Biology subjects

Straube, A.

Publications and source records attributed to Straube, A..

9 recordsLinked to original sources

bioRxiv2025

ShapeSpaceExplorer: Analysis of morphological transitions in migrating cells using similarity-based shape space mapping

Here we describe the development of ShapeSpaceExplorer, an interactive software for the extraction, visualisation and analysis of complex 2D shape series. We also demonstrate its application to the analysis of cell morphology changes during cell migration. Cell migration is essential for many physiological and pathological processes. Intracellular force generation and transmission of these forces to extracellular structures or neighbouring cells drives cell migration. The emergent property of the processes driving cell migration is a change in cell shape. We describe a machine learning approach to understand the relationship of cell shape dynamics and cell migration behaviour. Our algorithm analyses cell shape from time-lapse images and learns the intrinsic low-dimensional structure of cell shape space. We use the resultant shape space map to visualise differences in cell shape distribution following perturbation experiments and to analyse the quantitative relationships between shape and migration behaviour. The core of our algorithm is a new, rapid, and landmark-free shape difference measure that allows unbiased analysis of the widely varying morphologies exhibited by migrating mesenchymal cells. We used our method to predict cell turning from dynamic cell shape information. ShapeSpaceExplorer can be applied widely to visualise and analyse cell morphology changes during development, the cell cycle and stress response, but also to the outlines of clusters, tissues and inanimate objects.

cell biology↗

bioRxiv2023

KIF1C activates and extends dynein movement through the FHF cargo adaptor

Cellular cargos move bidirectionally on microtubules due to the presence of opposite polarity motors dynein and kinesin. Many studies show these motors are co-dependent, whereby one requires the activity of the other, although the mechanism is unknown. Here, using in vitro motility assays, we show that the kinesin-3 KIF1C acts both as an activator and a processivity factor for dynein. Activation only requires a fragment of the non-motor tail of KIF1C (KIF1C-stalk) to bind the cargo adaptor HOOK3. Cryo-EM, crosslinking mass spectrometry and AlphaFold2 predictions reveal this binding site to be separate from that of two constitutive factors (FTS and FHIP), which link HOOK3 to small G-proteins on cargos. We provide a structural model for how the FTS-HOOK3-FHIP1B (FHF) complex is auto-inhibited and explain how the KIF1C-stalk relieves this inhibition. Collectively, our work provides a molecular explanation for co-dependency by revealing that the mutual activation of dynein and kinesin is mediated through their shared adaptor. Many adaptors bind both dynein and kinesins, suggesting this mechanism could be generalised to other bidirectional complexes.

cell biology↗

bioRxiv2022

Motor adaptation does not differ when a perturbation is introduced abruptly or gradually

People continuously adapt their movements to ever-changing circumstances, and particularly in skills training and rehabilitation, it is crucial that we understand how to optimize implicit adaptation in order for these processes to require as little conscious effort as possible. Although it is generally assumed that the way to do this is by introducing perturbations gradually, the literature is ambivalent on the effectiveness of this approach. Here we test whether there are differences in motor performance when adapting to an abrupt compared to a ramped visuomotor rotation. Using a within-subjects design, we test this question under 3 different rotation sizes: 30{degrees}, 45{degrees}, and 60{degrees}, as well as in 3 different populations: younger adults, older adults, and patients with mild cerebellar ataxia. We find no significant differences in either the behavioural outcomes, or model fits, between abrupt and gradual learning across any of the different conditions. Neither age, nor cerebellar ataxia had any significant effect on motor adaptation either. These findings together indicate that motor adaptation is not modulated by introducing a perturbation abruptly compared to gradually, and is also unaffected by age or mild cerebellar ataxia.

neuroscience↗

bioRxiv2021

Intrinsic Network Activity Reflects the Fluctuating Experience of Tonic Pain

Although we know sensation is continuous, research on long-lasting and continuously changing stimuli is scarce and the dynamic nature of ongoing cortical processing is largely neglected. In a longitudinal study with 152 fMRI sessions, participants were asked to continuously rate the intensity of applied tonic heat pain for 20 minutes. Using group independent component analysis and dual-regression, we extracted the subjects time courses of intrinsic network activity. The relationship between the dynamic fluctuation of network activity with the varying time courses of three pain processing entities was computed: pain intensity, the direction of pain intensity changes and temperature. We were able to dissociate the spatio-temporal patterns of objective (temperature) and subjective (pain intensity/changes of pain intensity) aspects of pain processing in the human brain. We found two somatosensory networks with distinct functions: one network which encodes the small fluctuations in temperature and consists mainly of bilateral SI. A second right-lateralised network that encodes the intensity of the subjective experience of pain consists of SI, SII, the PCC, and the thalamus. We revealed the somatosensory dynamics that build up towards a current subjective percept of pain. The timing suggests a cascade of subsequent processing steps towards the current pain percept.

neuroscience↗

bioRxiv2021

Force generation of KIF1C is impaired by pathogenic mutations

Intracellular transport is essential for neuronal function and survival. The fastest neuronal transporter is the kinesin-3 KIF1C. Mutations in KIF1C cause hereditary spastic paraplegia and cerebellar dysfunction in human patients. However, neither the force generation of the KIF1C motor protein, nor the biophysical and functional properties of pathogenic mutant proteins have been studied thus far. Here we show that full length KIF1C is a processive motor that can generate forces up to 5.7 pN. We find that KIF1C single molecule processivity relies on its ability to slip and re-engage under load and that its slightly reduced stall force compared to kinesin-1 relates to its enhanced probability to backslip. Two pathogenic mutations P176L and R169W that cause hereditary spastic paraplegia in humans maintain fast, processive single molecule motility in vitro, but with decreased run length and slightly increased unloaded velocity compared to the wildtype motor. Under load in an optical trap, force generation by these mutants is severely reduced. In cells, the same mutants are impaired in producing sufficient force to efficiently relocate organelles. Our results establish a baseline for the single molecule mechanics of Kif1C and explain how pathogenic mutations at the microtubule-binding interface of KIF1C impair the cellular function of these long-distance transporters and result in neuronal disease.

cell biology↗

bioRxiv2020

Chronic Pain Patients Exhibit Individually Unique Cortical Signatures of Pain

We investigated how the trajectory of pain patients ongoing and fluctuating pain is encoded in the brain. In repeated fMRI sessions, 20 chronic back pain patients and 20 chronic migraineurs were asked to continuously rate the intensity of their endogenous pain. Linear mixed effects models were used to disentangle cortical processes related to pain intensity and to pain intensity changes. We found that the intensity of pain in chronic back pain patients is encoded in the anterior insula, the frontal operculum, and the pons; the change of pain of chronic back pain and chronic migraine patients is mainly encoded in the anterior insula. At the individual level, we identified a more complex picture where each patient exhibited their own signature of endogenous pain encoding. The diversity of the individual cortical signatures of chronic pain encoding results adds to the understanding of chronic pain as a complex and multifaceted disease.

neuroscience↗

bioRxiv2020

Activation of cytoplasmic dynein through microtubule crossbridging

Cytoplasmic dynein is the main microtubule-minus-end-directed transporter of cellular cargo in animal cells [1, 2]. Cytoplasmic dynein also functions in the organisation and positioning of mitotic spindles [3, 4] and the formation of ordered microtubule arrays in neurons and muscle [5, 6]. Activation of the motor for cargo transport is thought to require formation of a complex with dynactin and a cargo adapter [7-10]. Here we show that recombinant human dynein can crossbridge neighbouring microtubules and can be activated by this crossbridging to slide and polarity-sort microtubule bundles. While single molecules of human dynein are predominantly static or diffusive on single microtubules, they walk processively for 1.5 m on average along the microtubule bundles they form. Speed and force output of dynein are doubled on bundles compared to single microtubules, indicating that the crossbridging dynein steps equivalently on two microtubules. Our data are consistent with a model of autoactivation through the physical separation of dynein motor domains when crossbridging two microtubules. This enables cytoplasmic dynein to function effectively as a microtubule organiser and transporter without needing to first form a complex with dynactin and a cargo adapter.

biophysics↗

bioRxiv2018

Activation of intracellular transport by relieving KIF1C autoinhibition

The kinesin-3 KIF1C is a fast organelle transporter implicated in the transport of dense core vesicles in neurons and the delivery of integrins to cell adhesions. Here we report the mechanisms of autoinhibition and release that control the activity of KIF1C. We show that the microtubule binding surface of KIF1C motor domain interacts with its stalk and that these autoinhibitory interactions are released upon binding of protein tyrosine phosphatase PTPN21. The FERM domain of PTPN21 stimulates dense core vesicle transport in primary hippocampal neurons and rescues integrin trafficking in KIF1C-depleted cells. In vitro, human full-length KIF1C is a processive, plus-end directed motor. Its landing rate onto microtubules increases in the presence of either PTPN21 FERM domain or the cargo adapter Hook3 that binds the same region of KIF1C tail. This autoinhibition release mechanism allows cargo-activated transport and might enable motors to participate in bidirectional cargo transport without undertaking a tug-of-war.

cell biology↗

bioRxiv2018

Mitotic phosphorylation by Nek6 and Nek7 reduces microtubule affinity of EML4 to alter spindle dynamics and promote chromosome congression

EML4 is a microtubule-associated protein that promotes microtubule stability. We show here that EML4 is distributed as punctate foci along the microtubule lattice in interphase but exhibits reduced association with spindle microtubules in mitosis. Microtubule sedimentation and cryo-electron microscopy and 3D reconstruction reveal that EML4 binds via its basic N-terminal domain to the acidic C-terminal tails of - and {beta}-tubulin on the microtubule surface. The mitotic kinases Nek6 and Nek7 can phosphorylate EML4 N-terminal domain at S144 and S146 in vitro, and depletion of these kinases leads to increased EML4 binding to microtubules in mitosis. An S144A-S146A double mutant not only binds inappropriately to mitotic microtubules but also interferes with chromosome congression. Meanwhile, constitutive activation of Nek6 or Nek7 reduces EML4 association with interphase microtubules. Together, these data support a model in which Nek6 and Nek7-dependent phosphorylation promotes dissociation of EML4 from microtubules in mitosis thereby altering microtubule dynamics to enable chromosome congression.

cell biology↗