Self-extinguishing relay waves enable homeostatic control of human neutrophil swarming.

Neutrophils collectively migrate to sites of injury and infection. How these swarms are coordinated to ensure the proper level of recruitment is unknown. Using an ex vivo model of infection, we show that human neutrophil swarming is organized by multiple pulsatile chemoattractant waves.

Comparative study of immune response to local tumor destruction modalities in a murine breast cancer model.

Introduction: Immunotherapy is revolutionizing the management of multiple cancer types. However, only a subset of patients responds to immunotherapy. One mechanism of resistance is the absence of immune infiltrates within the tumor.

A non-symmetrical p97 conformation initiates a multistep recruitment of Ufd1/Npl4.

experiments and cryo-EM structures of p97 and its cofactor, Ufd1/Npl4 (UN), elucidated substrate processing. Yet, the structural transitions and the related ATPase cycle upon UN binding remain unresolved. We captured two discrete conformations: One in which D1 protomers are ATP bound, while the D2 subunits are in the ADP state, presumably required for substrate engagement with the D2 pore; and a heterologous nucleotide state within the D1 ring in which only two NTDs are in the "up" ATP state that favors UN binding.

Phospholipid Supply for Autophagosome Biogenesis.

Autophagy is a cellular degradation pathway where double-membrane autophagosomes form de novo to engulf cytoplasmic material destined for lysosomal degradation. This process requires regulated membrane remodeling, beginning with the initial autophagosomal precursor and progressing to its elongation and maturation into a fully enclosed, fusion-capable vesicle. While the core protein machinery involved in autophagosome formation has been extensively studied over the past two decades, the role of phospholipids in this process has only recently been studied.

Biomimetic Analogues of the Desferrioxamine E Siderophore for PET Imaging of Invasive Aspergillosis: Targeting Properties and Species Specificity.

The pathogenic fungus utilizes a cyclic ferrioxamine E (FOXE) siderophore to acquire iron from the host. Biomimetic FOXE analogues were labeled with gallium-68 for molecular imaging with PET. [Ga]Ga(III)-FOXE analogues were internalized in cells via Sit1.

Predicting the direction of phenotypic difference.

Predicting phenotypes from genomic data is a key goal in genetics, but for most complex phenotypes, predictions are hampered by incomplete genotype-to-phenotype mapping. Here, we describe a more attainable approach than quantitative predictions, which is aimed at qualitatively predicting phenotypic differences. Despite incomplete genotype-to-phenotype mapping, we show that it is relatively easy to determine which of two individuals has a greater phenotypic value.

Dasatinib induces endothelial dysfunction leading to impaired recovery from ischaemia.

Chronic myeloid leukaemia (CML) management is complicated by treatment-emergent vascular adverse events seen with tyrosine kinase inhibitors (TKIs) such as nilotinib, dasatinib and ponatinib. Pleural effusion and pulmonary arterial hypertension (PAH) have been associated with dasatinib treatment. Endothelial dysfunction and impaired angiogenesis are hallmarks of PAH.

The tumor-driven antibody-mediated immune response in cancer.

Immune cells in the tumor microenvironment play a crucial role in cancer prognosis and response to immunotherapy. Recent studies highlight the significance of tumor-infiltrating B cells and tertiary lymphoid structures as markers of favorable prognosis and patient-positive response to immune checkpoint blockers in some types of cancer. Although the presence of germinal center B cells and plasma cells in the tumor microenvironment has been established, determining their tumor reactivity remains challenging.

Elastic to plastic transition in amorphous solids.

The response of amorphous solids to mechanical loads is accompanied by plasticity that is generically associated with "non-affine" quadrupolar events seen in the resulting displacement field. To develop a continuum theory, one needs to assess when these quadrupolar events have a finite density, allowing the development of a field theory. Is there a transition, as a function of the material parameters and the nature of the loads, from isolated plastic events whose density is zero to a regime governed by a finite density? And if so, what is the nature of this transition? The aim of the paper is to explore this issue.

The physiological relevance of autophagosome morphogenesis.

Autophagy sequesters cytoplasmic portions into autophagosomes. While selective cargo is engulfed by elongation of cup-shaped isolation membranes (IMs), the morphogenesis of non-selective IMs remains elusive. Based on recent observations, we propose a novel model for autophagosome morphogenesis wherein active regulation of the IM rim serves the physiological roles of autophagy.

Establishing a Mouse Genotyping Core Facility Based on Automation, High-resolution Melting Analysis, and Purpose-developed MATLAB Applications for Sample Tracking, Data Analysis, and Report Generation.

An in-house genotyping facility should aim to be more cost-effective than outsourced service and more reliable than genotyping performed by short-term employees or students of individual research groups. Reliable genotyping allows efficient and economical management of mice colonies and promotes accurate and reproducible research results. Here we provide a detailed description of our approach to establishing a genotyping core facility, relying on automated PCR assembly and high-resolution melting (HRM) analysis (first derivative).

Mapping the tumor stress network reveals dynamic shifts in the stromal oxidative stress response.

The tumor microenvironment (TME) presents cells with challenges such as variable pH, hypoxia, and free radicals, triggering stress responses that affect cancer progression. In this study, we examine the stress response landscape in four carcinomas-breast, pancreas, ovary, and prostate-across five pathways: heat shock, oxidative stress, hypoxia, DNA damage, and unfolded protein stress. Using a combination of experimental and computational methods, we create an atlas of stress responses across various types of carcinomas.

Dynamic screening by plasticity in amorphous solids.

In recent work it was shown that elasticity theory can break down in amorphous solids subjected to nonuniform static loads. The elastic fields are screened by geometric dipoles; these stem from gradients of the quadrupole field associated with plastic responses. Here we study the dynamical responses induced by oscillatory loads.

Uncommon opsin's retinal isomer is involved in mammalian sperm thermotaxis.

In recent years it became apparent that, in mammals, rhodopsin and other opsins, known to act as photosensors in the visual system, are also present in spermatozoa, where they function as highly sensitive thermosensors for thermotaxis. The intriguing question how a well-conserved protein functions as a photosensor in one type of cells and as a thermosensor in another type of cells is unresolved. Since the moiety that confers photosensitivity on opsins is the chromophore retinal, we examined whether retinal is substituted in spermatozoa with a thermosensitive molecule.

Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification.

Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the parasite life cycle. Alterations in the level of a specific Ψ in helix 69 (H69) affected ribosome function.

Silica Biomineralization with Lignin Involves Si-O-C Bonds That Stabilize Radicals.

Plants undergo substantial biomineralization of silicon, which is deposited primarily in cell walls as amorphous silica. The mineral formation could be moderated by the structure and chemistry of lignin, a polyphenol polymer that is a major constituent of the secondary cell wall. However, the reactions between lignin and silica have not yet been well elucidated.

Phylogenomics and genetic analysis of solvent-producing Clostridium species.

The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C.

Unlocking the Role of Age-Related Changes to Fibroblasts in Pancreatic Cancer.

Pancreatic cancer prevalence increases with age, and disease prognosis is poorer in older individuals. The increased prevalence is driven, undoubtedly, by the multistep accumulation of oncogenic mutations in cancer cells with age. However, fibroblasts are major constituents and key players in pancreatic cancer, and they too undergo age-related changes that may contribute to disease severity.

The GARD Prebiotic Reproduction Model Described in Order and Complexity.

Early steps in the origin of life were necessarily connected to the unlikely formation of self-reproducing structures from chaotic chemistry. Simulations of chemical kinetics based on the graded autocatalysis replication domain (GARD) model demonstrate the ability of a micellar system to become self-reproducing units away from equilibrium. Even though they may be very rare in the initial state of the system, the property of their endogenous mutually catalytic networks being dynamic attractors greatly enhanced reproduction propensity, revealing their potential for selection and Darwinian evolution processes.

Deconvoluting low yield from weak potency in direct-to-biology workflows with machine learning.

High throughput and rapid biological evaluation of small molecules is an essential factor in drug discovery and development. Direct-to-biology (D2B), whereby compound purification is foregone, has emerged as a viable technique in time efficient screening, specifically for PROTAC design and biological evaluation. However, one notable limitation is the prerequisite of high yielding reactions to ensure the desired compound is indeed the compound responsible for biological activity.

A cellulosomal double-dockerin module from Clostridium thermocellum shows distinct structural and cohesin-binding features.

Cellulosomes are intricate cellulose-degrading multi-enzymatic complexes produced by anaerobic bacteria, which are valuable for bioenergy development and biotechnology. Cellulosome assembly relies on the selective interaction between cohesin modules in structural scaffolding proteins (scaffoldins) and dockerin modules in enzymes. Although the number of tandem cohesins in the scaffoldins is believed to determine the complexity of the cellulosomes, tandem dockerins also exist, albeit very rare, in some cellulosomal components whose assembly and functional roles are currently unclear.