A specific and adaptable approach to track CD206 macrophages by molecular MRI and fluorescence imaging.

The mannose receptor (CD206, expressed by the gene ) is a surface marker overexpressed by anti-inflammatory and pro-tumoral macrophages. As such, CD206 macrophages play key roles in the immune response to different pathophysiological conditions and represent a promising diagnostic and therapeutic target. However, methods to specifically target these cells remain challenging.

Loss of does not affect bone and lean tissue in zebrafish.

Human genetic studies have nominated cadherin-like and PC-esterase domain-containing 1 () as a candidate target gene mediating bone mineral density (BMD) and fracture risk heritability. Recent efforts to define the role of in bone in mouse and human models have revealed complex alternative splicing and inconsistent results arising from gene targeting, making its function in bone difficult to interpret. To better understand the role of in adult bone mass and morphology, we conducted a comprehensive genetic and phenotypic analysis of in zebrafish, an emerging model for bone and mineral research.

PCA-based spatial domain identification with state-of-the-art performance.

Motivation: The identification of biologically meaningful domains is a central step in the analysis of spatial transcriptomic data.

Results: Following Occam's razor, we show that a simple PCA-based algorithm for unsupervised spatial domain identification rivals the performance of ten competing state-of-the-art methods across six single-cell spatial transcriptomic datasets. Our reductionist approach, NichePCA, provides researchers with intuitive domain interpretation and excels in execution speed, robustness, and scalability.

Sparse keypoint segmentation of lung fissures: efficient geometric deep learning for abstracting volumetric images.

Purpose: Lung fissure segmentation on CT images often relies on 3D convolutional neural networks (CNNs). However, 3D-CNNs are inefficient for detecting thin structures like the fissures, which make up a tiny fraction of the entire image volume. We propose to make lung fissure segmentation more efficient by using geometric deep learning (GDL) on sparse point clouds.

Advancing macromolecular structure determination with microsecond X-ray pulses at a 4th generation synchrotron.

Serial macromolecular crystallography has become a powerful method to reveal room temperature structures of biological macromolecules and perform time-resolved studies. ID29, a flagship beamline of the ESRF 4th generation synchrotron, is the first synchrotron beamline in the world capable of delivering high brilliance microsecond X-ray pulses at high repetition rate for the structure determination of biological macromolecules at room temperature. The cardinal combination of microsecond exposure times, innovative beam characteristics and adaptable sample environment provides high quality complete data, even from an exceptionally small amount of crystalline material, enabling what we collectively term serial microsecond crystallography (SµX).

Low-dimensional controllability of brain networks.

Identifying the driver nodes of a network has crucial implications in biological systems from unveiling causal interactions to informing effective intervention strategies. Despite recent advances in network control theory, results remain inaccurate as the number of drivers becomes too small compared to the network size, thus limiting the concrete usability in many real-life applications. To overcome this issue, we introduced a framework that integrates principles from spectral graph theory and output controllability to project the network state into a smaller topological space formed by the Laplacian network structure.

Embracing plant plasticity or robustness as a means of ensuring food security.

The dual challenges of global population explosion and environmental deterioration represent major hurdles for 21 Century agriculture culminating in an unprecedented demand for food security. In this Review, we revisit historical concepts of plasticity and canalization before integrating them with contemporary studies of genotype-environment interactions (G×E) that are currently being carried out at the genome-wide level. In doing so we address both fundamental questions regarding G×E and potential strategies to best secure yields in both current and future climate scenarios.

DNA targeting by compact Cas9d and its resurrected ancestor.

Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion.

Structural characterization of pyruvic oxime dioxygenase, a key enzyme in heterotrophic nitrification.

Nitrification by heterotrophic microorganisms is an important part of the nitrogen cycle in the environment. The enzyme responsible for the core function of heterotrophic nitrification is pyruvic oxime dioxygenase (POD). POD is a non-heme, Fe(II)-dependent enzyme that catalyzes the dioxygenation of pyruvic oxime to produce pyruvate and nitrite.

Metagenomics reveals spatial variation in cyanobacterial composition, function, and biosynthetic potential in the Winam Gulf, Lake Victoria, Kenya.

The Winam Gulf in the Kenyan region of Lake Victoria experiences prolific, year-round cyanobacterial harmful algal blooms (cyanoHABs) which pose threats to human, livestock, and ecosystem health. To our knowledge, there is limited molecular research on the gulf's cyanoHABs, and thus, the strategies employed for survival and proliferation by toxigenic cyanobacteria in this region remain largely unexplored. Here, we used metagenomics to analyze the Winam Gulf's cyanobacterial composition, function, and biosynthetic potential.

Structure of WzxE the lipid III flippase for Enterobacterial Common Antigen polysaccharide.

The enterobacterial common antigen (ECA) is conserved in Gram-negative bacteria of the order although its function is debated. ECA biogenesis depends on the Wzx/Wzy-dependent strategy whereby the newly synthesized lipid-linked repeat units, lipid III, are transferred across the inner membrane by the lipid III flippase WzxE. WzxE is part of the Wzx family and required in many glycan assembly systems, but an understanding of its molecular mechanism is hindered due to a lack of structural evidence.

Antibiotic candidates for Gram-positive bacterial infections induce multidrug resistance.

Several antibiotic candidates are in development against Gram-positive bacterial pathogens, but their long-term utility is unclear. To investigate this issue, we studied the laboratory evolution of resistance to antibiotics that have not yet reached the market. We found that, with the exception of compound SCH79797, antibiotic resistance generally readily evolves in .

Comparative Analysis of Transcriptomic and Proteomic Expression between Two Non-Small Cell Lung Cancer Subtypes.

Non-small cell lung cancer (NSCLC) is frequently diagnosed late and has poor survival. The two predominant subtypes of NSCLC, adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), are currently differentially diagnosed using immunohistochemical markers; however, they are increasingly recognized as very different cancer types suggestive of potential for new, more targeted therapies. There are extensive efforts to find more precise and noninvasive differential diagnostic tools.

Membrane-Active Singlet Oxygen Photogenerators as a Paradigm for Broad-Spectrum Antivirals: The Case of Halogenated (BOron)-DIPYrromethenes.

Enveloped viruses, such as flaviviruses and coronaviruses, are pathogens of significant medical concern that cause severe infections in humans. Some photosensitizers are known to possess virucidal activity against enveloped viruses, targeting their lipid bilayer. Here we report a series of halogenated difluoroboron-dipyrromethene (BODIPYs) photosensitizers with strong virus-inactivating activity.

Protocol for fecal microbiota transplantation: A microaerophilic approach for mice housed in a specific pathogen-free facility.

Recently, studies have emerged exploring the potential application of fecal microbiota transplantation (FMT) in pre-clinical settings. Here, we present a protocol for FMT for mice housed in a specific pathogen-free (SPF) facility. We describe steps for sample collection, microaerophilic processing of freshly collected fecal pellets, and administration through oral gavage.

Discovery of Potent Dengue Virus NS2B-NS3 Protease Inhibitors Among Glycyrrhizic Acid Conjugates with Amino Acids and Dipeptides Esters.

This study investigated a library of known and novel glycyrrhizic acid (GL) conjugates with amino acids and dipeptide esters, as inhibitors of the DENV NS2B-NS3 protease. We utilized docking algorithms to evaluate the interactions of these GL derivatives with key residues (His51, Asp75, Ser135, and Gly153) within 10 Å of the DENV-2 NS2B-NS3 protease binding pocket (PDB ID: 2FOM). It was found that compounds and exhibited unique binding patterns, forming hydrogen bonds with Asp75, Tyr150, and Gly153.

Assessment of Favipiravir and Remdesivir in Combination for SARS-CoV-2 Infection in Syrian Golden Hamsters.

Favipiravir (FVP) and remdesivir (RDV) have demonstrable antiviral activity against SARS-CoV-2. Here, the efficacy of FVP, RDV, and FVP with RDV (FVP + RDV) in combination was assessed in Syrian golden hamsters challenged with SARS-CoV- 2 (B.1.

Amperometric Biosensor Based on Glutamate Oxidase to Determine Ast Activity.

This work presents the development of an amperometric biosensor for detecting aspartate aminotransferase (AST) activity in biological fluids using a platinum disk electrode as the working transducer. Optimal concentrations of substrates (aspartate, α-ketoglutarate) and the coenzyme (pyridoxal phosphate) were determined to ensure efficient biosensor operation. A semi-permeable poly-m-phenylenediamine membrane was applied to enhance selectivity against electroactive interferents.

Characterization of Odor-Active 2-Ethyldimethyl-1,3,6-trioxocane Isomers in Polyurethane Materials.

Polyurethane materials, widely used in indoor environments, occasionally exhibit unpleasant odors. An important source of polyurethane odorants is polyether polyols. Previous studies identified odorous 2-ethyldimethyl-1,3,6-trioxocanes in polyurethane materials and polyols but did not investigate the odor activity of the individual isomers.

Bovine Colostrum in Pediatric Nutrition and Health.

Bovine colostrum (BC), the first milk secreted by mammals after birth, is a trending alternative source for supplementing infants and children, offering benefits for gut and immune health. Its rich components, such as proteins, immunoglobulins, lactoferrin, and glycans, are used to fortify diets and support development. Preterm development is crucial, especially in the maturation of essential systems, and from 2010 to 2020, approximately 15% of all premature births occurred at less than 32 weeks of gestation worldwide.

Effective Inhibitor Removal from Wastewater Samples Increases Sensitivity of RT-dPCR and Sequencing Analyses and Enhances the Stability of Wastewater-Based Surveillance.

Wastewater-based surveillance (WBS) is a proven tool for monitoring population-level infection events. Wastewater contains high concentrations of inhibitors, which contaminate the total nucleic acids (TNA) extracted from these samples. We found that TNA extracts from raw influent of Berlin wastewater treatment plants contained highly variable amounts of inhibitors that impaired molecular analyses like dPCR and next-generation sequencing (NGS).

Unveiling the Bioleaching Versatility of .

is a Gram-negative bacterium that thrives in extreme acidic conditions. It has emerged as a key player in biomining and bioleaching technologies thanks to its unique ability to mobilize a wide spectrum of elements, such as Li, P, V, Cr, Fe, Ni, Cu, Zn, Ga, As, Mo, W, Pb, U, and its role in ferrous iron oxidation and reduction. catalyzes the extraction of elements by generating iron (III) ions in oxic conditions, which are able to react with metal sulfides.

Nanoconfined Chlorine-Substituted Monomethine Cyanine Dye with a Propionamide Function Based on the Thiazole Orange Scaffold-Use of a Fluorogenic Probe for Cell Staining and Nucleic Acid Visualization.

The development of fluorescence-based methods for bioassays and medical diagnostics requires the design and synthesis of specific markers to target biological microobjects. However, biomolecular recognition in real cellular systems is not always as selective as desired. A new concept for creating fluorescent biomolecular probes, utilizing a fluorogenic dye and biodegradable, biocompatible nanomaterials, is demonstrated.

Advances in Nanotheranostic Systems for Concurrent Cancer Imaging and Therapy: An Overview of the Last 5 Years.

The rapid development of nanotechnology during the last two decades has created new opportunities to design and generate more advanced nanotheranostics with diversified capabilities for diagnosis, drug delivery, and treatment response monitoring in a single platform. To date, several approaches have been employed in order to develop nanotheranostics. The purpose of this review is to briefly discuss the key components of nanotheranostic systems, to present the conventional and upcoming imaging and therapeutic modalities that employ nanotheranostic systems, and to evaluate recent progress in the field of cancer nanotheranostic systems in the past five years (2020-2024).