in the spinal cord. Mechanistic research of EA's analgesic impact would be beneficial in ensuring its prospective therapeutic effect on DNP as well as in extending EA's applicability.

Bubble-particle dynamics in multiphase flow of capillary foams in a porous micromodel.

Surfactant-free capillary foams (CFs) are known to be remarkably tolerant to oil, and possess unique stability and flow properties. These properties result from the presence of oil-and-particle-coated bubbles that are interconnected by a dense particle-oil capillary network. In this work, we present a study of the dynamics of capillary foams flowing through a porous micromodel. We determine that despite the presence of oil-particle networks, CFs can flow through a microporous environment and that above a threshold flowrate, >80% of foam pumped through the micromodel can be recovered. In addition, we highlight the absence of steady state in CF flow and identify the underlying phenomena including the increasing apparent viscosity, reconfigurable flow paths, and intermittent clogging of the micromodel from an oil-particle composite and bubbles trapped in pores. We also characterize bubble dynamics and show that CFs surprisingly exhibit the same bubble generation and destruction mechanisms as classical foams despite the absence of surfactants. Our observations suggest that the porous medium plays a key role in generating uniformly sized bubbles and that capillary foams in a microporous environment tend to reconfigure their flow paths in a manner that may provide opportunities for increased sweep efficiency in enhanced oil recovery.

An expanded GCaMP reporter toolkit for functional imaging in Caenorhabditis elegans.

In living organisms, changes in calcium flux are integral to many different cellular functions and are especially critical for the activity of neurons and myocytes. Genetically encoded calcium indicators (GECIs) have been popular tools for reporting changes in calcium levels in vivo. In particular, GCaMPs, derived from GFP, are the most widely used GECIs and have become an invaluable toolkit for neurophysiological studies. Recently, new variants of GCaMP, which offer a greater variety of temporal dynamics and improved brightness, have been developed. However, these variants are not readily available to the Caenorhabditis elegans research community. This work reports a set of GCaMP6 and jGCaMP7 reporters optimized for C. elegans studies. Our toolkit provides reporters with improved dynamic range, varied kinetics, and targeted subcellular localizations. Besides optimized routine uses, this set of reporters is also well suited for studies requiring fast imaging speeds and low magnification or low-cost platforms.

High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS).

High-throughput transgenesis using synthetic DNA libraries is a powerful method for systematically exploring genetic function. Diverse synthesized libraries have been used for protein engineering, identification of protein-protein interactions, characterization of promoter libraries, developmental and evolutionary lineage tracking, and various other exploratory assays. However, the need for library transgenesis has effectively restricted these approaches to single-cell models. Here, we present Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS), a simple yet powerful approach to large-scale transgenesis that overcomes typical limitations encountered in multicellular systems. TARDIS splits the transgenesis process into a two-step process: creation of individuals carrying experimentally introduced sequence libraries, followed by inducible extraction and integration of individual sequences/library components from the larger library cassette into engineered genomic sites. Thus, transformation of a single individual, followed by lineage expansion and functional transgenesis, gives rise to thousands of genetically unique transgenic individuals. We demonstrate the power of this system using engineered, split selectable TARDIS sites in Caenorhabditis elegans to generate (1) a large set of individually barcoded lineages and (2) transcriptional reporter lines from predefined promoter libraries. We find that this approach increases transformation yields up to approximately 1000-fold over current single-step methods. While we demonstrate the utility of TARDIS using C. elegans, in principle the process is adaptable to any system where experimentally generated genomic loci landing pads and diverse, heritable DNA elements can be generated.

Transgenesis ­ the ability to insert foreign genetic material (known as transgenes) in to the genome of an organism ­ has revolutionized biological research. This approach has made it possible for scientists to study the role of specific genes and to produce animal models which mimic aspects of human diseases. For transgenes to be maintained and passed down to future generations, they must be introduced into germ cells which will go on to form the egg and sperm of the organism. However, despite advances in genetic engineering, this process (called 'specific transgenesis') is still laborious and time-consuming, and limits researchers to working with only a small number of known DNA sequences at a time. In contrast, 'exploratory transgenesis' ­ where dozens of transgenes from a library of DNA sequences are introduced simultaneously into multiple individuals ­ is more efficient and allows for more large-scale experiments. However, this approach can only be done with single-celled organisms like bacteria, and remains virtually impossible in laboratory animals like worms or mice. Stevenson et al. therefore set out to boost the efficiency of exploratory transgenesis in a commonly used laboratory animal, the roundworm Caenorhabditis elegans. To do this, they used the 'library' principle of exploratory transgenesis in order to develop a new resource called TARDIS (short for, Transgenic Arrays Resulting in Diversity of Integrated Sequences). First, Stevenson et al. genetically engineered worms to carry a 'landing site' for foreign DNA. Next, a library of transgenes and a mechanism which cuts pieces of DNA and pastes them into the landing site were introduced into the germ cells of these worms using traditional methods. The worms were then bred to generate a large population of offspring that had inherited this array of foreign DNA sequences. Finally, the 'cut and paste' mechanism was switched on and a random transgene was inserted into the landing site in the genome. This resulted in thousands of worms which each had a unique genetic modification that can be passed on to future generations. These results show for the first time that larger-scale transgenesis experiments are possible in multi-cellular animals. In the future, Stevenson et al. hope that TARDIS can be adapted to different organisms and allow researchers to carry out experiments that were not previously possible.