Automated live-cell single-molecule tracking in enteroid monolayers reveals transcription factor dynamics probing lineage-determining function.

Lineage transcription factors (TFs) provide one regulatory level of differentiation crucial for the generation and maintenance of healthy tissues. To probe TF function by measuring their dynamics during adult intestinal homeostasis, we established HILO-illumination-based live-cell single-molecule tracking (SMT) in mouse small intestinal enteroid monolayers recapitulating tissue differentiation hierarchies in vitro. To increase the throughput, capture cellular features, and correlate morphological characteristics with diffusion parameters, we developed an automated imaging and analysis pipeline, broadly applicable to two-dimensional culture systems.

A comprehensive molecular phylogeny of the genus Sylvirana (Anura: Ranidae) highlights unrecognized diversity, revised classification and historical biogeography.

The genus Sylvirana includes 12 species widely distributed in South China and Southeast Asia. The phylogenetic relationships and species diversity for Sylvirana and allied genera remain unresolved and controversial due to insufficient data and incomplete taxon sampling. Using a combined dataset of mitochondrial genes (16S and COI) and 101 nuclear genes obtained through the amplicon sequence capture approach, we generated the most comprehensive phylogenetic analysis for the genus Sylvirana to date, inferring diversity, phylogenetic relationships, and historical biogeography with unprecedented levels of taxon and geographic sampling.

Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis.

Transcription factors (TFs) bind combinatorially to cis-regulatory elements, orchestrating transcriptional programs. Although studies of chromatin state and chromosomal interactions have demonstrated dynamic neurodevelopmental cis-regulatory landscapes, parallel understanding of TF interactions lags. To elucidate combinatorial TF binding driving mouse basal ganglia development, we integrated chromatin immunoprecipitation sequencing (ChIP-seq) for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and gene expression data, and functional enhancer assays.

Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche.

Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces.

VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers.

Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we present an updated VISTA Enhancer Browser (https://enhancer.lbl.

BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes.

Secondary metabolites are compounds not essential for an organism's development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis.

Correlative X-ray micro-nanotomography with scanning electron microscopy at the Advanced Light Source.

Geological samples are inherently multi-scale. Understanding their bulk physical and chemical properties requires characterization down to the nano-scale. A powerful technique to study the three-dimensional microstructure is X-ray tomography, but it lacks information about the chemistry of samples.

A general Bayesian algorithm for the autonomous alignment of beamlines.

Autonomous methods to align beamlines can decrease the amount of time spent on diagnostics, and also uncover better global optima leading to better beam quality. The alignment of these beamlines is a high-dimensional expensive-to-sample optimization problem involving the simultaneous treatment of many optical elements with correlated and nonlinear dynamics. Bayesian optimization is a strategy of efficient global optimization that has proved successful in similar regimes in a wide variety of beamline alignment applications, though it has typically been implemented for particular beamlines and optimization tasks.

Packaged delivery of CRISPR-Cas9 ribonucleoproteins accelerates genome editing.

Effective genome editing requires a sufficient dose of CRISPR-Cas9 ribonucleoproteins (RNPs) to enter the target cell while minimizing immune responses, off-target editing and cytotoxicity. Clinical use of Cas9 RNPs currently entails electroporation into cells , but no systematic comparison of this method to packaged RNP delivery has been made. Here we compared two delivery strategies, electroporation and enveloped delivery vehicles (EDVs), to investigate the Cas9 dosage requirements for genome editing.

A Pyrrole Modified 3,4-Propylenedioxythiophene Conjugated Polymer as Hole Transport Layer for Efficient and Stable Perovskite Solar Cells.

Despite the outstanding electric properties and cost-effectiveness of poly(3,4-ethylenedioxythiophene) (PEDOT) and its derivatives, their performance as hole transport layer (HTL) materials in conventional perovskite solar cells (PSCs) has lagged behind that of widely used spirobifluorene-based molecules or poly(triaryl amine). This gap is mainly from their poor solubility and energy alignment mismatch. In this work, the design and synthesis of a pyrrole-modified HTL (PPr) based on 3,4-propylenedioxythiophene (ProDOT) are presented for efficient and stable PSCs.

Development and Validation of a Diagnostic Algorithm for Down Syndrome Using Birth Certificate and International Classification of Diseases Codes.

Objective: We aimed to develop an algorithm that accurately identifies children with Down syndrome (DS) using administrative data.

Methods: We identified a cohort of children born between 2000 and 2017, enrolled in the Tennessee Medicaid Program (TennCare), who either had DS coded on their birth certificate or had a diagnosis listed using an International Classification of Diseases (ICD) code (suspected DS), and who received care at Vanderbilt University Medical Center, a comprehensive academic medical center, in the United States. Children with suspected DS were defined as having DS if they had (a) karyotype-confirmed DS indicated on their birth certificate; (b) karyotype-pending DS indicated on their birth certificate (or just DS if test type was not specified) and at least two healthcare encounters for DS during the first 6 years of life; or (c) at least three healthcare encounters for DS, with the first and last encounter separated by at least 30 days, during the first six years of life.

Functional Assessments of Gynecologic Cancer Models Highlight Differences Between Single-Node Inhibitors of the PI3K/AKT/mTOR Pathway and a Pan-PI3K/mTOR Inhibitor, Gedatolisib.

: The PI3K/AKT/mTOR (PAM) pathway is frequently activated in gynecological cancers. Many PAM inhibitors selectively target single PAM pathway nodes, which can lead to reduced efficacy and increased drug resistance. To address these limitations, multiple PAM pathway nodes may need to be inhibited.

Tailoring the Spin Reorientation Transition of Co Films by Pd Monolayer Capping.

We have characterized the magnetization easy-axis of ultra-thin Co films (2-5 atomic layers, AL) grown on Ru(0001) when they are capped with a monolayer of Pd. The addition of a Pd monolayer turns the magnetization of 3 and 4 AL-thick Co films from an in-plane to an out-of-plane alignment, but not that of a 5 AL-thick film. These observations are explained in terms of an enhancement of the surface anisotropy.

Energy and nutrient recovery from municipal and industrial waste and wastewater-a perspective.

Unlabelled: This publication highlights the latest advancements in the field of energy and nutrient recovery from organics rich municipal and industrial waste and wastewater. Energy and carbon rich waste streams are multifaceted, including municipal solid waste, industrial waste, agricultural by-products and residues, beached or residual seaweed biomass from post-harvest processing, and food waste, and are valuable resources to overcome current limitations with sustainable feedstock supply chains for biorefining approaches. The emphasis will be on the most recent scientific progress in the area, including the development of new and innovative technologies, such as microbial processes and the role of biofilms for the degradation of organic pollutants in wastewater, as well as the production of biofuels and value-added products from organic waste and wastewater streams.

Reductive pathways in molten inorganic salts enable colloidal synthesis of III-V semiconductor nanocrystals.

Colloidal quantum dots, with their size-tunable optoelectronic properties and scalable synthesis, enable applications in which inexpensive high-performance semiconductors are needed. Synthesis science breakthroughs have been key to the realization of quantum dot technologies, but important group III-group V semiconductors, including colloidal gallium arsenide (GaAs), still cannot be synthesized with existing approaches. The high-temperature molten salt colloidal synthesis introduced in this work enables the preparation of previously intractable colloidal materials.

Soft hydrogel semiconductors with augmented biointeractive functions.

Hydrogels, known for their mechanical and chemical similarity to biological tissues, are widely used in biotechnologies, whereas semiconductors provide advanced electronic and optoelectronic functionalities such as signal amplification, sensing, and photomodulation. Combining semiconducting properties with hydrogel designs can enhance biointeractive functions and intimacy at biointerfaces, but this is challenging owing to the low hydrophilicity of polymer semiconductors. We developed a solvent affinity-induced assembly method that incorporates water-insoluble polymer semiconductors into double-network hydrogels.

Highly sensitive multiplexed colorimetric lateral flow immunoassay by plasmon-controlled metal-silica isoform nanocomposites: PINs.

Lateral flow assay (LFA) systems use metal nanoparticles for rapid and convenient target detection and are extensively studied for the diagnostics of various diseases. Gold nanoparticles (AuNPs) are often used as probes in LFAs, displaying a single red color. However, there is a high demand for colorimetric LFAs to detect multiple biomarkers, requiring the use of multicolored NPs.

Learning protocols for the fast and efficient control of active matter.

Exact analytic calculation shows that optimal control protocols for passive molecular systems often involve rapid variations and discontinuities. However, similar analytic baselines are not generally available for active-matter systems, because it is more difficult to treat active systems exactly. Here we use machine learning to derive efficient control protocols for active-matter systems, and find that they are characterized by sharp features similar to those seen in passive systems.

Synthetic Control of Water-Stable Hybrid Perovskitoid Semiconductors.

Hybrid metal-halide perovskites and their derived materials have emerged as the next-generation semiconductors with a wide range of applications, including photovoltaics, light-emitting devices, and other optoelectronics. Over the past decade, numerous single-crystalline perovskite derivatives have been synthesized and developed. However, the synthetic methods for these derivatives mainly rely on acidic crystallization conditions.