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arXiv2013

Time-of-flight secondary ion mass spectrometry-based molecular distribution distinguishing healthy and osteoarthritic human cartilage

Osteoarthritis (OA) is a pathology that ultimately causes joint destruction. The cartilage is one of the principal affected tissues. Alterations in the lipid mediators and an imbalance in the metabolism of cells that form the cartilage (chondrocytes) have been described as contributors to the OA development. In this study, we have studied the distribution of lipids and chemical elements in healthy and OA human cartilage. Time of flight-secondary ion mass spectrometry (TOF-SIMS) allows us to study the spatial distribution of molecules at a high resolution on a tissue section. TOF-SIMS revealed a specific peak profile that distinguishes healthy from OA cartilages. The spatial distribution of cholesterol-related peaks exhibited a remarkable difference between healthy and OA cartilages. A distinctive colocalization of cholesterol and other lipids in the superficial area of the cartilage was found. A higher intensity of oleic acid and other fatty acids in the OA cartilages exhibited a similar localization. On the other hand, CN(-) was observed with a higher intensity in the healthy samples. Finally, we observed an accumulation of calcium and phosphate ions exclusively in areas surrounding the chondrocyte in OA tissues. To our knowledge, this is the first time that TOF-SIMS revealed combined changes in the molecular distribution in the OA human cartilage.

physics.bio-ph↗

arXiv2018

Relevance of the speed and direction of pulling in simple modular proteins

A theoretical analysis of the unfolding pathway of simple modular proteins in length- controlled pulling experiments is put forward. Within this framework, we predict the first module to unfold in a chain of identical units, emphasizing the ranges of pulling speeds in which we expect our theory to hold. These theoretical predictions are checked by means of steered molecular dynamics of a simple construct, specifically a chain composed of two coiled-coils motives, where anisotropic features are revealed. These simulations also allow us to give an estimate for the range of pulling velocities in which our theoretical approach is valid.

cond-mat.soft↗

arXiv2012

Three-Way Electrochemical Sensing of Ultra-Low MicroRNA Levels

MicroRNAs (miRNAs) are an emerging class of biomarkers that are frequently deregulated in cancer cells and have shown a great promise for cancer classification and prognosis. In this work, we developed a three-way electrochemical sensor for detection and quantitation of ultra-low amounts of miRNAs in a wide dynamic range of measured concentrations. The sensor facilitates three detection modes based on hybridization (H-SENS), p19 protein binding (P-SENS) and protein displacement (D-SENS). The combined HPD sensor (HPD-SENS) identifies as low as 5 aM or 90 molecules of miRNA per 30\muL of sample without PCR amplification, and can be operated within the dynamic range from 10 aM to 1 \muM. The HPD senor is made on a commercially-available gold nanoparticles-modified electrode and suitable for analysing multiple miRNAs on a single electrode. This three-way sensor exhibits high selectivity and specificity and was successfully used for sequential analysis of miR-32 and miR-122 on one electrode. Furthermore, the P-SENS was employed for profiling of three endogenous microRNAs (miR-21, miR-32 and miR-122) in human blood serum.

q-bio.BM↗

arXiv2013

Atomistic study of energy funneling in the light-harvesting complex of green sulfur bacteria

Phototrophic organisms such as plants, photosynthetic bacteria and algae use microscopic complexes of pigment molecules to absorb sunlight. Within the light-harvesting complexes, which frequently have several functional and structural subunits, the energy is transferred in the form of molecular excitations with very high efficiency. Green sulfur bacteria are considered to be amongst the most efficient light-harvesting organisms. Despite multiple experimental and theoretical studies of these bacteria the physical origin of the efficient and robust energy transfer in their light-harvesting complexes is not well understood. To study excitation dynamics at the systems level we introduce an atomistic model that mimics a complete light-harvesting apparatus of green sulfur bacteria. The model contains approximately 4000 pigment molecules and comprises a double wall roll for the chlorosome, a baseplate and six Fenna-Matthews-Olson trimer complexes. We show that the fast relaxation within functional subunits combined with the transfer between collective excited states of pigments can result in robust energy funneling. Energy transfer is robust on the initial excitation conditions and temperature changes. Moreover, the same mechanism describes the coexistence of multiple timescales of excitation dynamics frequently observed in ultrafast optical experiments. While our findings support the hypothesis of supertransfer, the model reveals energy transport through multiple channels on different length scales.

physics.chem-ph↗

arXiv2013

Ab-Initio Calculation of Molecular Aggregation Effects: a Coumarin-343 Case Study

We present time-dependent density functional theory (TDDFT) calculations for single and dimerized Coumarin-343 molecules in order to investigate the quantum mechanical effects of chromophore aggregation in extended systems designed to function as a new generation of sensors and light-harvesting devices. Using the single-chromophore results, we describe the construction of effective Hamiltonians to predict the excitonic properties of aggregate systems. We compare the electronic coupling properties predicted by such effective Hamiltonians to those obtained from TDDFT calculations of dimers, and to the coupling predicted by the transition density cube (TDC) method. We determine the accuracy of the dipole-dipole approximation and TDC with respect to the separation distance and orientation of the dimers. In particular, we investigate the effects of including Coulomb coupling terms ignored in the typical tight-binding effective Hamiltonian. We also examine effects of orbital relaxation which cannot be captured by either of these models.

physics.chem-ph↗

arXiv2013

Disentangling electronic and vibronic coherences in two-dimensional echo spectra

The prevalence of long-lasting oscillatory signals in the 2d echo-spectroscopy of light-harvesting complexes has led to a search for possible mechanisms. We investigate how two causes of oscillatory signals are intertwined: (i) electronic coherences supporting delocalized wave-like motion, and (ii) narrow bands in the vibronic spectral density. To disentangle the vibronic and electronic contributions we introduce a time-windowed Fourier transform of the signal amplitude. We find that 2d spectra can be dominated by excitations of pathways which are absent in excitonic energy transport. This leads to an underestimation of the life-time of electronic coherences by 2d spectra.

physics.bio-ph↗

arXiv2013

Internal water and microsecond dynamics in myoglobin

Myoglobin (Mb) binds diatomic ligands, like O$_2$, CO, and NO, in a cavity that is only transiently accessible. Crystallography and molecular simulations show that the ligands can migrate through an extensive network of transiently connected cavities, but disagree on the locations and occupancy of internal hydration sites. Here, we use water $^2$H and $^{17}$O magnetic relaxation dispersion (MRD) to characterize the internal water molecules in Mb under physiological conditions. We find that equine carbonmonoxy Mb contains 4.5 $\pm$ 1.0 ordered internal water molecules with a mean survival time of 5.6 $\pm$ 0.5 $μ$s at 25 $^\circ$C. The likely location of these water molecules are the four polar hydration sites, including one of the xenon-binding cavities, that are fully occupied in all high-resolution crystal structures of equine Mb. The finding that water escapes from these sites, located 17 -- 31 Å apart in the protein, on the same $μ$s time scale suggests a global exchange mechanism. We propose that this mechanism involves transient penetration of the protein by H-bonded water chains. Such a mechanism could play a functional role by eliminating trapped ligands. In addition, the MRD results indicate that two or three of the 11 histidine residues of equine Mb undergo intramolecular hydrogen exchange on a $μ$s time scale.

q-bio.BM↗

arXiv2013

Tracking single particles on supported lipid membranes: multi-mobility diffusion and nanoscopic confinement

Supported lipid bilayers have been studied intensively over the past two decades. In this work, we study the diffusion of single gold nanoparticles (GNPs) with diameter of 20 nm attached to GM1 ganglioside or DOPE lipids at different concentrations in supported DOPC bilayers. The indefinite photostability of GNPs combined with the high sensitivity of interferometric scattering microscopy (iSCAT) allows us to achieve 1.9 nm spatial precision at 1 ms temporal resolution, while maintaining long recording times. Our trajectories visualize strong transient confinements within domains as small as 20 nm, and the statistical analysis of the data reveals multiple mobilities and deviations from normal diffusion. We present a detailed analysis of our findings and provide interpretations regarding the effect of the supporting substrate and GM1 clustering. We also comment on the use of high-speed iSCAT for investigating diffusion of lipids, proteins or viruses in lipid membranes with unprecedented spatial and temporal resolution.

physics.bio-ph↗

arXiv2013

Clustered Geometries Exploiting Quantum Coherence Effects for Efficient Energy Transfer in Light Harvesting

Elucidating quantum coherence effects and geometrical factors for efficient energy transfer in photosynthesis has the potential to uncover non-classical design principles for advanced organic materials. We study energy transfer in a linear light-harvesting model to reveal that dimerized geometries with strong electronic coherences within donor and acceptor pairs exhibit significantly improved efficiency, which is in marked contrast to predictions of the classical Förster theory. We reveal that energy tuning due to coherent delocalization of photoexcitations is mainly responsible for the efficiency optimization. This coherence-assisted energy-tuning mechanism also explains the energetics and chlorophyll arrangements in the widely-studied Fenna-Matthews-Olson complex. We argue that a clustered network with rapid energy relaxation among donors and resonant energy transfer from donor to acceptor states provides a basic formula for constructing efficient light-harvesting systems, and the general principles revealed here can be generalized to larger systems and benefit future innovation of efficient molecular light-harvesting materials.

physics.bio-ph↗

arXiv2014

Non-classicality of the molecular vibrations assisting exciton energy transfer at room temperature

Advancing the debate on quantum effects in light-initiated reactions in biology requires clear identification of non-classical features that these processes can exhibit and utilise. Here we show that in prototype dimers present in a variety of photosynthetic antennae, efficient vibration-assisted energy transfer in the subpicosecond timescale and at room temperature can manifest and benefit from non-classical fluctuations of collective pigment motions. Non-classicality of initially thermalised vibrations is induced via coherent exciton-vibration interactions and is unambiguously indicated by negativities in the phase-space quasi-probability distribution of the effective collective mode coupled to the electronic dynamics. These quantum effects can be prompted upon incoherent input of excitation. Our results therefore suggest that investigation of the non-classical properties of vibrational motions assisting excitation and charge transport, photoreception and chemical sensing processes could be a touchstone for revealing a role for non-trivial quantum phenomena in biology.

quant-ph↗

arXiv2014

Ultra-Fast Fluorescence Imaging in Vivo with Conjugated Polymer Fluorophores in the Second Near-Infrared Window

In vivo fluorescence imaging in the second near-infrared window (1.0-1.7 microns) can afford deep tissue penetration and high spatial resolution, owing to the reduced scattering of long-wavelength photons. Here, we synthesize a series of low-bandgap donor/acceptor copolymers with tunable emission wavelengths of 1050-1350 nm in this window. Non-covalent functionalization with phospholipid-polyethylene glycol results in water-soluble and biocompatible polymeric nanoparticles, allowing for live cell molecular imaging at > 1000 nm with polymer fluorophores for the first time. Importantly, the high quantum yield of the polymer allows for in vivo, deep-tissue and ultrafast imaging of mouse arterial blood flow with an unprecedented frame rate of > 25 frames per second. The high time resolution results in spatially and time resolved imaging of the blood flow pattern in cardiogram waveform over a single cardiac cycle (~ 200 ms) of a mouse, which has not been observed with fluorescence imaging in this window before.

physics.bio-ph↗

arXiv2018

Finding influential nodes for integration in brain networks using optimal percolation theory

Global integration of information in the brain results from complex interactions of segregated brain networks. Identifying the most influential neuronal populations that efficiently bind these networks is a fundamental problem of systems neuroscience. Here we apply optimal percolation theory and pharmacogenetic interventions in-vivo to predict and subsequently target nodes that are essential for global integration of a memory network in rodents. The theory predicts that integration in the memory network is mediated by a set of low-degree nodes located in the nucleus accumbens. This result is confirmed with pharmacogenetic inactivation of the nucleus accumbens, which eliminates the formation of the memory network, while inactivations of other brain areas leave the network intact. Thus, optimal percolation theory predicts essential nodes in brain networks. This could be used to identify targets of interventions to modulate brain function.

q-bio.NC↗

arXiv2021

Large field-of-view non-invasive imaging through scattering layers using fluctuating random illumination

On-invasive optical imaging techniques are essential diagnostic tools in many fields. Although various recent methods have been proposed to utilize and control light in multiple scattering media, non-invasive optical imaging through and inside scattering layers across a large field of view remains elusive due to the physical limits set by the optical memory effect, especially without wavefront shaping techniques. Here, we demonstrate an approach that enables non-invasive fluorescence imaging behind scattering layers with field-of-views extending well beyond the optical memory effect. The method consists in demixing the speckle patterns emitted by a fluorescent object under variable unknown random illumination, using matrix factorization and a novel fingerprint-based reconstruction. Experimental validation shows the efficiency and robustness of the method with various fluorescent samples, covering a field of view up to three times the optical memory effect range. Our non-invasive imaging technique is simple, neither requires a spatial light modulator nor a guide star, and can be generalized to a wide range of incoherent contrast mechanisms and illumination schemes.

physics.optics↗

arXiv2017

Universal geometric constraints during epithelial jamming

As an injury heals, an embryo develops, or a carcinoma spreads, epithelial cells systematically change their shape. In each of these processes cell shape is studied extensively, whereas variation of shape from cell-to-cell is dismissed most often as biological noise. But where do cell shape and variation of cell shape come from? Here we report that cell shape and shape variation are mutually constrained through a relationship that is purely geometrical. That relationship is shown to govern maturation of the pseudostratified bronchial epithelial layer cultured from both non-asthmatic and asthmatic donors as well as formation of the ventral furrow in the epithelial monolayer of the Drosophila embryo in vivo. Across these and other vastly different epithelial systems, cell shape variation collapses to a family of distributions that is common to all and potentially universal. That distribution, in turn, is accounted for quantitatively by a mechanistic theory of cell-cell interaction showing that cell shape becomes progressively less elongated and less variable as the layer becomes progressively more jammed. These findings thus uncover a connection between jamming and geometry that is generic -spanning jammed living and inert systems alike- and demonstrate that proximity of the cell layer to the jammed state is the principal determinant of the most primitive features of epithelial cell shape and shape variation.

physics.bio-ph↗

arXiv2012

Malaria pigment crystals as magnetic micro-rotors: key for high-sensitivity diagnosis

The need to develop new methods for the high-sensitivity diagnosis of malaria has initiated a global activity in medical and interdisciplinary sciences. Most of the diverse variety of emerging techniques are based on research-grade instruments, sophisticated reagent-based assays or rely on expertise. Here, we suggest an alternative optical methodology with an easy-to-use and cost-effective instrumentation based on unique properties of malaria pigment reported previously and determined quantitatively in the present study. Malaria pigment, also called hemozoin, is an insoluble microcrystalline form of heme. These crystallites show remarkable magnetic and optical anisotropy distinctly from any other components of blood. As a consequence, they can simultaneously act as magnetically driven micro-rotors and spinning polarizers in suspensions. These properties can gain importance not only in malaria diagnosis and therapies, where hemozoin is considered as drug target or immune modulator, but also in the magnetic manipulation of cells and tissues on the microscopic scale.

physics.bio-ph↗

arXiv2013

Hydrodynamic Instabilities Provide A Generic Route To Spontaneous Biomimetic Oscillations In Chemomechanically Active Filaments

Non-equilibrium processes which convert chemical energy into mechanical motion enable the motility of organisms. Bundles of inextensible filaments driven by energy transduction of molecular motors form essential components of micron-scale motility engines like cilia and flagella. The mimicry of cilia-like motion in recent experiments on synthetic active filaments supports the idea that generic physical mechanisms may be sufficient to generate such motion. Here we show, theoretically, that the competition between the destabilising effect of hydrodynamic interactions induced by force-free and torque-free chemomechanically active flows, and the stabilising effect of nonlinear elasticity, provides a generic route to spontaneous oscillations in active filaments. These oscillations, reminiscent of prokaryotic and eukaryotic flagellar motion, are obtained without having to invoke structural complexity or biochemical regulation. This minimality implies that biomimetic oscillations, previously observed only in complex bundles of active filaments, can be replicated in simple chains of generic chemomechanically active beads.

cond-mat.soft↗

arXiv2013

Identification and super-resolution imaging of ligand-activated receptor dimers in live cells

Molecular interactions are key to many chemical and biological processes like protein function. In many signaling processes they occur in sub-cellular areas displaying nanoscale organizations and involving molecular assemblies. The nanometric dimensions and the dynamic nature of the interactions make their investigations complex in live cells. While super-resolution fluorescence microscopies offer live-cell molecular imaging with sub-wavelength resolutions, they lack specificity for distinguishing interacting molecule populations. Here we combine super-resolution microscopy and single-molecule Förster Resonance Energy Transfer (FRET) to identify dimers of receptors induced by ligand binding and provide super-resolved images of their membrane distribution in live cells. By developing a two-color universal-Point-Accumulation-In-the-Nanoscale-Topography (uPAINT) method, dimers of epidermal growth factor receptors (EGFR) activated by EGF are studied at ultra-high densities, revealing preferential cell-edge sub-localization. This methodology which is specifically devoted to the study of molecules in interaction, may find other applications in biological systems where understanding of molecular organization is crucial.

physics.bio-ph↗

arXiv2013

Single-Neuron Criticality Optimizes Analog Dendritic Computation

Neurons are thought of as the building blocks of excitable brain tissue. However, at the single neuron level, the neuronal membrane, the dendritic arbor and the axonal projections can also be considered an extended active medium. Active dendritic branchlets enable the propagation of dendritic spikes, whose computational functions, despite several proposals, remain an open question. Here we propose a concrete function to the active channels in large dendritic trees. By using a probabilistic cellular automaton approach, we model the input-output response of large active dendritic arbors subjected to complex spatio-temporal inputs and exhibiting non-stereotyped dendritic spikes. We find that, if dendritic spikes have a non-deterministic duration, the dendritic arbor can undergo a continuous phase transition from a quiescent to an active state, thereby exhibiting spontaneous and self-sustained localized activity as suggested by experiments. Analogously to the critical brain hypothesis, which states that neuronal networks self-organize near a phase transition to take advantage of specific properties of the critical state, here we propose that neurons with large dendritic arbors optimize their capacity to distinguish incoming stimuli at the critical state. We suggest that "computation at the edge of a phase transition" is more compatible with the view that dendritic arbors perform an analog rather than a digital dendritic computation.

q-bio.NC↗