Non-Newtonian dynamics modelled with non-linear transport coefficients at the mesoscale by using dissipative particle dynamics.

We derive the algorithms for the dynamics of the standard dissipative particle dynamics model (DPD) for a velocity-dependent friction coefficient. By introducing simple estimators of the local rate of strain we propose an interparticle friction coefficient that decreases for high deformation rates, eventually leading to the macroscopic shear-thinning behaviour. We have derived the appropriate fluctuation-dissipation theorems that include the correction of the spurious behaviour due to the coupling of the non-linear friction and the fluctuations.

Light-Induced Nanobody-Mediated Targeted Protein Degradation for Metabolic Flux Control.

In metabolic engineering, increasing chemical production usually involves manipulating the expression levels of key enzymes. However, limited synthetic tools exist for modulating enzyme activity beyond the transcription level. Inspired by natural post-translational mechanisms, we present targeted enzyme degradation mediated by optically controlled nanobodies.

The plasma proteome reveals markers of recent and repeated stress in free-ranging seals.

Animals in nature potentially experience multiple stressors, and those of anthropogenic origin are likely to be repeated or chronic. However, stress hormone levels are highly context-dependent and are not consistent predictors of chronic stress in wildlife. Profiling the downstream consequences of repeated stress responses, such as changes in metabolism or gene expression, may be more informative for predicting their individual-level health consequences and population-level impacts, which are key objectives for wildlife conservation.

Mevalonate secretion is not mediated by a singular non-essential transporter in .

Isoprenoids are highly valued targets for microbial chemical production, allowing the creation of fragrances, biofuels, and pharmaceuticals from renewable carbon feedstocks. To increase isoprenoid production, previous efforts have manipulated pyruvate dehydrogenase (PDH) bypass pathway flux to increase cytosolic acetyl-coA; however, this results in mevalonate secretion and does not necessarily translate into higher isoprenoid production. Identification and disruption of the transporter mediating mevalonate secretion would allow us to determine whether increasing PDH bypass activity in the absence of secretion improves conversion of mevalonate into downstream isoprenoids.

A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic .

Soilborne species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives.

A High-Speed Acoustic Echo Canceller Based on Grey Wolf Optimization and Particle Swarm Optimization Algorithms.

Currently, the use of acoustic echo cancellers (AECs) plays a crucial role in IoT applications, such as voice control appliances, hands-free telephony and intelligent voice control devices, among others. Therefore, these IoT devices are mostly controlled by voice commands. However, the performance of these devices is significantly affected by echo noise in real acoustic environments.

The RNAi Machinery in the Fungus Is Not Very Active in Synthetic Medium and Is Related to Transposable Elements.

Small RNAS (sRNAs) participate in regulatory RNA interference (RNAi) mechanisms in a wide range of eukaryotic organisms, including fungi. The fungus , a model for the study of secondary metabolism, contains a complete set of genes for RNAi pathways. We have analyzed by high-throughput sequencing the content of sRNAs in total RNA samples of grown in synthetic medium in the dark or after 1 h of illumination, using libraries below 150 nt, covering sRNAs and their precursors.

Solutions From Mexican-Descent Perinatal Women To Pandemic-Related Food, Mental Health, And Health And Safety Stressors.

Latina women in the US were disproportionately affected by the COVID-19 pandemic because of structural racism, including discrimination, reduced care access, and elevated risk for illness and death. Although several US policies were implemented to offset the economic toll of the pandemic, few addressed complex stressors, particularly those among Mexican-descent mothers. This qualitative study with thirty-eight perinatal women and mothers of young children who were of Mexican descent sought to identify pandemic-related stressors and solicit recommendations for addressing them during future large-scale crises.

Three Genes Involved in Different Signaling Pathways, , , and , Participate in the Regulation of Fusarin Biosynthesis in .

The phytopathogenic fungus has a rich secondary metabolism which includes the synthesis of very different metabolites in response to diverse environmental cues, such as light or nitrogen. Here, we focused our attention on fusarins, a class of mycotoxins whose synthesis is downregulated by nitrogen starvation. Previous data showed that mutants of genes involved in carotenoid regulation (, encoding a RING finger protein repressor), light detection (, White Collar photoreceptor), and cAMP signaling (AcyA, adenylate cyclase) affect the synthesis of different metabolites.

Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility.

Endogenous biomolecular condensates, composed of a multitude of proteins and RNAs, can organize into multiphasic structures with compositionally distinct phases. This multiphasic organization is generally understood to be critical for facilitating their proper biological function. However, the biophysical principles driving multiphase formation are not completely understood.

Using MitER for 3D analysis of mitochondrial morphology and ER contacts.

We have developed an open-source workflow that allows for quantitative single-cell analysis of organelle morphology, distribution, and inter-organelle contacts with an emphasis on the analysis of mitochondria and mitochondria-endoplasmic reticulum (mito-ER) contact sites. As the importance of inter-organelle contacts becomes more widely recognized, there is a concomitant increase in demand for tools to analyze subcellular architecture. Here, we describe a workflow we call MitER (pronounced "mightier"), which allows for automated calculation of organelle morphology, distribution, and inter-organelle contacts from 3D renderings by employing the animation software Blender.

Green-Kubo expressions for transport coefficients from dissipative particle dynamics simulations revisited.

This article addresses the debate about the correct application of Green-Kubo expressions for transport coefficients from dissipative particle dynamics simulations. We demonstrate that the Green-Kubo expressions are valid provided that (i) the dynamic model conserves the physical property, whose transport is studied, and (ii) the fluctuations satisfy detailed balance. As a result, the traditional expressions used in molecular dynamics can also be applied to dissipative particle dynamics simulations.

Intracellular negative feedback mechanisms in blubber and muscle moderate acute stress responses in fasting seals.

Animals may limit the cost of stress responses during key life history stages such as breeding and molting by reducing tissue sensitivity to energy-mobilizing stress hormones (e.g. cortisol).

High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates.

The ability to perform sophisticated, high-throughput optogenetic experiments has been greatly enhanced by recent open-source illumination devices that allow independent programming of light patterns in single wells of microwell plates. However, there is currently a lack of instrumentation to monitor such experiments in real time, necessitating repeated transfers of the samples to stand-alone analytical instruments, thus limiting the types of experiments that could be performed. Here we address this gap with the development of the optoPlateReader (oPR), an open-source, solid-state, compact device that allows automated optogenetic stimulation and spectroscopy in each well of a 96-well plate.

Bioavailability and provitamin A activity of neurosporaxanthin in mice.

Various species of ascomycete fungi synthesize the carboxylic carotenoid neurosporaxanthin. The unique chemical structure of this xanthophyll reveals that: (1) Its carboxylic end and shorter length increase the polarity of neurosporaxanthin in comparison to other carotenoids, and (2) it contains an unsubstituted β-ionone ring, conferring the potential to form vitamin A. Previously, neurosporaxanthin production was optimized in Fusarium fujikuroi, which allowed us to characterize its antioxidant properties in in vitro assays.

HmbC, a Protein of the HMG Family, Participates in the Regulation of Carotenoid Biosynthesis in .

In the fungus , carotenoid production is up-regulated by light and down-regulated by the CarS RING finger protein, which modulates the mRNA levels of carotenoid pathway genes ( genes). To identify new potential regulators of genes, we used a biotin-mediated pull-down procedure to detect proteins capable of binding to their promoters. We focused our attention on one of the proteins found in the screening, belonging to the High-Mobility Group (HMG) family that was named HmbC.

Water treatment membranes embedded with a stable and bactericidal nanodiamond material.

Filtration has emerged as a critical technology to reduce waterborne diseases caused by poor water quality. Filtration technology presents key challenges, such as membrane selectivity, permeability and biofouling. Nanomaterials can offer solutions to these challenges by varying the membranes' mechanical and bactericidal properties.

Transport coefficients from Einstein-Helfand relations using standard and energy-conserving dissipative particle dynamics methods.

In this article we demonstrate that contrary to general belief, the standard Einstein-Helfand (EH) formulas are valid for the evaluation of transport coefficients of systems containing dissipative and random forces provided that for these mesoscopic systems: (i) the corresponding conservation laws are satisfied, and (ii) the transition probabilities satisfy detailed balance. Dissipative particle dynamics (DPD) and energy-conserving DPD methods (DPDE), for instance, are archetypical of such mesoscopic approaches satisfying these properties. To verify this statement, we have derived a mesoscopic heat flux form for the DPDE method, suitable for the calculation of the thermal conductivity from an EH expression.

Photoreceptors.

Light is an important modulating signal in fungi. species stand out as research models for their phytopathogenic activity and their complex secondary metabolism. This includes the synthesis of carotenoids, whose induction by light is their best known photoregulated process.

Generalized Energy-Conserving Dissipative Particle Dynamics with Mass Transfer. Part 2: Applications and Demonstrations.

We present the second part of a two-part paper series intended to address a gap in computational capability for coarse-grain particle modeling and simulation, namely, the simulation of phenomena in which diffusion via mass transfer is a contributing mechanism. In part 1, we presented a formulation of a dissipative particle dynamics method to simulate interparticle mass transfer, termed generalized energy-conserving dissipative particle dynamics with mass transfer (GenDPDE-M). In the GenDPDE-M method, the mass of each mesoparticle remains constant following the interparticle mass exchange.

Generalized Energy-Conserving Dissipative Particle Dynamics with Mass Transfer. Part 1: Theoretical Foundation and Algorithm.

An extension of the generalized energy-conserving dissipative particle dynamics method (GenDPDE) that allows mass transfer between mesoparticles via a diffusion process is presented. By considering the concept of the mesoparticles as , the complexity and flexibility of the GenDPDE framework were enhanced to allow for interparticle mass transfer under isoenergetic conditions, notated here as GenDPDE-M. In the formulation, diffusion is described via the theory of mesoscale irreversible processes based on linear relationships between the fluxes and thermodynamic forces, where their fluctuations are described by Langevin-like equations.

Relation between CarS expression and activation of carotenogenesis by stress in .

a model organism for secondary metabolism in fungi, produces carotenoids, terpenoid pigments with antioxidant activity. Previous results indicate that carotenoid synthesis in is stimulated by light or by different stress conditions and downregulated by a RING finger protein encoded by gene. Here, we have analyzed the effects of three stressors, nitrogen scarcity, heat shock, and oxidative stress.

Confidentiality in medical images through a genetic-based steganography algorithm in artificial intelligence.

Nowadays, image steganography has an important role in hiding information in advanced applications, such as medical image communication, confidential communication and secret data storing, protection of data alteration, access control system for digital content distribution and media database systems. In these applications, one of the most important aspects is to hide information in a cover image whithout suffering any alteration. Currently, all existing approaches used to hide a secret message in a cover image produce some level of distortion in this image.