A High-Throughput Workflow to Analyze Sequence-Conformation Relationships and Explore Hydrophobic Patterning in Disordered Peptoids.

Understanding how a macromolecule's primary sequence governs its conformational landscape is crucial for elucidating its function, yet these design principles are still emerging for macromolecules with intrinsic disorder. Herein, we introduce a high-throughput workflow that implements a practical colorimetric conformational assay, introduces a semi-automated sequencing protocol using MALDI-MS/MS, and develops a generalizable sequence-structure algorithm. Using a model system of 20mer peptidomimetics containing polar glycine and hydrophobic -butylglycine residues, we identified nine classifications of conformational disorder and isolated 122 unique sequences across varied compositions and conformations.

Digital hologram reconstruction algorithm based on the Fractional Fourier transform in non-telecentric digital holographic microscopy.

A hologram reconstruction algorithm is proposed based on the fractional Fourier transform (FRFT) in non-telecentric digital holographic microscopy. The optimal fractional order representing the recorded hologram is estimated based on an evaluation metric. The FRFT-based hologram reconstruction enables noise robust amplitude and phase imaging with enhanced resolution.

Microglia Mediate Contact-Independent Neuronal Network Remodeling via Secreted Neuraminidase-3 Associated with Extracellular Vesicles.

Neurons communicate with each other through electrochemical transmission at synapses. Microglia, the resident immune cells of the central nervous system, modulate this communication through a variety of contact-dependent and -independent means. Microglial secretion of active sialidase enzymes upon exposure to inflammatory stimuli is one unexplored mechanism of modulation.

State-space modeling approach for fringe pattern demodulation.

A spatial carrier fringe demodulation technique is proposed based on a state-space modeling approach for phase estimation. The fringe background intensity, carrier frequency, and phase quadrature components are considered to be the elements of the state vector, which are estimated simultaneously. The state estimation is performed using the extended Kalman filter.

Microglia mediate contact-independent neuronal pruning via secreted Neuraminidase-3 associated with extracellular vesicles.

Neurons communicate with each other through electrochemical transmission at synapses. Microglia, the resident immune cells of the central nervous system, can prune these synapses through a variety of contact-dependent and -independent means. Microglial secretion of active sialidase enzymes upon exposure to inflammatory stimuli is one unexplored mechanism of pruning.

Phase-shifting interferometry based on dynamic mode decomposition.

A phase retrieval algorithm in phase-shifting interferometry is presented based on dynamic mode decomposition (DMD). The complex-valued spatial mode obtained from the DMD of phase-shifted interferograms allows the derivation of the phase estimate. At the same time, the oscillation frequency associated with the spatial mode provides the phase step estimate.

Objective speckle pattern-based surface roughness measurement using matrix factorization.

A method for the measurement of profile parameters of both isotropic and anisotropic surfaces is presented using the objective laser speckle imaging technique. The surface parameters are characterized in terms of a singular value decomposition method-based metric derived from the initial key contributing singular values of the speckle pattern. A simulation study is performed with random Gaussian anisotropic surfaces generated as a function of the correlation lengths in both and directions.

Fringe pattern demodulation using Zernike polynomials and a 1-norm regularized extended Kalman filter.

A novel algorithm for closed fringe demodulation for an absolute phase estimation, to the best of our knowledge, is proposed. The two-dimensional phase is represented as a weighted linear combination of a certain number of Zernike polynomials (ZPs). Essentially, the problem of phase estimation is converted into the estimation of ZP coefficients.

Analyzing nested experimental designs-A user-friendly resampling method to determine experimental significance.

While hierarchical experimental designs are near-ubiquitous in neuroscience and biomedical research, researchers often do not take the structure of their datasets into account while performing statistical hypothesis tests. Resampling-based methods are a flexible strategy for performing these analyses but are difficult due to the lack of open-source software to automate test construction and execution. To address this, we present Hierarch, a Python package to perform hypothesis tests and compute confidence intervals on hierarchical experimental designs.

Improving particle detection and size estimation accuracy in digital in-line holography using autoregressive interpolation.

The accuracy of particle detection and size estimation is limited by the physical size of the digital sensor used to record the hologram in a digital in-line holographic imaging system. In this paper, we propose to utilize the autoregressive (AR) interpolation of the hologram to increase pixel density and, effectively, the quality of hologram reconstruction. Simulation studies are conducted to evaluate the influence of AR interpolation of a hologram on the accuracy of detection and size estimation of single and multiple particles of varying sizes.

Autofocusing in digital holography using eigenvalues.

A new autofocusing algorithm for digital holography is proposed based on the eigenvalues of the images reconstructed at different distances in the measurement volume. An image quality metric evaluated based on the distribution of its eigenvalues is compared in function of the reconstruction distance to identify the location of the focal plane. The proposed automatic focal plane detection algorithm is capable of working with amplitude objects, phase objects, and mixed type objects.

BODIPY Fluorophores for Membrane Potential Imaging.

Fluorophores based on the BODIPY scaffold are prized for their tunable excitation and emission profiles, mild syntheses, and biological compatibility. Improving the water-solubility of BODIPY dyes remains an outstanding challenge. The development of water-soluble BODIPY dyes usually involves direct modification of the BODIPY fluorophore core with ionizable groups or substitution at the boron center.

Two-Photon Voltage Imaging with Sulfonated Rhodamine Dyes.

Optical methods that rely on fluorescence for mapping changes in neuronal membrane potential in the brains of awake animals provide a powerful way to interrogate the activity of neurons that underlie neural computations ranging from sensation and perception to learning and memory. To achieve this goal, fluorescent indicators should be bright, highly sensitive to small changes in membrane potential, nontoxic, and excitable with infrared light. We report a new class of fluorescent, voltage-sensitive dyes: sulfonated rhodamine voltage reporters (sRhoVR), synthetic fluorophores with high voltage sensitivity, excellent two-photon performance, and compatibility in intact mouse brains.

hPSC-Derived Striatal Cells Generated Using a Scalable 3D Hydrogel Promote Recovery in a Huntington Disease Mouse Model.

Huntington disease (HD) is an inherited, progressive neurological disorder characterized by degenerating striatal medium spiny neurons (MSNs). One promising approach for treating HD is cell replacement therapy, where lost cells are replaced by MSN progenitors derived from human pluripotent stem cells (hPSCs). While there has been remarkable progress in generating hPSC-derived MSNs, current production methods rely on two-dimensional culture systems that can include poorly defined components, limit scalability, and yield differing preclinical results.

Diet-induced obesity suppresses cortical bone accrual by a neuropeptide Y-dependent mechanism.

Objective: To determine whether age and neuropeptide Y (NPY) were involved in the skeletal response to extended periods of diet-induced obesity.

Methods: Male wild-type (WT) and NPY null (NPYKO) mice were fed a mild (23% fat) high-fat diet for 10 weeks from 6 or 16 weeks of age. Metabolism and bone density were assessed during feeding.

Phase unwrapping algorithm using polynomial phase approximation and linear Kalman filter.

A noise-robust phase unwrapping algorithm is proposed based on state space analysis and polynomial phase approximation using wrapped phase measurement. The true phase is approximated as a two-dimensional first order polynomial function within a small sized window around each pixel. The estimates of polynomial coefficients provide the measurement of phase and local fringe frequencies.

Voltage Imaging: Pitfalls and Potential.

Optical methods for interrogating membrane potential changes in neurons promise to revolutionize our ability to dissect the activity of individual cells embedded in neural circuits underlying behavior and sensation. A number of voltage imaging strategies have emerged in the past few years. This Perspective discusses developments in both small-molecule and genetically encoded fluorescent indicators of membrane potential.

Insulin controls food intake and energy balance via NPY neurons.

Objectives: Insulin signaling in the brain has been implicated in the control of satiety, glucose homeostasis and energy balance. However, insulin signaling is dispensable in energy homeostasis controlling AgRP or POMC neurons and it is unclear which other neurons regulate these effects. Here we describe an ancient insulin/NPY neuronal network that governs energy homeostasis across phyla.

Engineered hydrogels increase the post-transplantation survival of encapsulated hESC-derived midbrain dopaminergic neurons.

Cell replacement therapies have broad biomedical potential; however, low cell survival and poor functional integration post-transplantation are major hurdles that hamper clinical benefit. For example, following striatal transplantation of midbrain dopaminergic (mDA) neurons for the treatment of Parkinson's disease (PD), only 1-5% of the neurons typically survive in preclinical models and in clinical trials. In general, resource-intensive generation and implantation of larger numbers of cells are used to compensate for the low post-transplantation cell-survival.

A modular platform to develop peptoid-based selective fluorescent metal sensors.

Despite the reduction in industrial use of toxic heavy metals, there remain contaminated natural water sources across the world. Herein we present a modular platform for developing selective sensors for toxic metal ions using N-substituted glycine, or peptoid, oligomers coupled to a fluorophore. As a preliminary evaluation of this strategy, structures based on previously identified metal-binding peptoids were synthesized with terminal pyrene moieties.

Voltage-sensitive rhodol with enhanced two-photon brightness.

We have designed, synthesized, and applied a rhodol-based chromophore to a molecular wire-based platform for voltage sensing to achieve fast, sensitive, and bright voltage sensing using two-photon (2P) illumination. Rhodol VoltageFluor-5 (RVF5) is a voltage-sensitive dye with improved 2P cross-section for use in thick tissue or brain samples. RVF5 features a dichlororhodol core with pyrrolidyl substitution at the nitrogen center.

Efficient generation of hPSC-derived midbrain dopaminergic neurons in a fully defined, scalable, 3D biomaterial platform.

Pluripotent stem cells (PSCs) have major potential as an unlimited source of functional cells for many biomedical applications; however, the development of cell manufacturing systems to enable this promise faces many challenges. For example, there have been major recent advances in the generation of midbrain dopaminergic (mDA) neurons from stem cells for Parkinson's Disease (PD) therapy; however, production of these cells typically involves undefined components and difficult to scale 2D culture formats. Here, we used a fully defined, 3D, thermoresponsive biomaterial platform to rapidly generate large numbers of action-potential firing mDA neurons after 25 days of differentiation (~40% tyrosine hydroxylase (TH) positive, maturing into 25% cells exhibiting mDA neuron-like spiking behavior).

A Rationally Designed, General Strategy for Membrane Orientation of Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes.

Voltage imaging with fluorescent dyes offers promise for interrogating the complex roles of membrane potential in coordinating the activity of neurons in the brain. Yet, low sensitivity often limits the broad applicability of optical voltage indicators. In this paper, we use molecular dynamics (MD) simulations to guide the design of new, ultrasensitive fluorescent voltage indicators that use photoinduced electron transfer (PeT) as a voltage-sensing switch.

Isomerically Pure Tetramethylrhodamine Voltage Reporters.

We present the design, synthesis, and application of a new family of fluorescent voltage indicators based on isomerically pure tetramethylrhodamines. These new Rhodamine Voltage Reporters, or RhoVRs, use photoinduced electron transfer (PeT) as a trigger for voltage sensing, display excitation and emission profiles in the green to orange region of the visible spectrum, demonstrate high sensitivity to membrane potential changes (up to 47% ΔF/F per 100 mV), and employ a tertiary amide derived from sarcosine, which aids in membrane localization and simultaneously simplifies the synthetic route to the voltage sensors. The most sensitive of the RhoVR dyes, RhoVR 1, features a methoxy-substituted diethylaniline donor and phenylenevinylene molecular wire at the 5'-position of the rhodamine aryl ring, exhibits the highest voltage sensitivity to date for red-shifted PeT-based voltage sensors, and is compatible with simultaneous imaging alongside green fluorescent protein-based indicators.