ModularImageAnalysis (MIA): Assembly of modularised image and object analysis workflows in ImageJ.

ModularImageAnalysis (MIA) is an ImageJ plugin providing a code-free graphical environment in which complex automated analysis workflows can be constructed and distributed. The broad range of included modules cover all stages of a typical analysis workflow, from image loading through image processing, object detection, extraction of measurements, measurement-based filtering, visualisation and data exporting. MIA provides out-of-the-box compatibility with many advanced image processing plugins for ImageJ including Bio-Formats, DeepImageJ, MorphoLibJ and TrackMate, allowing these tools and their outputs to be directly incorporated into analysis workflows.

Correction: Back et al. A New Strain with Antibiotic Activity Isolated from the Microbiome of a Mid-Atlantic Deep-Sea Sponge. 2021, , 105.

After publication of this article [...

Ultrasound modulates neuronal potassium currents via ionotropic glutamate receptors.

Background: Focused ultrasound stimulation (FUS) has the potential to provide non-invasive neuromodulation of deep brain regions with unparalleled spatial precision. However, the cellular and molecular consequences of ultrasound stimulation on neurons remains poorly understood. We previously reported that ultrasound stimulation induces increases in neuronal excitability that persist for hours following stimulation in vitro.

PDIA3/ERp57 promotes a matrix-rich secretome that stimulates fibroblast adhesion through CCN2.

The matricellular glycoprotein thrombospondin-1 (TSP1) has complex roles in the extracellular matrix (ECM) and at cell surfaces, but relatively little is known about its intracellular associations prior to secretion. To search for novel intracellular interactions of TSP1 in situ, we carried out a biotin ligase-based TSP1 interactome screen and identified protein disulfide isomerase A3 (PDIA3/ERp57) as a novel candidate binding protein. In validation, TSP1 and PDIA3 were established to bind in vitro and to colocalize in the endoplasmic reticulum of human dermal fibroblasts (HDF).

Understanding the Matrix: The Role of Extracellular DNA in Oral Biofilms.

Dental plaque is the key etiological agent in caries formation and the development of the prevalent chronic oral inflammatory disease, periodontitis. The dental plaque biofilm comprises a diverse range of microbial species encased within a rich extracellular matrix, of which extracellular DNA (eDNA) has been identified as an important component. The molecular mechanisms of eDNA release and the structure of eDNA have yet to be fully characterized.

A New Strain with Antibiotic Activity Isolated from the Microbiome of a Mid-Atlantic Deep-Sea Sponge.

To tackle the growing problem of antibiotic resistance, it is essential to identify new bioactive compounds that are effective against resistant microbes and safe to use. Natural products and their derivatives are, and will continue to be, an important source of these molecules. Sea sponges harbour a diverse microbiome that co-exists with the sponge, and these bacterial communities produce a rich array of bioactive metabolites for protection and resource competition.

Excitation-Energy-Dependent Molecular Beacon Detects Early Stage Neurotoxic Aβ Aggregates in the Presence of Cortical Neurons.

There is now crucial medical importance placed on understanding the role of early stage, subvisible protein aggregation, particularly in neurodegenerative disease. While there are strategies for detecting such aggregates in vitro, there is no approach at present that can detect these toxic species associated with cells and specific subcellular compartments. We have exploited excitation-energy-dependent fluorescence edge-shift of recombinant protein labeled with a molecular beacon, to provide a sensitive read out for the presence of subvisible protein aggregates.

Effects of food-borne nanomaterials on gastrointestinal tissues and microbiota.

Ingestion of engineered nanomaterials is inevitable due to their addition to food and prevalence in food packaging and domestic products such as toothpaste and sun cream. In the absence of robust dosimetry and particokinetic data, it is currently challenging to accurately assess the potential toxicity of food-borne nanomaterials. Herein, we review current understanding of gastrointestinal uptake mechanisms, consider some data on the potential for toxicity of the most commonly encountered classes of food-borne nanomaterials (including TiO , SiO ZnO, and Ag nanoparticles), and discuss the potential impact of the luminal environment on nanoparticle properties and toxicity.

Detection of a fluorescent-labeled avidin-nucleic acid nanoassembly by confocal laser endomicroscopy in the microvasculature of chronically inflamed intestinal mucosa.

Inflammatory bowel diseases are chronic gastrointestinal pathologies causing great discomfort in both children and adults. The pathogenesis of inflammatory bowel diseases is not yet fully understood and their diagnosis and treatment are often challenging. Nanoparticle-based strategies have been tested in local drug delivery to the inflamed colon.

Streptococcus gordonii comCDE (competence) operon modulates biofilm formation with Candida albicans.

Candida albicans is a pleiomorphic fungus that forms mixed species biofilms with Streptococcus gordonii, an early colonizer of oral cavity surfaces. Activation of quorum sensing (QS; intercellular signalling) promotes monospecies biofilm development by these micro-organisms, but the role of QS in mixed species communities is not understood. The comCDE genes in S.

Applications of microscopy in Salmonella research.

Salmonella enterica is a Gram-negative enteropathogen that can cause localized infections, typically resulting in gastroenteritis, or systemic infection, e.g., typhoid fever, in humans and many other animals.

Axenic culture of a candidate division TM7 bacterium from the human oral cavity and biofilm interactions with other oral bacteria.

The diversity of bacterial species in the human oral cavity is well recognized, but a high proportion of them are presently uncultivable. Candidate division TM7 bacteria are almost always detected in metagenomic studies but have not yet been cultivated. In this paper, we identified candidate division TM7 bacterial phylotypes in mature plaque samples from around orthodontic bonds in subjects undergoing orthodontic treatment.

O-mannosylation in Candida albicans enables development of interkingdom biofilm communities.

Candida albicans is a fungus that colonizes oral cavity surfaces, the gut, and the genital tract. Streptococcus gordonii is a ubiquitous oral bacterium that has been shown to form biofilm communities with C. albicans.

Regulatory function of trefoil peptides (TFF) on intestinal cell junctional complexes.

Abstract Trefoil peptides (TFF) are constitutively expressed in the gastrointestinal tract and are involved in gastrointestinal defence and repair by promoting epithelial restitution. Although there is a general consensus regarding the pro-motogenic activity of trefoil peptides, the cellular mechanisms through which they mediate these processes are not completely understood. Pertubation of the E-cadherin/catenin complex at intercellular junctions appears to be a functional pathway through which TFF2 and TFF3 promote cell migration.

Characterization of cerium oxide nanoparticles-part 2: nonsize measurements.

Part 1 (see companion paper) of the present study discussed the application of a multimethod approach in characterizing the size of cerium oxide nanoparticles (NPs). However, other properties less routinely investigated, such as shape and morphology, structure, chemical composition, and surface properties, are likely to play an important role in determining the behavior, reactivity, and potential toxicity of these NPs. The present study describes the measurement of the aforementioned physicochemical properties of NPs (applied also to nanomaterials [NMs]) compared with micrometer particles (MPs).

Characterization of cerium oxide nanoparticles-part 1: size measurements.

The present study gives an overview of some of the major aspects for consideration in the characterization of nanomaterials (NMs). Part 1 focuses on the measurement of particle size and size-related parameters using several analytical techniques such as transmission electron microscopy, atomic force microscopy, dynamic light scattering, X-ray diffraction, and Brunauer, Emmett, and Teller surface area measurements as applied to commercially available cerium oxide nanoparticles (NPs) and microparticles (MPs). Part 2 (see companion paper) considers nonsize-related characterization and analysis.

Interspecies comparisons on the uptake and toxicity of silver and cerium dioxide nanoparticles.

An increasing number and quantity of manufactured nanoparticles are entering the environment as the diversity of their applications increases, and this will lead to the exposure of both humans and wildlife. However, little is known regarding their potential health effects. We compared the potential biological effects of silver (Ag; nominally 35 and 600-1,600 nm) and cerium dioxide (CeO(2;) nominally <25 nm and 1-5 µm) particles in a range of cell (human hepatocyte and intestinal and fish hepatocyte) and animal (Daphnia magna, Cyprinus carpio) models to assess possible commonalities in toxicity across taxa.

Resolution limits of secondary electron dopant contrast in helium ion and scanning electron microscopy.

As the miniaturization of semiconductor devices continues, characterization of dopant distribution within the structures becomes increasingly challenging. One potential solution is the use of the secondary electron signal produced in scanning electron (SEMs) or helium ion microscopes (HeIMs) to image the changes in electrical potential caused by the dopant atoms. In this article, the contrast mechanisms and resolution limits of secondary electron dopant contrast are explored.

Streptococcus pyogenes antigen I/II-family polypeptide AspA shows differential ligand-binding properties and mediates biofilm formation.

The streptococcal antigen I/II (AgI/II)-family polypeptides are cell wall-anchored adhesins expressed by most indigenous oral streptococci. Proteins sharing 30-40% overall amino acid sequence similarities with AgI/II-family proteins are also expressed by Streptococcus pyogenes. The S.

Effects of silver and cerium dioxide micro- and nano-sized particles on Daphnia magna.

Acute (96 h) and chronic (21 d) exposures of Daphnia magna neonates were carried out with nano- and micro-sized Ag and CeO(2) particles to assess the influence of both material and size of particles on mortality and moulting. Mortality rates for silver in the acute exposures were: AgNP, 56.7 ± 23.

Differences in Salmonella enterica serovar Typhimurium strain invasiveness are associated with heterogeneity in SPI-1 gene expression.

Most studies on Salmonella enterica serovar Typhimurium infection focus on strains ATCC SL1344 or NTCC 12023 (ATCC 14028). We have compared the abilities of these strains to induce membrane ruffles and invade epithelial cells. S.

Enhanced recovery of Salmonella Typhimurium DT104 from exposure to stress at low temperature.

Salmonella enterica serovar Typhimurium (S. Typhimurium) remains an important cause of food-borne infection in the developed world. In order to establish infection within a host, Salmonella must survive and recover from a range of environmental stresses.