Automated matching of two-time X-ray photon correlation maps from phase-separating proteins with Cahn-Hilliard-type simulations using auto-encoder networks.

Machine learning methods are used for an automated classification of experimental two-time X-ray photon correlation maps from an arrested liquid-liquid phase separation of a protein solution. The correlation maps are matched with correlation maps generated with Cahn-Hilliard-type simulations of liquid-liquid phase separations according to two simulation parameters and in the last step interpreted in the framework of the simulation. The matching routine employs an auto-encoder network and a differential evolution based algorithm.

Reverse-engineering method for XPCS studies of non-equilibrium dynamics.

X-ray photon correlation spectroscopy (XPCS) is a powerful tool in the investigation of dynamics covering a broad time and length scale. It has been widely used to probe dynamics for systems in both equilibrium and non-equilibrium states; in particular, for systems undergoing a phase transition where the structural growth kinetics and the microscopic dynamics are strongly intertwined. The resulting time-dependent dynamic behavior can be described using the two-time correlation function (TTC), which, however, often contains more interesting features than the component along the diagonal, and cannot be easily interpreted via the classical simulation methods.

Interplay between Kinetics and Dynamics of Liquid-Liquid Phase Separation in a Protein Solution Revealed by Coherent X-ray Spectroscopy.

Microscopic dynamics of complex fluids in the early stage of spinodal decomposition (SD) is strongly intertwined with the kinetics of structural evolution, which makes a quantitative characterization challenging. In this work, we use X-ray photon correlation spectroscopy to study the dynamics and kinetics of a protein solution undergoing liquid-liquid phase separation (LLPS). We demonstrate that in the early stage of SD, the kinetics relaxation is up to 40 times slower than the dynamics and thus can be decoupled.

Microscopic Dynamics of Liquid-Liquid Phase Separation and Domain Coarsening in a Protein Solution Revealed by X-Ray Photon Correlation Spectroscopy.

While the interplay between liquid-liquid phase separation (LLPS) and glass formation in biological systems is highly relevant for their structure formation and thus function, the exact underlying mechanisms are not well known. The kinetic arrest originates from the slowdown at the molecular level, but how this propagates to the dynamics of microscopic phase domains is not clear. Since with diffusion, viscoelasticity, and hydrodynamics, distinctly different mechanisms are at play, the dynamics needs to be monitored on the relevant time and length scales and compared to theories of phase separation.

Kinetics of Network Formation and Heterogeneous Dynamics of an Egg White Gel Revealed by Coherent X-Ray Scattering.

The kinetics of heat-induced gelation and the microscopic dynamics of a hen egg white gel are probed using x-ray photon correlation spectroscopy along with ultrasmall-angle x-ray scattering. The kinetics of structural growth reveals a reaction-limited aggregation process with a gel fractal dimension of ≈2 and an average network mesh size of ca. 400 nm.

Nanoscale Transient Magnetization Gratings Created and Probed by Femtosecond Extreme Ultraviolet Pulses.

We utilize coherent femtosecond extreme ultraviolet (EUV) pulses from a free electron laser (FEL) to generate transient periodic magnetization patterns with periods as short as 44 nm. Combining spatially periodic excitation with resonant probing at the M-edge of cobalt allows us to create and probe transient gratings of electronic and magnetic excitations in a CoGd alloy. In a demagnetized sample, we observe an electronic excitation with a rise time close to the FEL pulse duration and ∼0.

Implications of disturbed photon-counting statistics of Eiger detectors for X-ray speckle visibility experiments.

This paper reports on coherent scattering experiments in the low-count regime with less than one photon per pixel per acquisition on average, conducted with two detectors based on the Eiger single-photon-counting chip. The obtained photon-count distributions show systematic deviations from the expected Poisson-gamma distribution, which result in a strong overestimation of the measured speckle contrast. It is shown that these deviations originate from an artificial increase of double-photon events, which is proportional to the detected intensity and inversely proportional to the exposure time.

Size and cell number of the utricle in kinetotically swimming fish: a parabolic aircraft flight study.

Humans taking part in parabolic aircraft flights (PAFs) may suffer from space motion sickness (SMS, a kinetosis). Since it has been repeatedly shown earlier that some fish of a given batch also reveal a kinetotic behavior during PAFs (especially so-called spinning movements and looping responses) and due to the homology of the vestibular apparatus among all vertebrates, fish can be used as model systems to investigate the origin of susceptibility to motion sickness. Therefore, we examined the utricular maculae (they are responsible for the internalization of gravity in teleosteans) of fish swimming kinetotically at microgravity in comparison with animals from the same batch who swam normally.

Calcium-tracers disclose the site of biomineralization in inner ear otoliths of fish.

Since changing gravity (concerning direction and amplitude) strongly affects inner ear otolith growth and otolithic calcium incorporation in developing fish, it was the aim of the present study to locate the site of mineralization in order to gain cues and insights into the provenance of the otoliths inorganic compounds. Therefore, larval cichlid fish (Oreochromis mossambicus) were incubated in the calcium-tracer alizarin complexone (AC; red fluorescence). After maintenance in aquarium water for various periods (1, 2, 3, 6, 9 and 12 h; 1, 2, 3, 5, 6, 7, 15, 29, 36 and 87 d), the animals were incubated in the calcium-tracer calcein (CAL; green fluorescence).

No correlation between multilamellar bodies in the inner ear and further organs of mutant (backstroke, bks) and wildtype zebrafish embryos.

The origin of the proteinacious matrix of the inner ear stones (otoliths) of vertebrates has not yet been clarified. Using the backstroke mutant (bks) of the zebrafish Danio rerio, which is characterized by a complete lack of otoliths, we searched for possibly missing or aberrant structural components within the macular epithelia of the inner ears of embryos on the ultrastructural level. Numerous multilamellar bodies (MLBs) were found.

Extremely elongated mitochondria in ionocytes of the saccular epithelium of a teleost, Oreochromis mossambicus (Cichlidae).

Unusually large mitochondria are a rather scarce feature in normal biological tissue and string-like giant mitochondria have hitherto not been reported in animals. Investigating the role of inner ear ionocytes for otolith growth, large ionocytes of the saccular epithelium of the cichlid fish Oreochromis mossambicus were analyzed by imaging of thick sections with energy-filtering transmission electron microscopy. We report here that ionocytes do not contain numerous small-sized mitochondria as has been suggested earlier but rather few, extremely elongated megamitochondria.

Calcium gradients in the fish inner ear sensory epithelium and otolithic membrane visualized by energy filtering transmission electron microscopy (EFTEM).

Inner ear otolith formation in fish is supposed to be performed by the molecular release of proteinacious precursor material from the sensory epithelia, followed by an undirected and diffuse precipitation of calcium carbonate (which is mainly responsible for the functionally important weight of otoliths). The pathway of calcium into the endolymph, however, still remains obscure. Therefore, the presence of calcium within the utricle of larval cichlid fish Oreochromis mossambicus was analyzed by means of energy filtering transmission electron microscopy (EFTEM).

Swimming behaviour and calcium incorporation into inner ear otoliths of fish after vestibular nerve transection.

Previous investigations on neonate swordtail fish (Xiphophorus helleri) revealed that otolithic calcium incorporation (visualized using the calcium tracer alizarin complexone) and thus otolith growth had ceased after nerve transection, supporting a hypothesis according to which the gravity-dependent otolith growth is regulated neuronally. Subsequent investigations on larval cichlid fish (Oreochromis mossambicus) yielded contrasting results, repeatedly depending on the particular batch of cichlids investigated. Like most neonate swordtails, Type I cichlids revealed a stop of calcium incorporation after unilateral vestibular nerve transection.

Effect of hypergravity on carboanhydrase reactivity in inner ear ionocytes of developing cichlid fish.

It has been shown earlier that hypergravity slows down inner ear otolith growth in developing fish. Otolith growth in terms of mineralization mainly depends on the enzyme carboanhydrase (CA), which is responsible for the provision of the pH-value necessary for calcium carbonate deposition. Larval siblings of cichlid fish (Oreochromis mossambicus) were subjected to hypergravity (3 g, hg; 6 h) during development and separated into normally and kinetotically swimming individuals following the transfer to 1 g (i.

Hypergravity decreases carbonic anhydrase-reactivity in inner ear maculae of fish.

Previous investigations revealed that fish inner ear otolith growth depends on the amplitude and the direction of gravity. Both otolith total size, otolith bilateral size-asymmetry and the total and bilateral calcium-incorporation are also affected by gravity. Hypergravity, e.

Endolymphatic calcium supply for fish otolith growth takes place via the proximal portion of the otocyst.

The presence of calcium within the utricle of larval cichlid fish Oreochromis mossambicus was analysed by means of energy-filtering transmission electron microscopy. Electron-spectroscopic imaging and electron energy loss spectra revealed discrete calcium precipitations that were more numerous in the proximal endolymph than in the distal endolymph, clearly indicating a decreasing proximo-distal gradient. This decreasing proximo-distal gradient was also present within the proximal endolymph between the sensory epithelium and the otolith.

Histology of the utricle in kinetotically swimming fish: a parabolic aircraft flight study.

Objectives: Humans taking part in parabolic aircraft flights (PAFs) may suffer from space motion sickness, which is a form of kinetosis. As it has been repeatedly shown that some fish in a given batch also reveal kinetotic behaviour (especially so-called spinning movements and looping responses) during PAFs, and as a result of the homology of the vestibular apparatus of all vertebrates, fish can be used as model systems to investigate the origin of susceptibility to motion sickness. Therefore.

Neuronal regulation of otolith growth and kinetotic behaviour.

Inner ear stones (otoliths) of larval cichlid fish were labelled with the calcium-tracer alizarin-complexone (AC) before animals were subjected to hypergravity (hg; 3 g). After the experiment, the otoliths' area between the two AC-labellings was measured. Growth of hg-otoliths was significantly slowed down as compared to 1 g-control specimens.

Susceptibility to motion sickness in fish: a parabolic aircraft flight study.

Juvenile swordtail fish and larval cichlids were subjected to parabolic aircraft flights (PAFs) and individually observed. After the PAFs, inner ear otoliths and sensory epithelia were examined on the light microscopical level. Otolith asymmetry (differences in otolith size between the left and the right side) was especially pronounced in those fish, who exhibited a kinetotic behaviour (e.

Gravitation biology using fish as model systems for understanding motion sickness susceptibility.

During the entire evolution of life on Earth, the development of all organisms took place under constant gravity conditions, against which they achieved specific countermeasures for compensation and adaptation. On this background, it is still an open question to which extent altered gravity such as hyper- or microgravity (centrifuge/spaceflight) affects the normal individual development, either on the systemic level of the whole organism or on the level of individual organs or even single cells. The present short review provides information on this topic, focusing on the effects of altered gravity on developing fish as model systems even for higher vertebrates including humans, with special emphasis on the effect of altered gravity on behaviour and particularly on the developing brain and vestibular system.

On the origin of susceptibility to kinetotic swimming behaviour in fish: a parabolic aircraft flight study.

Humans taking part in parabolic aircraft flights (PAFs) may suffer from motion sickness (SMS, a kinetosis; it comprises a dynamic and a static component). It has been argued that the so-called static variety of SMS during PAFs might be based on asymmetric statoliths (i.e.

Effects of hypergravity on the development of cell number and asymmetry in fish brain nuclei.

Larval cichlid fish (Oreochromis mossambicus) siblings were subjected to 3 g hypergravity (hg) and total darkness for 21 days during development and subsequently processed for conventional histology. Further siblings reared at 1 g and alternating light/dark (12h:12h) conditions served as controls. Cell number counts of the visual Nucleus isthmi (Ni) versus the vestibular Nucleus magnocellularis (Nm) revealed that in experimental animals total cell number was decreased in the Ni, possibly due to retarded growth as a result of the lack of visual input whereas no effect was observed in the Nm.

Microgravity (STS-90 Neurolab-Mission) influences synapse formation in a vestibular nucleus of fish brain.

Synapse counting was undertaken by conventional electron microscopy in primary vestibular integration centers (i.e., Nucleus descendens, Nd, and Nucleus magnocellularis, Nm, of the brainstem Area octavolateralis) and in the diencephalic visual Nucleus corticalis (Nc) of spaceflown neonate swordtail fish Xiphophorus helleri as well as in 1 g control siblings.

Effects of altered gravity on the swimming behaviour of fish.

Humans taking part in parabolic aircraft flights (PAFs) may suffer from space motion sickness-phenomena (SMS, a kinetosis). It has been argued that SMS during PAFs might not be based on microgravity alone but rather on changing accelerations from 0 g to 2 g. We test here the hypothesis that PAF-induced kinetosis is based on asymmetric statoliths (i.

Neuronal feedback between brain and inner ear for growth of otoliths in fish.

Previous investigations revealed that fish inner ear otolith growth (concerning otolith size and calcium-incorporation) depends on the amplitude and the direction of gravity, suggesting the existence of a (negative) feedback mechanism. In search for the regulating unit, the vestibular nerve was unilaterally transected in neonate swordtail fish (Xiphophorus helleri) which were subsequently incubated in the calcium-tracer alizarin-complexone. Calcium incorporation ceased on the transected head sides, indicating that calcium uptake is neurally regulated.