ResearchPad - immunology-and-microbiology https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[A pull-down assay using DNA/RNA-conjugated beads with a customized competition strategy: An effective approach to identify DNA/RNA binding proteins]]> https://www.researchpad.co/article/N8e56d6de-361d-4676-bbf9-3665cb7a57a6 Image, graphical abstract

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<![CDATA[Data showing differential expression of Monocyte chemoattractant protein-1 in response to symptomatic and asymptomatic T. vaginalis infection]]> https://www.researchpad.co/article/Nbb59ccb4-75d4-4bd3-aada-07c8f7d0c4a3

Trichomoniasis is caused by Trichomonas vaginalis (a protozoan parasite). About 80% of the infected cases remain asymptomatic [1]. The differential response of showing symptoms or no symptoms is not yet explored. However, some studies gave us some insights on the pathogenesis of trichomonas and also about host defense mechanism. Host secretes pro-inflammatory cytokines and chemokines to evade infection. Monocyte chemoattractant protein-1 (MCP-1/CCL2) is a strong chemoattractant of monocytes, NK-cells and T-lymphocytes. Many reports have shown high MCP-1 levels during trichomonas infection [2], [3], [4], [5] in human prostate stromal myofibroblast cells (WPMY-1), HeLa cells, vaginal epithelial cells (VECs) but levels in response to symptomatic and asymptomatic isolates is not yet reported. In this article, we have reported MCP-1 levels in the vaginal washes and serum samples of BALB/c mouse infected with symptomatic and asymptomatic T. vaginalis isolates for different time points. We found higher levels of MCP-1 in vaginal washes of symptomatic group on 2nd day post infection (dpi) than control uninfected group. While on 4th dpi and 14th dpi, higher levels of MCP-1 in vaginal washes was observed in asymptomatic group as compared to control group. However, significant level of MCP-1 was observed in asymptomatic group on 14th dpi as compared to symptomatic group in vaginal washes. We have also observed significantly higher levels of MCP-1 in the serum samples of symptomatic group on 2nd, 4th and 14th dpi as compared to control group. A higher level of MCP-1 was found at all the time points in serum samples of asymptomatic group as compared to control group. Interestingly, a significant higher level of MCP-1 was found in the serum samples of BALB/c mice in asymptomatic as compared to symptomatic group. The MCP-1 levels in both vaginal washes and serum were significantly higher in asymptomatic group at later time points.

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<![CDATA[Dataset on phenotypic characterization, on protein and genome analysis of three fluorescent Pseudomonas strains from mid-mountain water]]> https://www.researchpad.co/article/Nf998420b-8bbb-4152-8b7b-175a2bd99f77

The identification of non-fermentative Gram negative bacilli from run-off and spring water, including fluorescent Pseudomonas is very complex and investigations are needed to contribute to the systematic of these bacteria. In this dataset, the phenotypical profiles of three strains isolated from Vosges mountains first identified as Pseudomonas fluorescens were determined using API 50 CH galleries. Then, the identification of their proteins released directly into water was carried out using tandem/mass spectrometry after separating proteins on native two-dimensional polyacrylamide gels. Finally, genotypic analysis data is presented, that illustrates biodiversity in this fluorescent bacterial group.

This data is referred by a research article entitled “Fluorescent Pseudomonas strains from mid-mountain water able to release antioxidant proteins directly into water”.

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<![CDATA[An ex vivo cornea infection model]]> https://www.researchpad.co/article/Nc6931390-d2cb-4fd4-aa47-dd1e4d2fc991

In vitro screening and testing of drugs and devices is necessary, but in vitro conditions differ greatly from those found in vivo. These differences can lead to false promises of efficacy, or can hide problems of tissue compatibility. Models with ex vivo tissues can be highly valuable bridges which provide relevant matrices for testing [1], [2], [3], [4], [5], [6], [7], [8], [9]. Ex vivo tissue models which are closer both biochemically and biophysically can provide useful feedback in a more time- and cost-efficient manner. Herein we describe an ex vivo corneal model for use in drug delivery testing and corneal infection modeling [10]. The protocol covers the tissue harvesting, sterilization, inoculation, and bacterial load quantification. We envision that the model can be used to study bacterial physiology on metabolizable matrices and to study the direct effects of microbial colonization on the cornea's integrity and clarity.

  • Devitalized cornea.

  • Non-submersed conditions.

  • Contact lens compatible.

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<![CDATA[An improved protocol to establish experimental tuberculous meningitis in the rabbit]]> https://www.researchpad.co/article/Nd28710fa-db2c-4bfb-9f07-a0cf1d5fa122

Tuberculous meningitis (TBM), caused by Mycobacterium tuberculosis (Mtb), is the deadliest form of tuberculosis in humans, particularly in children and the geriatric population. However, the host-pathogen interactions underlying TBM is not well understood. Rabbits are a valuable model system to study TB in humans. The rabbit model of TB recapitulates several pathophysiological characteristics, including heterogeneity, architecture, and development of granulomas at the site of infection as observed in Mtb-infected human organs. Previously, our group has established a rabbit model of TBM that has been used to understand the host immune response to Mtb infection and to evaluate novel intervention therapies for TBM. In this model, rabbits infected intracisternally with Mtb showed histopathologic manifestations in the brain and meninges that are hallmarks of TBM in humans, including inflammatory cell accumulation and thickening of the leptomeninges. However, in this model, a helmet made of dental acrylic was attached to rabbit's skull with screws under anesthesia. At 24 h post-procedure, the animals were injected intracisternally with Mtb using a spinal needle. The rabbits were necropsied at various experimental time points up to 2 weeks post-infection. Although this method has been successful in establishing TBM, placement of the dental acrylic helmet on rabbit skull with screws that stays until the experimental endpoint poses stress to the animals and increases the chances of secondary infection. To alleviate these issues, we have developed an improved protocol, in which sedated rabbits are placed on specialised stereotaxic equipment and injected with Mtb intracisternally. This method is less cumbersome, faster, and more efficient in delivering the bacteria. Besides, the animals are not stressed by this method, compared to the previous one.

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<![CDATA[An invitro dataset on infectious potential of transmitted/founder (TF) and non-TF (NT) HIV-1 viruses generated from Interferon alpha-treated primary CD4+ T cells]]> https://www.researchpad.co/article/Nfb14245a-20fa-46db-8fe4-30e9d0e16e5c

This data article describes the infectivity of transmitted/founder (TF) and non-TF (NT) HIV-1 viruses derived from primary CD4+ T cells treated with or without IFN-α, over a period of 12 days. TF and NT viruses described in this article were derived from the same individual (one of each from 8 infants who acquired HIV infection through mother-to-child transmission (MTCT). IFN-α resistance to both TF and NT viruses was studied by infecting TZM-bl cells and measuring luciferase expression (expressed as relative light units, RLU). Measurement of luciferase expression is extremely sensitive and allows quantification of even small changes in gene expression at the transcriptional level.

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<![CDATA[Metagenomic data of the microbial community of lab-scale nitritation-anammox sequencing-batch bioreactor performing nitrogen removal from synthetic wastewater]]> https://www.researchpad.co/article/N11760d1b-6489-4cda-8cda-15368c0fd18a

The nitritation-anammox process, which involves partial aerobic oxidation of the ammonium to nitrite and following oxidation of ammonium by nitrite to molecular nitrogen, is an efficient and cost-effective approach for biological nitrogen removal from wastewater. To characterize the microbial communities involved in the nitrogen and carbon cycles in wastewater treatment bioreactors employing this process, we sequenced the metagenome of a sludge sample collected from the lab-scale nitritation-anammox sequencing-batch reactor. At the phylum level, Proteobacteria and Chloroflexi were the most numerous groups. Anammox bacteria belonged to the genus Candidatus Brocadia. The obtained data will help to investigate the taxonomical and functional diversity the microbial communities involved in nitritation-anammox process, and will be used for genome-based analysis of uncultured bacterial lineages. The raw sequencing data is available from the NCBI Sequence Read Archive (SRR9831403) database under the BioProject PRJN0A55627.

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<![CDATA[Data on antigen recognition hindrance by antibodies covalently immobilized to Protein G magnetic beads by dimethyl pimelimidate (DMP) cross-linking]]> https://www.researchpad.co/article/5c50f65ed5eed0c48462c49a

The data presented herein is related to the article entitled "Trypanosoma cruzi immunoproteome: calpain-like CAP5.5 differentially detected throughout distinct stages of human Chagas disease cardiomyopathy" [1]. Electrophoretic analyses under denaturing and reducing conditions indicate that covalent immobilization of human IgG to Protein G magnetic beads by cross-linking with 50 mM dimethyl pimelimidate hinders the recognition of T. cruzi antigens in immunoprecipitation assays.

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<![CDATA[Escherichia coli O157:H7 transcriptome datasets for comparison of RNA-seq and microarray platforms]]> https://www.researchpad.co/article/5c26b4b9d5eed0c484763c2d

Whole transcriptome analysis to investigate differential gene expression and regulatory adaption can be carried out on two different technological platforms: by probe hybridisation to microarrays or by RNAseq for deep sequencing. Since there are difference in terms of their genome coverage, sensitivity and cost, there is a requirement for robust comparisons to determine the platform of choice. Here, we present datasets for the whole transcriptional response verocytoxigenic Escherichia coli (VTEC) obtained from RNA-seq and microarray platforms in response to spinach, together with a comparison between the datasets (available at Array Express: E-MTAB-3249, E-MTAB-4120, E-MTAB-7441).

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<![CDATA[Data on the generation of rabbit infections and RPR titre changes in serum samples from syphilis patients at follow-up]]> https://www.researchpad.co/article/5c1d86d5d5eed0c48476c940

The data presented in this article are related to the research article entitled “Performance of novel infection phase-dependent antigens in syphilis serodiagnosis and treatment efficacy determination”. The rabbit model [1], [2] is an appropriate animal model for studying syphilis, a classic sexually transmitted disease (STD). Live Treponema pallidum (T. pallidum, Tp) and inactivated T. pallidum were inoculated in the backs of New Zealand rabbits. RT-PCR was performed to determine whether T. pallidum DNA could be detected in different groups. Sixty paired serum samples from patients at follow-up were tested by RPR and recombinant Tp0971-, Tp0768-, Tp0462- and Tp92-based ELISA.

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<![CDATA[Identifying novel strategies for treating human hair loss disorders: Cyclosporine A suppresses the Wnt inhibitor, SFRP1, in the dermal papilla of human scalp hair follicles]]> https://www.researchpad.co/article/5afd46cd463d7e6ee57105ce

Hair growth disorders often carry a major psychological burden. Therefore, more effective human hair growth–modulatory agents urgently need to be developed. Here, we used the hypertrichosis-inducing immunosuppressant, Cyclosporine A (CsA), as a lead compound to identify new hair growth–promoting molecular targets. Through microarray analysis we identified the Wnt inhibitor, secreted frizzled related protein 1 (SFRP1), as being down-regulated in the dermal papilla (DP) of CsA-treated human scalp hair follicles (HFs) ex vivo. Therefore, we further investigated the function of SFRP1 using a pharmacological approach and found that SFRP1 regulates intrafollicular canonical Wnt/β-catenin activity through inhibition of Wnt ligands in the human hair bulb. Conversely, inhibiting SFRP1 activity through the SFRP1 antagonist, WAY-316606, enhanced hair shaft production, hair shaft keratin expression, and inhibited spontaneous HF regression (catagen) ex vivo. Collectively, these data (a) identify Wnt signalling as a novel, non–immune-inhibitory CsA target; (b) introduce SFRP1 as a physiologically important regulator of canonical β-catenin activity in a human (mini-)organ; and (c) demonstrate WAY-316606 to be a promising new promoter of human hair growth. Since inhibiting SFRP1 only facilitates Wnt signalling through ligands that are already present, this ‘ligand-limited’ therapeutic strategy for promoting human hair growth may circumvent potential oncological risks associated with chronic Wnt over-activation.

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<![CDATA[The neural system of metacognition accompanying decision-making in the prefrontal cortex]]> https://www.researchpad.co/article/5ae95a3c463d7e06f246c069

Decision-making is usually accompanied by metacognition, through which a decision maker monitors uncertainty regarding a decision and may then consequently revise the decision. These metacognitive processes can occur prior to or in the absence of feedback. However, the neural mechanisms of metacognition remain controversial. One theory proposes an independent neural system for metacognition in the prefrontal cortex (PFC); the other, that metacognitive processes coincide and overlap with the systems used for the decision-making process per se. In this study, we devised a novel “decision–redecision” paradigm to investigate the neural metacognitive processes involved in redecision as compared to the initial decision-making process. The participants underwent a perceptual decision-making task and a rule-based decision-making task during functional magnetic resonance imaging (fMRI). We found that the anterior PFC, including the dorsal anterior cingulate cortex (dACC) and lateral frontopolar cortex (lFPC), were more extensively activated after the initial decision. The dACC activity in redecision positively scaled with decision uncertainty and correlated with individual metacognitive uncertainty monitoring abilities—commonly occurring in both tasks—indicating that the dACC was specifically involved in decision uncertainty monitoring. In contrast, the lFPC activity seen in redecision processing was scaled with decision uncertainty reduction and correlated with individual accuracy changes—positively in the rule-based decision-making task and negatively in the perceptual decision-making task. Our results show that the lFPC was specifically involved in metacognitive control of decision adjustment and was subject to different control demands of the tasks. Therefore, our findings support that a separate neural system in the PFC is essentially involved in metacognition and further, that functions of the PFC in metacognition are dissociable.

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<![CDATA[In vivo clonal analysis reveals spatiotemporal regulation of thalamic nucleogenesis]]> https://www.researchpad.co/article/5ae95a3e463d7e06f246c06a

The thalamus, a crucial regulator of cortical functions, is composed of many nuclei arranged in a spatially complex pattern. Thalamic neurogenesis occurs over a short period during mammalian embryonic development. These features have hampered the effort to understand how regionalization, cell divisions, and fate specification are coordinated and produce a wide array of nuclei that exhibit distinct patterns of gene expression and functions. Here, we performed in vivo clonal analysis to track the divisions of individual progenitor cells and spatial allocation of their progeny in the developing mouse thalamus. Quantitative analysis of clone compositions revealed evidence for sequential generation of distinct sets of thalamic nuclei based on the location of the founder progenitor cells. Furthermore, we identified intermediate progenitor cells that produced neurons populating more than one thalamic nuclei, indicating a prolonged specification of nuclear fate. Our study reveals an organizational principle that governs the spatial and temporal progression of cell divisions and fate specification and provides a framework for studying cellular heterogeneity and connectivity in the mammalian thalamus.

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<![CDATA[How measurement science can improve confidence in research results]]> https://www.researchpad.co/article/5ae95a46463d7e06f246c06e

The current push for rigor and reproducibility is driven by a desire for confidence in research results. Here, we suggest a framework for a systematic process, based on consensus principles of measurement science, to guide researchers and reviewers in assessing, documenting, and mitigating the sources of uncertainty in a study. All study results have associated ambiguities that are not always clarified by simply establishing reproducibility. By explicitly considering sources of uncertainty, noting aspects of the experimental system that are difficult to characterize quantitatively, and proposing alternative interpretations, the researcher provides information that enhances comparability and reproducibility.

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<![CDATA[Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry]]> https://www.researchpad.co/article/5b59a321463d7e789700d0d6

Post-translational modification (PTM) of protein lysine residues by NƐ-acylation induces structural changes that can dynamically regulate protein functions, for example, by changing enzymatic activity or by mediating interactions. Precise quantification of site-specific protein acylation occupancy, or stoichiometry, is essential for understanding the functional consequences of both global low-level stoichiometry and individual high-level acylation stoichiometry of specific lysine residues. Other groups have reported measurement of lysine acetylation stoichiometry by comparing the ratio of peptide precursor isotopes from endogenous, natural abundance acylation and exogenous, heavy isotope-labeled acylation introduced after quantitative chemical acetylation of proteins using stable isotope-labeled acetic anhydride. This protocol describes an optimized approach featuring several improvements, including: (1) increased chemical acylation efficiency, (2) the ability to measure protein succinylation in addition to acetylation, and (3) improved quantitative accuracy due to reduced interferences using fragment ion quantification from data-independent acquisitions (DIA) instead of precursor ion signal from data-dependent acquisition (DDA). The use of extracted peak areas from fragment ions for quantification also uniquely enables differentiation of site-level acylation stoichiometry from proteolytic peptides containing more than one lysine residue, which is not possible using precursor ion signals for quantification. Data visualization in Skyline, an open source quantitative proteomics environment, allows for convenient data inspection and review. Together, this workflow offers unbiased, precise, and accurate quantification of site-specific lysine acetylation and succinylation occupancy of an entire proteome, which may reveal and prioritize biologically relevant acylation sites.

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<![CDATA[Biocuration: Distilling data into knowledge]]> https://www.researchpad.co/article/5ae5cb72463d7e39eef05ada

Data, including information generated from them by processing and analysis, are an asset with measurable value. The assets that biological research funding produces are the data generated, the information derived from these data, and, ultimately, the discoveries and knowledge these lead to. From the time when Henry Oldenburg published the first scientific journal in 1665 (Proceedings of the Royal Society) to the founding of the United States National Library of Medicine in 1879 to the present, there has been a sustained drive to improve how researchers can record and discover what is known. Researchers’ experimental work builds upon years and (collectively) billions of dollars’ worth of earlier work. Today, researchers are generating data at ever-faster rates because of advances in instrumentation and technology, coupled with decreases in production costs. Unfortunately, the ability of researchers to manage and disseminate their results has not kept pace, so their work cannot achieve its maximal impact. Strides have recently been made, but more awareness is needed of the essential role that biological data resources, including biocuration, play in maintaining and linking this ever-growing flood of data and information. The aim of this paper is to describe the nature of data as an asset, the role biocurators play in increasing its value, and consistent, practical means to measure effectiveness that can guide planning and justify costs in biological research information resources’ development and management.

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<![CDATA[Organic cation transporter 1 (OCT1) modulates multiple cardiometabolic traits through effects on hepatic thiamine content]]> https://www.researchpad.co/article/5ae5cb71463d7e39eef05ad9

A constellation of metabolic disorders, including obesity, dysregulated lipids, and elevations in blood glucose levels, has been associated with cardiovascular disease and diabetes. Analysis of data from recently published genome-wide association studies (GWAS) demonstrated that reduced-function polymorphisms in the organic cation transporter, OCT1 (SLC22A1), are significantly associated with higher total cholesterol, low-density lipoprotein (LDL) cholesterol, and triglyceride (TG) levels and an increased risk for type 2 diabetes mellitus, yet the mechanism linking OCT1 to these metabolic traits remains puzzling. Here, we show that OCT1, widely characterized as a drug transporter, plays a key role in modulating hepatic glucose and lipid metabolism, potentially by mediating thiamine (vitamin B1) uptake and hence its levels in the liver. Deletion of Oct1 in mice resulted in reduced activity of thiamine-dependent enzymes, including pyruvate dehydrogenase (PDH), which disrupted the hepatic glucose–fatty acid cycle and shifted the source of energy production from glucose to fatty acids, leading to a reduction in glucose utilization, increased gluconeogenesis, and altered lipid metabolism. In turn, these effects resulted in increased total body adiposity and systemic levels of glucose and lipids. Importantly, wild-type mice on thiamine deficient diets (TDs) exhibited impaired glucose metabolism that phenocopied Oct1 deficient mice. Collectively, our study reveals a critical role of hepatic thiamine deficiency through OCT1 deficiency in promoting the metabolic inflexibility that leads to the pathogenesis of cardiometabolic disease.

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<![CDATA[The rostromedial tegmental nucleus is essential for non-rapid eye movement sleep]]> https://www.researchpad.co/article/5ae5a51d463d7e33ca31f530

The rostromedial tegmental nucleus (RMTg), also called the GABAergic tail of the ventral tegmental area, projects to the midbrain dopaminergic system, dorsal raphe nucleus, locus coeruleus, and other regions. Whether the RMTg is involved in sleep–wake regulation is unknown. In the present study, pharmacogenetic activation of rat RMTg neurons promoted non-rapid eye movement (NREM) sleep with increased slow-wave activity (SWA). Conversely, rats after neurotoxic lesions of 8 or 16 days showed decreased NREM sleep with reduced SWA at lights on. The reduced SWA persisted at least 25 days after lesions. Similarly, pharmacological and pharmacogenetic inactivation of rat RMTg neurons decreased NREM sleep. Electrophysiological experiments combined with optogenetics showed a direct inhibitory connection between the terminals of RMTg neurons and midbrain dopaminergic neurons. The bidirectional effects of the RMTg on the sleep–wake cycle were mimicked by the modulation of ventral tegmental area (VTA)/substantia nigra compacta (SNc) dopaminergic neuronal activity using a pharmacogenetic approach. Furthermore, during the 2-hour recovery period following 6-hour sleep deprivation, the amount of NREM sleep in both the lesion and control rats was significantly increased compared with baseline levels; however, only the control rats showed a significant increase in SWA compared with baseline levels. Collectively, our findings reveal an essential role of the RMTg in the promotion of NREM sleep and homeostatic regulation.

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<![CDATA[Simple Generation of a High Yield Culture of Induced Neurons from Human Adult Skin Fibroblasts]]> https://www.researchpad.co/article/5bff41f0d5eed0c484aa2063

Induced neurons (iNs), the product of somatic cells directly converted to neurons, are a way to obtain patient-derived neurons from tissue that is easily accessible. Through this route, mature neurons can be obtained in a matter of a few weeks. Here, we describe a straightforward and rapid one-step protocol to obtain iNs from dermal fibroblasts obtained through biopsy samples from adult human donors. We explain each step of the process, including the maintenance of the dermal fibroblasts, the freezing procedure to build a stock of the cell line, seeding of the cells for reprogramming, as well as the culture conditions during the conversion process. In addition, we describe the preparation of glass coverslips for electrophysiological recordings, long-term coating conditions, and fluorescence activated cell sorting (FACS). We also illustrate examples of the results to be expected. The protocol described here is easy to perform and can be applied to human fibroblasts derived from human skin biopsies from patients with various different diagnoses and ages. This protocol generates a sufficient amount of iNs which can be used for a wide array of biomedical applications, including disease modeling, drug screening, and target validation.

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<![CDATA[In Vivo Imaging of Muscle-tendon Morphogenesis in Drosophila Pupae]]> https://www.researchpad.co/article/5bff41f3d5eed0c484aa20c4

Muscles together with tendons and the skeleton enable animals including humans to move their body parts. Muscle morphogenesis is highly conserved from animals to humans. Therefore, the powerful Drosophila model system can be used to study concepts of muscle-tendon development that can also be applied to human muscle biology. Here, we describe in detail how morphogenesis of the adult muscle-tendon system can be easily imaged in living, developing Drosophila pupae. Hence, the method allows investigating proteins, cells and tissues in their physiological environment. In addition to a step-by-step protocol with helpful tips, we provide a comprehensive overview of fluorescently tagged marker proteins that are suitable for studying the muscle-tendon system. To highlight the versatile applications of the protocol, we show example movies ranging from visualization of long-term morphogenetic events – occurring on the time scale of hours and days – to visualization of short-term dynamic processes like muscle twitching occurring on time scale of seconds. Taken together, this protocol should enable the reader to design and perform live-imaging experiments for investigating muscle-tendon morphogenesis in the intact organism.

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