Nfinder: automatic inference of cell neighborhood in 2D and 3D using nuclear markers.

Background: In tissues and organisms, the coordination of neighboring cells is essential to maintain their properties and functions. Therefore, knowing which cells are adjacent is crucial to understand biological processes that involve physical interactions among them, e.g.

Extensive programmed centriole elimination unveiled in embryos.

Centrioles are critical for fundamental cellular processes, including signaling, motility, and division. The extent to which centrioles are present after cell cycle exit in a developing organism is not known. The stereotypical lineage of makes it uniquely well-suited to investigate this question.

Unlikely intersections on the -adic formal ball.

We investigate generalizations along the lines of the Mordell-Lang conjecture of the author's -adic formal Manin-Mumford results for -dimensional -divisible formal groups . In particular, given a finitely generated subgroup of and a closed subscheme , we show under suitable assumptions that for any points satisfying for some , the minimal such orders are uniformly bounded whenever does not contain a formal subgroup translate of positive dimension. In contrast, we then provide counter-examples to a full -adic formal Mordell-Lang result.

Demonstration of a Plasmonic Nonlinear Pseudodiode.

We demonstrate a nonlinear plasmonic metasurface that exhibits strongly asymmetric second-harmonic generation: nonlinear scattering is efficient upon excitation in one direction, and it is substantially suppressed when the excitation direction is reversed, thus enabling a diode-like functionality. A significant (approximately 10 dB) extinction ratio of SHG upon opposite excitations is measured experimentally, and those findings are substantiated with full-wave simulations. This effect is achieved by employing a combination of two commonly used metals─aluminum and silver─producing a material composition asymmetry that results in a bianisotropic response of the system, as confirmed by performing homogenization analysis and extracting an effective susceptibility tensor.

Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox responses in larval fish.

This Protocol Extension describes the adaptation of an existing Protocol detailing the use of targetable reactive electrophiles and oxidants, an on-demand redox targeting toolset in cultured cells. The adaptation described here is for use of reactive electrophiles and oxidants technologies in live zebrafish embryos (Z-REX). Zebrafish embryos expressing a Halo-tagged protein of interest (POI)-either ubiquitously or tissue specifically-are treated with a HaloTag-specific small-molecule probe housing a photocaged reactive electrophile (either natural electrophiles or synthetic electrophilic drug-like fragments).

Sperm-contributed centrioles segregate stochastically into blastomeres of 4-cell stage Caenorhabditis elegans embryos.

Whereas both sperm and egg contribute nuclear genetic material to the zygote in metazoan organisms, the inheritance of other cellular constituents is unequal between the 2 gametes. Thus, 2 copies of the centriole are contributed solely by the sperm to the zygote in most species. Centrioles can have a stereotyped distribution in some asymmetric divisions, but whether sperm-contributed centrioles are distributed in a stereotyped manner in the resulting embryo is not known.

Trap-and-Track for Characterizing Surfactants at Interfaces.

Understanding the behavior of surfactants at interfaces is crucial for many applications in materials science and chemistry. Optical tweezers combined with trajectory analysis can become a powerful tool for investigating surfactant characteristics. In this study, we perform trap-and-track analysis to compare the behavior of cetyltrimethylammonium bromide (CTAB) and cetyltrimethylammonium chloride (CTAC) at water-glass interfaces.

Label-Free Long-Term Methods for Live Cell Imaging of Neurons: New Opportunities.

Time-lapse light microscopy combined with in vitro neuronal cultures has provided a significant contribution to the field of Developmental Neuroscience. The establishment of the neuronal polarity, i.e.

Large-scale morphometry of the subarachnoid space of the optic nerve.

Background: The meninges, formed by dura, arachnoid and pia mater, cover the central nervous system and provide important barrier functions. Located between arachnoid and pia mater, the cerebrospinal fluid (CSF)-filled subarachnoid space (SAS) features a variety of trabeculae, septae and pillars. Like the arachnoid and the pia mater, these structures are covered with leptomeningeal or meningothelial cells (MECs) that form a barrier between CSF and the parenchyma of the optic nerve (ON).

Ultrafast tunable lasers using lithium niobate integrated photonics.

Early works and recent advances in thin-film lithium niobate (LiNbO) on insulator have enabled low-loss photonic integrated circuits, modulators with improved half-wave voltage, electro-optic frequency combs and on-chip electro-optic devices, with applications ranging from microwave photonics to microwave-to-optical quantum interfaces. Although recent advances have demonstrated tunable integrated lasers based on LiNbO (refs. ), the full potential of this platform to demonstrate frequency-agile, narrow-linewidth integrated lasers has not been achieved.

Cancer hallmarks intersect with neuroscience in the tumor microenvironment.

The mechanisms underlying the multistep process of tumorigenesis can be distilled into a logical framework involving the acquisition of functional capabilities, the so-called hallmarks of cancer, which are collectively envisaged to be necessary for malignancy. These capabilities, embodied both in transformed cancer cells as well as in the heterotypic accessory cells that together constitute the tumor microenvironment (TME), are conveyed by certain abnormal characteristics of the cancerous phenotype. This perspective discusses the link between the nervous system and the induction of hallmark capabilities, revealing neurons and neuronal projections (axons) as hallmark-inducing constituents of the TME.

Grand canonical Brownian dynamics simulations of adsorption and self-assembly of SAS-6 rings on a surface.

The Spindle Assembly Abnormal Protein 6 (SAS-6) forms dimers, which then self-assemble into rings that are critical for the nine-fold symmetry of the centriole organelle. It has recently been shown experimentally that the self-assembly of SAS-6 rings is strongly facilitated on a surface, shifting the reaction equilibrium by four orders of magnitude compared to the bulk. Moreover, a fraction of non-canonical symmetries (i.

Multitarget-Directed Gallium(III) Tris(acyl-pyrazolonate) Complexes Induce Ferroptosis in Cancer Cells via Dysregulation of Cell Redox Homeostasis and Inhibition of the Mevalonate Pathway.

A series of Ga(Q) coordination compounds have been synthesized, where HQ is 1-phenyl-3-methyl-4-RC(═O)-pyrazolo-5-one. The complexes have been characterized through analytical data, NMR and IR spectroscopy, ESI mass spectrometry, elemental analysis, X-ray crystallography, and density functional theory (DFT) studies. Cytotoxic activity against a panel of human cancer cell lines was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, with interesting results in terms of both cell line selectivity and toxicity values compared with cisplatin.

Finding a vocation for validation: taking proteomics beyond association and location.

First established in the seventies, proteomics, chemoproteomics, and most recently, spatial/proximity-proteomics technologies have empowered researchers with new capabilities to illuminate cellular communication networks that govern sophisticated decision-making processes. With an ever-growing inventory of these advanced proteomics tools, the onus is upon the researchers to understand their individual advantages and limitations, such that we can ensure rigorous implementation and conclusions derived from critical data interpretations backed up by orthogonal series of functional validations. This perspective-based on the authors' experience in applying varied proteomics workflows in complex living models-underlines key book-keeping considerations, comparing and contrasting most-commonly-deployed modern proteomics profiling technologies.

Electromagnetic Forces and Torques: From Dielectrophoresis to Optical Tweezers.

Electromagnetic forces and torques enable many key technologies, including optical tweezers or dielectrophoresis. Interestingly, both techniques rely on the same physical process: the interaction of an oscillating electric field with a particle of matter. This work provides a unified framework to understand this interaction both when considering fields oscillating at low frequencies─dielectrophoresis─and high frequencies─optical tweezers.

Protein Dielectrophoresis with Gradient Array of Conductive Electrodes Sheds New Light on Empirical Theory.

Dielectrophoresis (DEP) is a versatile tool for the precise microscale manipulation of a broad range of substances. To unleash the full potential of DEP for the manipulation of complex molecular-sized particulates such as proteins requires the development of appropriate theoretical models and their comprehensive experimental verification. Here, we construct an original DEP platform and test the Hölzel-Pethig empirical model for protein DEP.

Out With a Bang: Celebrating Global Chemical Biology.

On November 8-10, 2022, 163 participants from all over the world gathered at the Campus Biotech in Geneva, Switzerland to share in the latest research in chemical biology. The fourth international symposium of the Swiss National Centres of Competence in Research (NCCR) Chemical Biology coincided with the end of this successful research consortium, and as such this event marked a celebration of the past 12 years of chemical biology research in Switzerland. The inspiring talks delivered by the 15 well-known scientists, balanced in gender, expertise, and geographic location, as well as the numerous poster presentations by junior scientists showcased the breadth of global chemical biology and the bright future ahead.

Topological lattices realized in superconducting circuit optomechanics.

Cavity optomechanics enables the control of mechanical motion through the radiation-pressure interaction, and has contributed to the quantum control of engineered mechanical systems ranging from kilogramme-scale Laser Interferometer Gravitational-wave Observatory (LIGO) mirrors to nanomechanical systems, enabling ground-state preparation, entanglement, squeezing of mechanical objects, position measurements at the standard quantum limit and quantum transduction. Yet nearly all previous schemes have used single- or few-mode optomechanical systems. By contrast, new dynamics and applications are expected when using optomechanical lattices, which enable the synthesis of non-trivial band structures, and these lattices have been actively studied in the field of circuit quantum electrodynamics.

Ultrahigh dynamic range and low noise figure programmable integrated microwave photonic filter.

Microwave photonics has adopted a number of important concepts and technologies over the recent pasts, including photonic integration, versatile programmability, and techniques for enhancing key radio frequency performance metrics such as the noise figure and the dynamic range. However, to date, these aspects have not been achieved simultaneously in a single circuit. Here, we report a multi-functional photonic integrated circuit that enables programmable filtering functions with record-high performance.

The cGAS-STING pathway and cancer.

The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway has emerged as a critical innate immune pathway that, following engagement by DNA, promotes distinct immune effector responses that can impact virtually all aspects of tumorigenesis, from malignant cell transformation to metastasis. Here we address how natural tumor-associated processes and traditional cancer therapies are shaped by cGAS-STING signaling, and how this contributes to beneficial or detrimental outcomes of cancer. We consider current efforts to target the cGAS-STING axis in tumors and highlight new frontiers in cGAS-STING biology to inspire thinking about their connection to cancer.

Microbiome Toolbox: methodological approaches to derive and visualize microbiome trajectories.

Motivation: The gut microbiome changes rapidly under the influence of different factors such as age, dietary changes or medications to name just a few. To analyze and understand such changes, we present a Microbiome Toolbox. We implemented several methods for analysis and exploration to provide interactive visualizations for easy comprehension and reporting of longitudinal microbiome data.

A photonic integrated continuous-travelling-wave parametric amplifier.

The ability to amplify optical signals is of pivotal importance across science and technology typically using rare-earth-doped fibres or gain media based on III-V semiconductors. A different physical process to amplify optical signals is to use the Kerr nonlinearity of optical fibres through parametric interactions. Pioneering work demonstrated continuous-wave net-gain travelling-wave parametric amplification in fibres, enabling, for example, phase-sensitive (that is, noiseless) amplification, link span increase, signal regeneration and nonlinear phase noise mitigation.

High precision, high throughput generation of droplets containing single cells.

The Poisson limit is a major problem for the isolation of single cells in different single-cell technologies and applications. In droplet-based single-cell assays, a scheme that is increasingly popular, the intrinsic randomness during single-cell encapsulation in droplets requires most of the created droplets to be empty, which has a profound impact on the efficiency and throughput of such techniques, and on the predictability of the combinatory droplet assays. Here we present a simple passive microfluidic system overcoming this limitation with unprecedented efficacy, allowing the generation of single-cell droplets for a wide range of operating conditions, with extremely high throughput (more than 22 000 single-cell loaded droplets per minute) and with an extremely low fault ratio (doublets or empty droplets), applicable to any cells and deformable particles.

CFD Simulation of Particle-Laden Flow in a 3D Differentially Heated Cavity Using Coarse Large Eddy Simulation.

Particulate flow in closed space is involved in many engineering applications. In this paper, the prediction of particle removal is investigated in a thermally driven 3D cavity at turbulent Rayleigh number Ra = 10 using Coarse Large Eddy Simulation (CLES). The depletion dynamics of SiO aerosol with aerodynamic diameters between 1.

Aberrant hyperexpression of the RNA binding protein FMRP in tumors mediates immune evasion.

Many human cancers manifest the capability to circumvent attack by the adaptive immune system. In this work, we identified a component of immune evasion that involves frequent up-regulation of fragile X mental retardation protein (FMRP) in solid tumors. FMRP represses immune attack, as revealed by cancer cells engineered to lack its expression.