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opencc-by-4.0Jan 2020View details →

Dataset for: Entrainment of mammalian motile cilia in the brain with hydrodynamic forces

Please read the README.md for information on how to handle the dataset.

opencc-by-4.0Feb 2020View details →

Video for: The role of hydrodynamic forces in synchronisation and alignment of mammalian motile cilia

Here you can find all the videos of the PhD thesis:   The role of hydrodynamic forces in synchronisation and alignment of mammalian motile cilia. by Nicola Pellicciotta Video1: This example shows a movie of a single cell, being subjected to an external oscillatory flow. Images were acquired at 500\,fps using a 60X objective, then analysed using background subtraction and spatial median filter of 3x3 pixels.  Chapter 3 Video 2:  we show the entrainment of a group of cells with very strong oscillatory external flow $v_\mathrm{EX}= 2$\,mm/s at $f_\mathrm{EX}=12$\,Hz. This s flow induced entrainment and also alignment of beating direction of some cells that were beating misaligned to the external flow. The original direction of beating was recovered after the flow stopped. Chapter 3 Video3 and Video4: we depolymerised cell actin by adding 2uM Cytochalasin-D in the cell culture medium for 48hr. After imaging, cells (control and dug treated) were stained in 4\% PFA for 10 minutes, permeabilised with Triton x-100 0.1\% in PBS, and incubated for 1 hour with Nucblue R37605 (1 drop for mL of PBS) and with phalloidin for actin (Sir-Actin, 0.2 uM) following proprietary protocols. Z-stack were taken with confocal microscope (slices of distance of 0.15um each) and can be found at the following links: DMSO treated cells (control) Video 3, and Cytochalasin-D treated,  Video 4. Chapter 3 Video5: The maximal beating amplitude for a cilium within each cell was measured by inspecting the recordings from top view and marking two extreme points at the power and recovery stroke. Chapter 3 Video6: Experimental procedure  and the image analysis methods for Chapter 4. Continuous fluid flow is applied for three days on cells cultured in Transwell-chips. The chips are then removed from the flow and cilia motility is imaged with the microscope. From high speed Bright Field movies we identify ciliary beating frequency and cell position, while from tracer particles we measure ciliary beating direction.  Video7: Video of Propelled particles in a culture at 29 DIV and treated with shear stress τ ≈0.8 dyne/cm2. Chapter 4

dryad32/100

Pathogenic LRRK2 control of primary cilia and Hedgehog signaling in neurons and astrocytes of mouse brain

Previously, we showed that cholinergic interneurons of the dorsal striatum lose cilia in mice harboring the Parkinson's disease associated, kinase activating, R1441C LRRK2 mutation (<a href="https://www.biorxiv.org/content/10.1101/2021.03.02.433576v1#ref-8">Dhekne et al., 2018</a>). Here we show that this phenotype is also seen in two mouse strains carrying the most common human G2019S LRRK2 mutation. Heterozygous loss of the PPM1H phosphatase that is specific for LRRK2-phosphorylated Rab GTPases (<a href="https://www.biorxiv.org/content/10.1101/2021.03.02.433576v1#ref-3">Berndsen et al., 2019</a>) yields the same cilia loss phenotype, strongly supporting a connection between Rab GTPase phosphorylation and cilia loss. In addition, astrocytes throughout the striatum show a ciliation defect in LRRK2 and PPM1H-/+ mutant models. Hedgehog signaling requires cilia, and loss of cilia correlates here with a loss in induction of Hedgehog signaling as monitored by in situ hybridization of Gli1 transcripts. These data support a model in which LRRK2 and PPM1H mutant mice struggle to receive and respond to critical Hedgehog signals in the nigral-striatal pathway.

opencc-zeroOct 2021View details →

opennotspecifiedJan 2022View details →

◂Fig. 6 Scanning electronmicroscopy images of Ramisyllis kingghidorahi n. sp. A Anterior region up to first 17 segments, dorsal view. B Prostomium in detail, anterodorsal view (broken antennae on stub). C Prostomium and first segments in detail showing dorsal bands of cilia, dorsal view. D–F Pores on dorsal cirri. Scale bars: 1 mm A, 200 µm B, 300 µm C, 50 µm E, 30 µm D, F in Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan

◂Fig. 6 Scanning electronmicroscopy images of Ramisyllis kingghidorahi n. sp. A Anterior region up to first 17 segments, dorsal view. B Prostomium in detail, anterodorsal view (broken antennae on stub). C Prostomium and first segments in detail showing dorsal bands of cilia, dorsal view. D–F Pores on dorsal cirri. Scale bars: 1 mm A, 200 µm B, 300 µm C, 50 µm E, 30 µm D, F

opennotspecifiedJan 2022View details →

◂Fig. 10 Scanning electron microscopy images of Ramisyllis kingghidorahi n. sp., posterior-most regions and epithelium details. A–D Posterior ends. Arrow in C and D points to heavily ciliated anus. E– G Minute crests on the dorsal surface of midbody segments. Arrows point to crests laterally located on the dorsal surface. H Dorsal surface of posterior segments. I Clumps of cilia on dorsal surface of proventricular segments. Arrows pointing to pores in H. Scale bars: 100 µm A, B, I, 50 um C, G, 5 µm D, E,4 µm F, and 3 µm H in Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan

◂Fig. 10 Scanning electron microscopy images of Ramisyllis kingghidorahi n. sp., posterior-most regions and epithelium details. A–D Posterior ends. Arrow in C and D points to heavily ciliated anus. E– G Minute crests on the dorsal surface of midbody segments. Arrows point to crests laterally located on the dorsal surface. H Dorsal surface of posterior segments. I Clumps of cilia on dorsal surface of proventricular segments. Arrows pointing to pores in H. Scale bars: 100 µm A, B, I, 50 um C, G, 5 µm D, E,4 µm F, and 3 µm H

opencc-byOct 2019View details →

Dataset for: Motile cilia hydrodynamics: Entrainment versus synchronisation when coupling through flow

This archive contains the dataset for the article "Motile cilia hydrodynamics: Entrainment versus synchronisation when coupling through flow". We gathered videos of cilia dynamics from different sources. For each animal/microorganism we upload the videos in different formats depending on the source: - .tiffs  usually in a directory, it is composed by a series of images - .movie    a format that we use in our lab and that it is combatible with our software in Matlab to tack cilium waveform - .avi          For each video we also have the results from the tracking with our software. The resuts from a single video are all in a Matlab  variable that has the same name but with the extension .clclk_force for example for the video "filename", the results are in "filename.clclk_force". In Matlab these can be loaded as force = load('filename.clclk_force','-mat'); For all the videos these can be directly be found in the directory cilium waveforms force files.

opencc-by-4.0Sep 2024View details →

Cilia structure and intraflagellar transport differentially regulate sensory response dynamics within and between C. elegans chemosensory neurons

List of data with corresponding files Figure 1 A)    File name: Figure 1A- ASH_IFT_mutants_length_copy.pzfx B)    File names: (Folder) ASH_1Mglycerol_IFT_mutants and (Folder) ASH_10-2IAA_IFT_mutants C)    File names: (Folder) ASH_1Mglycerol_IFT_mutants > Peak_responses and (Folder) ASH_10-2IAA_IFT_mutants > Peak_responses - first pulse D)   File names: Figure 1D – ASH Cher and Marianas Lengths Truncation osm-3(ts) 27 and 30 degree graph and Figure 1D – ASH Cher and Marianas Lengths Truncation osm-3(ts) 27 degrees E)    File name: Figure 1E – ASH IFT Quantification.xlsx F)    File name: (Folder) ASH_1Mglycerol_osm3ts G)   File names: Figure 1 – Glycerol_Assays_Data.pzfx and Figure 1 – Glycerol_Assays_Data.xlsx H)   File name: Figure 1H – ALL ASH Marianas and Cher Lengths che-3(nx159ts) I)     File names: Figure 1- ASH IFT PY12007 v AP457 and Figure 1- ASH IFT PY12007 v AP457.xlsx J)    File name: (Folder) ASH_1Mglycerol_che3ts K)   File names: Figure 1 – Glycerol_Assays_Data.pzfx and Figure 1 – Glycerol_Assays_Data.xlsx Figure 2 B)  File name: (Folder) 10-7Diacetyl_Calcium_IFT_mutants C)  File names: (Folder) 10-6Pyrazine_Calcium_IFT_mutants and (Folder) 10-7Pyrazine_Calcium_IFT_mutants D)  File names: (Folder) Microfluidics > (Folder) 10-6pyrazine and (Folder) 10-7diacetyl E)  File names: (Folder) Microfluidics > Diacetyl_Chemotaxis_index_osm6_osm3kap1.pzfx and Pyrazine_Chemotaxis_index_pyrazine_osm3kap1_osm6.pzfx G)  File name: (Folder) 10-6Pyrazine_Calcium_misexpression Figure 3 A)   File name: Figure 3A- AWA IFT AP303 v AP379.xlsx C)  File names: (Folder) AWA_Calcium_Diacetyl and (Folder) AWA_Calcium_Pyrazine D)  File names: (Folder) AWA_Calcium_Diacetyl and (Folder) AWA_Calcium_Pyrazine E)  File name: Figure 3E- SRX64 and ODR10 within dendritic branches.pzfx Figure 4 A)   File name: (Folder) AWA_Calcium_Diacetyl_grk2 B)   File name: (Folder) AWA_Calcium_Pyrazine_grk2 C)   File name: (Folder) Microfluidics_diacetyl D)   File name: (Folder) Microfluidics_pyrazine E)    File name: Figure 4E- GRK2tRFP_kap1osm3ts.pzfx Figure 5 A)   File names: (Folder) AWA_Diacetyl_Adaptation_osm3ts and (Folder) AWA_Pyrazine_Adaptation_osm3ts B)    File name: Figure 5B and S7B- FRAP.pzfx C)    File names: Figure 5C- SRX64_bbs7jhu590.pzfx and Figure 5C- SRX64_bbs7ok1351.pzfx and Figure 5C- oy158_bbs7jhu590.pzfx and Figure 5C- oy158_bbs7ok1351.pzfx D)   File names: (Folder) AWA_Diacetyl_Adaptation_bbs7 and (Folder) AWA_Pyrazine_Adaptation_bbs7 E)    File name: Figure 5E- Marianas_EV_ODR10_SRX64_osm3tskap1.pzfx Figure S1 A)   File names: (Folder) ASH_IFTmutants_0.5and2Mglycerol > (Folder) 0.5Mglycerol and (Folder) 2Mglycerol B)    File names: (Folder) ASH_IFTmutants_quinine > (Folder) 5mM_quinine and (Folder) 10mM_quinine C)    File name: ASH_IAA_t1/2 D)   File names: (Folder) ASH_IFTmutants_heptanol > (Folder) 10-3_heptanol and (Folder) 10-4_heptanol E)    File names: (Folder) ASH_IFTmutants_2Mglycerol_GABA and (Folder) ASH_IFTmutants_2Mglycerol_bicuculline Figure S2 B)    File name: Figure S2B- Dye-filling_data C)    File name: Figure S2C- ASH_IFT_mutants_length.pzfx D)   File names: Figure S2D- ASH IFT PY6345 v PY12007 and Figure S2D- ASH IFT Quantification Figure S3 A)   File name: (Folder) AWA_10-7Diacetyl_IFTmutants B)    File names: (Folder) AWA_Calcium_heptanone > (Folder) 10-4_heptanone and (Folder) 10-5_heptanone C)    File name: (Folder) AWA_10-5Pyrazine_IFTmutants D)   File names: (Folder) AWA_Calcium_methylpyrazine > (Folder) 10-8_methylpyrazine and (Folder) 10-9_methylpyrazine E)    File name: Figure S3- Chemotaxis IFT_mutants.pzfx Figure S4 A)  File name: Figure S4A – AP419_pyrazine_Chemotaxis.pzfx C)  File name: Figure S4C – srx64SL2gfp_osm5.pzfx Figure S6 A)   File names: Diacetyl_prism_decay_grk2 and Pyrazine_prism_decay_grk2 Figure S7  A)  File name: (Folder) AWA_Calcium_Adaptation_diacetyl_IFT_mutant  B)  File name: Figure 5B and S7B- FRAP  C)  File name: Figure S7C- oy158_grk2_rescue.pzfx  F)  File names: (Folder) AWA_Calcium_Adaptation_diacetyl_grk2 > (Folder) grk2 and (Folder) grk2bbs7double Additional materials             All code is listed under Code from Github > MF.matR-master and Additional Methods

opennotspecifiedMay 2020View details →

FIGURE 2. Paepalanthus atratus. A. Capitulum detail. B. Leaf blade detail. C, D. Leaf apex detail. E. Scape detail. F. Spathe and scape detail. G. Spathe apex detail. H. Involucral bract, abaxial surface. I. Involucral bract, adaxial surface. J. Floral bract, abaxial surface. K. Floral bract, adaxial surface with deciduous cilia. L in Notes on an overlooked Paepalanthus (Eriocaulaceae) from central Brazil: identity, taxonomic placement, and morphological details

FIGURE 2. Paepalanthus atratus. A. Capitulum detail. B. Leaf blade detail. C, D. Leaf apex detail. E. Scape detail. F. Spathe and scape detail. G. Spathe apex detail. H. Involucral bract, abaxial surface. I. Involucral bract, adaxial surface. J. Floral bract, abaxial surface. K. Floral bract, adaxial surface with deciduous cilia. L. Staminate flower (pre-anthesis). M. Staminate flower (pre-anthesis) with sepals removed. N. Staminate flower (pre-anthesis) with sepals and petals removed. O. Pistillate flower with sepals and petals opened and lacking the stigmatic branches. P. Pistillate flower with sepals opened. Q. Pistillate flower with sepals removed and lacking the stigmatic branches. R. Gynoecium with bifid early developing stigmatic branches.

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Pathogenic LRRK2 control of primary cilia and Hedgehog signaling in neurons and astrocytes of mouse brain

Open the record for dataset details and reuse information.

publicNov 2021View details →

opencc-zeroAug 2019View details →

Data from: Stabilization of primary cilia reduces abortive cell cyle re-entry to protect injured adult CNS neurons from apoptosis

Abortive cell cycle (ACC) re-entry of apoptotic neurons is a recently characterized phenomenon that occurs after central nervous system (CNS) injury or over the course of CNS disease. Consequently, inhibiting cell cycle progression is neuroprotective in numerous CNS pathology models. Primary cilia are ubiquitous, centriole-based cellular organelles that prevent cell cycling, but their ability to modulate abortive cell cycle has not been described. Here, we show that neuronal cilia are ablated in-vitro and in-vivo following injury by hypoxia or optic nerve transection (ONT), respectively. Furthermore, forced cilia resorption sensitized neurons to these injuries and enhanced cell death. In contrast, pharmacological inhibition or shRNA knockdown of the proteins that disassemble the cilia increased neuron survival and decreased the phosphorylation of retinoblastoma (Rb), a master switch for cell cycle re-entry. Our findings show that the stabilization of neuronal primary cilia inhibits apoptotic cell cycling, which has implications for future therapeutic strategies that halt or slow the progression of neurodegenerative diseases and acute CNS injuries.

opencc-zeroDec 2016View details →

Data from: Dynamics of cilia length in left–right development

Reduction in the length of motile cilia in the zebrafish left–right organizer (LRO), also known as Kupffer's vesicle, has a large impact on left–right development. Here we demonstrate through genetic overexpression in zebrafish embryos and mathematical modelling that the impact of increased motile cilia length in embryonic LRO fluid flow is milder than that of short cilia. Through Arl13b overexpression, which increases cilia length without impacting cilia beat frequency, we show that the increase in cilium length is associated with a decrease in beat amplitude, resulting in similar flow strengths for Arl13b overexpression and wild-type (WT) embryos, which were not predicted by current theory. Longer cilia exhibit pronounced helical beat patterns and, consequently, lower beat amplitudes relative to WT, a result of an elastohydrodynamic shape transition. For long helical cilia, fluid dynamics modelling predicts a mild (approx. 12%) reduction in the torque exerted on the fluid relative to the WT, resulting in a proportional reduction in flow generation. This mild reduction is corroborated by experiments, providing a mechanism for the mild impact on organ situs.

publicAug 2019View details →

Data from: Stabilization of primary cilia reduces abortive cell cyle re-entry to protect injured adult CNS neurons from apoptosis

Open the record for dataset details and reuse information.

publicFeb 2017View details →

Data from: Dynamics of cilia length in left–right development

Open the record for dataset details and reuse information.

publicJul 2018View details →

Data from: Simulation of the nodal flow of mutant embryos with small number of cilia: comparison of mechanosensing and vesicle transport hypotheses

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openGEO-OpenSep 2023View details →

Abnormal accumulation of extracellular vesicles in hippocampal dystrophic axons and regulation by the primary cilia gene intraflagellar transport homolog 88 in Alzheimer's disease

GEO Series GSE230240. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.

openGEO-OpenSep 2017View details →

Cilia-dependent GLI processing in neural crest cells is required for tongue development

GEO Series GSE103822. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.

openGEO-OpenJul 2025View details →

Cholangiocytes’ Primary Cilia Regulate DNA Damage Response and Repair

GEO Series GSE280249. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.