BJ Articles Ahead of Print

Host lipid composition influences many stages of the influenza A virus (IAV) entry process, including: initial binding of IAV to sialylated glycans, fusion between the viral envelope and the host membrane, and the formation of a fusion pore through which the viral genome is transferred into a target cell. In particular, target membrane cholesterol has been shown to preferentially associate with virus receptors and alter physical properties of the membrane like fluidity and curvature. These properties affect both IAV binding and fusion, which makes it difficult to isolate the role of cholesterol in IAV fusion from receptor binding effects.

Large macromolecules, including proteins and their complexes, very often adopt multiple conformations. Some of them can be seen experimentally, for example with X-ray crystallography or cryo-electron microscopy. This structural heterogeneity is not occasional and is frequently linked with specific biological function. Thus, the accurate description of macromolecular conformational transitions is crucial for understanding fundamental mechanisms of life’s machinery. We report on a real-time method to predict such transitions by extrapolating from instantaneous eigen-motions, computed using the normal mode analysis, to a series of twists.

Microfluidic technologies are commonly used for the manipulation of red blood cell (RBC) suspensions and analyses of flow-mediated biomechanics. To enhance the performance of microfluidic devices, understanding the dynamics of the suspensions processed within is crucial. We report novel aspects of the spatio-temporal dynamics of RBC suspensions flowing through a typical microchannel at low Reynolds number. Through experiments with dilute RBC suspensions, we find an off-centre two-peak (OCTP) profile of cells contrary to the centralised distribution commonly reported for low-inertia flows.

High-throughput in vitro drug assays have been impacted by recent advances in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) technology and by contact-free all-optical systems simultaneously measuring action potential (AP) and Ca2+ transient (CaTr). Parallel computational advances have shown that in silico simulations can predict drug effects with high accuracy. We combine these in vitro and in silico technologies and demonstrate the utility of high-throughput experimental data to refine in silico hiPSC-CM populations, and to predict and explain drug action mechanisms.

We expand the standard FRAP model introduced by Axelrod et al. in 1976. Our goal is to capture some common artifacts observed in the fluorescence measurements obtained with a confocal laser scanning microscope (CLSM) in biofilms: 1) linear drift, 2) exponential decrease (due to bleaching during the measurements), 3) stochastic Gaussian noise, and 4) uncertainty in the exact time point of the onset of fluorescence recovery. In order to fit the resulting stochastic model to data from FRAP measurements and to estimate all unknown model parameters, we apply a suitably adapted Metropolis-Hastings algorithm.

Intrinsic Optical Signal (IOS) imaging has been widely used to map the patterns of brain activity in vivo in a label-free manner. Traditional IOS refers to changes in light transmission, absorption, reflectance and scattering of the brain tissue. Here we use polarized light for IOS imaging to monitor structural changes of cellular and sub-cellular architectures due to their neuronal activity in isolated brain slices. In order to reveal fast spatio-temporal changes of subcellular structures associated with neuronal activity, we developed the instantaneous polarized light microscope (instantaneous PolScope), which allows us to observe birefringence changes in neuronal cells and tissues while stimulating neuronal activity.

Single-particle tracking experiments have measured escape times of DNA-binding species diffusing in living cells: CRISPR-Cas9, TetR, and LacI. The observed distribution is a truncated power law. Working backward from the experimental results, the observed distribution appears inconsistent with a Gaussian distribution of binding energies. Working forward, the observed distribution leads to transient anomalous subdiffusion, in which diffusion is anomalous at short times and normal at long times, here only mildly anomalous.

Chromatin can be viewed as a hierarchically structured fiber that regulates gene expression. It consists of a complex network of DNA and proteins whose characteristic dynamical modes facilitate compaction and rearrangement in the cell nucleus. These modes stem from chromatin’s fundamental unit, the nucleosome, and their effects are propagated across length-scales. Understanding the effects of nucleosome dynamics on the chromatin fiber is of central importance to epigenetics, primarily through post-translational modifications that occur on the histones.

(Biophysical Journal 118, 1248–1260; March 24, 2020)

Cytoplasmic dynein is a two-headed molecular motor that moves to the minus end of a microtubule (MT) by ATP hydrolysis free energy. By employing its two heads (motor domains), cytoplasmic dynein exhibits various bipedal stepping motions; inchworm and hand-over-hand motions, as well as non-alternating steps of one head. However, the molecular basis to achieve such diverse stepping manners remains unclear because of the lack of an experimental method to observe stepping and ATPase reaction of dynein simultaneously.

Many membrane proteins are thought to function as dimers or higher oligomers, but measuring membrane protein oligomerization in lipid membranes is particularly challenging. Förster resonance energy transfer (FRET) and fluorescence cross-correlation spectroscopy (FCCS) are non-invasive, optical methods of choice that have been applied to the analysis of dimerization of single-spanning membrane proteins. However, the effects inherent to such two-dimensional systems, such as excluded volume of polytopic transmembrane proteins, proximity FRET, and rotational diffusion of fluorophore dipoles, complicate interpretation of FRET data and have not been typically accounted for.

Laurdan fluorescence, novel spectral fitting and Dynamic Light Scattering (DLS) were combined to determine lateral lipid organization in mixed lipid membranes of the oxidized lipid, 1-palmitoyl-2-glutaryl-sn-glycero-3-phosphocholine (PGPC) and each of the three bilayer lipids: 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-Palmitoyl-2-oleoylphosphatidylcholine (POPC). Second harmonic spectra were computed to determine the number of elementary emissions present.