Multi-omics and biochemical reconstitution reveal CDK7-dependent mechanisms controlling RNA polymerase II function at gene 5'- and 3'-ends.

CDK7 regulates RNA polymerase II (RNAPII) initiation, elongation, and termination through incompletely understood mechanisms. Because contaminating kinases precluded CDK7 analysis with nuclear extracts, we completed biochemical assays with purified factors. Reconstitution of RNAPII transcription initiation showed CDK7 inhibition slowed and/or paused RNAPII promoter-proximal transcription, which reduced re-initiation.

Pooled PPIseq: Screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform.

Protein-Protein Interactions (PPIs) are a key interface between virus and host, and these interactions are important to both viral reprogramming of the host and to host restriction of viral infection. In particular, viral-host PPI networks can be used to further our understanding of the molecular mechanisms of tissue specificity, host range, and virulence. At higher scales, viral-host PPI screening could also be used to screen for small-molecule antivirals that interfere with essential viral-host interactions, or to explore how the PPI networks between interacting viral and host genomes co-evolve.

Programmed shape transformations in cell-laden granular composites.

Tissues form during development through mechanical compaction of their extracellular matrix (ECM) and shape morphing, processes that result in complex-shaped structures that contribute to tissue function. While observed in vivo, control over these processes in vitro to understand both tissue development and guide tissue formation has remained challenging. Here, we use combinations of mesenchymal stromal cell spheroids and hydrogel microparticles (microgels) with varied hydrolytic stability to fabricate programmable and dynamic granular composites that control compaction and tissue formation over time.

CDK2 activity crosstalk on the ERK kinase translocation reporter can be resolved computationally.

The mitogen-activated protein kinase (MAPK) pathway integrates growth factor signaling through extracellular signal-regulated kinase (ERK) to control cell proliferation. To study ERK dynamics, many researchers use an ERK activity kinase translocation reporter (KTR). Our study reveals that this ERK KTR also partially senses cyclin-dependent kinase 2 (CDK2) activity, making it appear as if ERK activity rises as cells progress through the cell cycle.

Regulation of Cajal bodies: Unexpected connection to 60S ribosomes.

Cajal bodies are essential sites for the biogenesis of small nuclear and nucleolar ribonucleoproteins. In this issue, Courvan and Parker discuss new work from Neugebauer and colleagues (https://doi.org/10.

BRAF and ErbB inhibitors directly activate GCN2 in an off-target manner to limit cancer cell proliferation.

Targeted kinase inhibitors are well known for their promiscuity and off-target effects. Herein, we define an off-target effect in which several clinical BRAF inhibitors, including the widely used dabrafenib and encorafenib, interact directly with GCN2 to activate the Integrated Stress Response and ATF4. Blocking this off-target effect by co-drugging with a GCN2 inhibitor in A375 melanoma cells causes enhancement rather than suppression of cancer cell outgrowth, suggesting that the off-target activation of GCN2 is detrimental to these cells.

A bacterial NLR-related protein recognizes multiple unrelated phage triggers to sense infection.

Immune systems must rapidly sense viral infections to initiate antiviral signaling and protect the host. Bacteria encode >100 distinct viral (phage) defense systems and each has evolved to sense crucial components or activities associated with the viral lifecycle. Here we used a high-throughput AlphaFold-multimer screen to discover that a bacterial NLR-related protein directly senses multiple phage proteins, thereby limiting immune evasion.

Unveiling the promise of peptide nucleic acids as functional linkers for an RNA imaging platform.

Linkers in chemical biology provide more than just connectivity between molecules; their intrinsic properties can be harnessed to enhance the stability and functionality of chemical probes. In this study, we explored the incorporation of a peptide nucleic acid (PNA)-based linker into RNA-targeting probes to improve their affinity and specificity. By integrating a PNA linker into a small molecule probe of the Riboglow platform, we enabled dual binding events: cobalamin (Cbl)-RNA structure-based recognition and sequence-specific PNA-RNA interaction.

High-fidelity computational fluid dynamics modeling to simulate perfusion through a bone-mimicking scaffold.

Breast cancer cells sense shear stresses in response to interstitial fluid flow in bone and induce specific biological responses. Computational fluid dynamics models have been instrumental in estimating these shear stresses to relate the cell mechanoresponse to exact mechanical signals, better informing experiment design. Most computational models greatly simplify the experimental and cell mechanical environments for ease of computation, but these simplifications may overlook complex cell-substrate mechanical interactions that significantly change shear stresses experienced by cells.

Machine Learning Models for Segmentation and Classification of Cyanobacterial Cells.

Timelapse microscopy has recently been employed to study the metabolism and physiology of cyanobacteria at the single-cell level. However, the identification of individual cells in brightfield images remains a significant challenge. Traditional intensity-based segmentation algorithms perform poorly when identifying individual cells in dense colonies due to a lack of contrast between neighboring cells.

Pregnancy and age differentially affect stiffness, injury susceptibility, and composition of murine uterosacral ligaments.

Pelvic organ prolapse is a debilitating condition that diminishes quality of life, and it has been linked to pregnancy and aging. Injury of the uterosacral ligaments (USLs), which provide apical support to the pelvic organs, is a major cause of uterine prolapse. In this study, we examined the effect of pregnancy and age on the apparent elastic modulus, susceptibility to collagen damage, and extracellular matrix (ECM) composition of the murine USL.

Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity.

Background: Understanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible.

Regulation of human interferon signaling by transposon exonization.

Innate immune signaling is essential for clearing pathogens and damaged cells and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2.

Photoresponsive Chemistries for User-Directed Hydrogel Network Modulation to Investigate Cell-Matrix Interactions.

ConspectusSynthetic extracellular matrix (ECM) engineering is a highly interdisciplinary field integrating materials and polymer science and engineering, chemistry, cell biology, and medicine to develop innovative strategies to investigate and control cell-matrix interactions. Cellular microenvironments are complex and highly dynamic, changing in response to injury and disease. To capture some of these critical dynamics , biomaterial matrices have been developed with tailorable properties that can be modulated in the presence of cells.

Advanced Antibacterial Strategies for Combatting Biomaterial-Associated Infections: A Comprehensive Review.

Biomaterial-associated infections (BAIs) pose significant challenges in modern medical technologies, being a major postoperative complication and leading cause of implant failure. These infections significantly risk patient health, resulting in prolonged hospitalization, increased morbidity and mortality rates, and elevated treatment expenses. This comprehensive review examines the mechanisms driving bacterial adhesion and biofilm formation on biomaterial surfaces, offering an in-depth analysis of current antimicrobial strategies for preventing BAIs.

Synergistic Effect in Hybrid Plasmonic Conjugates for Photothermal Applications.

Photothermal conversion efficiency (η) plays a crucial role in selecting suitable gold nanoparticles for photothermal therapeutic applications. The photothermal efficiency depends on the material used for the nanoparticles as well as their various parameters, such as size and shape. By maximizing the light-to-heat conversion efficiency (η), one can reduce the concentration of nanoparticle drugs for photothermal cancer treatment and apply lower laser power to irradiate the tumor.

Photodegradable polyacrylamide tanglemers enable spatiotemporal control over chain lengthening in high-strength and low-hysteresis hydrogels.

Covalent hydrogel networks suffer from a stiffness-toughness conflict, where increased crosslinking density enhances the modulus of the material but also leads to embrittlement and diminished extensibility. Recently, strategies have been developed to form highly entangled hydrogels, colloquially referred to as tanglemers, by optimizing polymerization conditions to maximize the density and length of polymer chains and minimize the crosslinker concentration. It is challenging to assess entanglements in crosslinked networks beyond approximating their theoretical contribution to mechanical properties; thus, in this work, we synthesize and characterize polyacrylamide tanglemers using a photolabile crosslinker, which allows for direct assessment of covalent trapping of entanglements under tension.

Myofibers cultured in viscoelastic hydrogels reveal the effects of integrin-binding and mechanosensing on muscle satellite cells.

Quiescent skeletal muscle satellite cells (SCs) located on myofibers activate in response to muscle injury to regenerate muscle; however, identifying the role of specific matrix signals on SC behavior in vivo is difficult. Therefore, we developed a viscoelastic hydrogel with tunable properties to encapsulate myofibers while maintaining stem cell niche polarity and SC-myofiber interactions to investigate how matrix signals, including viscoelasticity and the integrin-binding ligand arginyl-glycyl-aspartic acid (RGD), influence SC behavior during muscle regeneration. Viscoelastic hydrogels support myofiber culture while preserving SC stemness for up to 72 hours post-encapsulation, minimizing myofiber hypercontraction and SC hyperproliferation compared to Matrigel.

GenoSiS: A Biobank-Scale Genotype Similarity Search Architecture for Creating Dynamic Patient-Match Cohorts.

Many patients do not experience optimal benefits from medical advances because clinical research does not adequately represent them. While the diversity of biomedical research cohorts is improving, ensuring that individual patients are adequately represented remains challenging. We propose a new approach, GenoSiS, which leverages machine learning-based similarity search to dynamically find patient-matched cohorts across different populations quickly.

Dopaminergic Axon Tracts Within a Hyaluronic Acid Hydrogel Encasement to Restore the Nigrostriatal Pathway.

Parkinson's disease is characterized by motor deficits emerging from insufficient dopamine in the striatum after degeneration of dopaminergic neurons and their long-projecting axons comprising the nigrostriatal pathway. To address this, a tissue-engineered nigrostriatal pathway (TE-NSP) featuring a tubular hydrogel with a collagen/laminin core that encases aggregated dopaminergic neurons and their axonal tracts is developed. This engineered microtissue can be implanted to replace neurons and axons with fidelity to the lost pathway and thus may provide dopamine according to feedback from host circuitry.

Proteome profiling of polyomavirus nuclear replication centers using iPOND.

Polyomaviruses (PyVs) cause diverse diseases in a variety of mammalian hosts. During the life cycle, PyVs recruit nuclear host factors to viral genomes to facilitate replication and transcription. While host factors involved in DNA replication, DNA damage sensing and repair, and cell cycle regulation have been observed to bind PyV DNA, the complete set of viral and host proteins comprising the PyV replisome remains incompletely characterized.

2D co-culture model reveals a biophysical interplay between activated fibroblasts and cancer cells.

The tumor microenvironment (TME) comprises diverse cell types within an altered extracellular matrix (ECM) and plays a pivotal role in metastasis through intricate cell-cell and cell-ECM interactions. Fibroblasts, as key constituents of the TME, contribute significantly to cancer metastasis through their involvement in matrix deposition and remodeling mechanisms, modulated by their quiescent or activated states. Despite their recognized importance, the precise role of fibroblasts in cancer cell invasion remains incompletely understood.