Three Microbial Musketeers of the Seas: Shewanella baltica,Aliivibrio fischeri and Vibrio harveyi,and Their Adaptation to Different Salinity Probed by a Proteomic Approach

Osmotic changes are common challenges for marine microorganisms. Bacteria have developed numerous ways of dealing with this stress, including reprogramming of global cellular processes. However, specific molecular adaptation mechanisms to osmotic stress have mainly been investigated in terrestrial model bacteria. In this work, we aimed to elucidate the basis of adjustment to prolonged salinity challenges at the proteome level in marine bacteria. The objects of our studies were three representatives of bacteria inhabiting various marine environments, Shewanella baltica, Vibrio harveyi and Aliivibrio fischeri. The proteomic studies were performed with bacteria cultivated in increased and decreased salinity, followed by proteolytic digestion of samples which were then subjected to liquid chromatography with tandem mass spectrometry analysis. We show that bacteria adjust at all levels of their biological processes, from DNA topology through gene expression regulation and proteasome assembly, to transport and cellular metabolism. The finding that many similar adaptation strategies were observed for both low- and high-salinity conditions is particularly striking. The results show that adaptation to salinity challenge involves the accumulation of DNA-binding proteins and increased polyamine uptake. We hypothesize that their function is to coat and protect the nucleoid to counteract adverse changes in DNA topology due to ionic shifts.     

Investigating the Potential Use of Chemical Biopsy Devices to Characterize Brain Tumor Lipidomes

The development of a fast and accurate intraoperative method that enables the differentiation and stratification of cancerous lesions is still a challenging problem in laboratory medicine. Therefore, it is important to find and optimize a simple and effective analytical method of enabling the selection of distinctive metabolites. This study aims to assess the usefulness of solid-phase microextraction (SPME) probes as a sampling method for the lipidomic analysis of brain tumors. To this end, SPME was applied to sample brain tumors immediately after excision, followed by lipidomic analysis via liquid chromatography-high resolution mass spectrometry (LC-HRMS). The results showed that long fibers were a good option for extracting analytes from an entire lesion to obtain an average lipidomic profile. Moreover, significant differences between tumors of different histological origin were observed. In-depth investigation of the glioma samples revealed that malignancy grade and isocitrate dehydrogenase (IDH) mutation status impact the lipidomic composition of the tumor, whereas 1p/19q co-deletion did not appear to alter the lipid profile. This first on-site lipidomic analysis of intact tumors proved that chemical biopsy with SPME is a promising tool for the simple and fast extraction of lipid markers in neurooncology.     

Maximum vertex occupation time and inert fugitive: Recontamination does help

Given a simple graph G, we consider the node search problem with inert fugitive. We are interested in minimizing the maximum vertex occupation time, i.e. the maximum number of steps in which a vertex is occupied by a searcher during a search of G. We prove that a search program which does not allow a recontamination may not find an optimal solution to this problem. Moreover, the difference between the minimum maximum vertex occupation time computed by a monotone search program and a program without such a restriction may be arbitrarily large.     

The influence of protein–flavonoid interactions on protein digestibility in vitro and the antioxidant quality of breads enriched with onion skin

Different types of breads enriched with onion skin were studied. The objectives were twofold: to show and examine protein–phenolic interactions and to discuss results concerning phenolic content, antioxidant activity and protein digestibility in the light of in vitro bioaccessibility. Phenolic contents and antiradical abilities were linked with the level of onion skin supplement however, the amounts determined were significantly lower than expected. Fortification influenced protein digestibility (a reduction from 78.4% for control breads to 55% for breads with a 4% supplement). Electrophoretic and chromatographic studies showed the presence of indigestible protein–flavonoid complexes – with molecular weights about 25 kDa and 14.5 kDa; however, the reduction of free amino group levels and the increase in chromatogram areas suggest that flavonoids also bind to other bread proteins. The interaction of phenolics with proteins affects antioxidant efficacy and protein digestibility; thus, they have multiple effects on food quality and pro-health properties.     

Behaviour of Dietary Fibre Supplements During Bread Dough Development Evaluated Using Novel Farinograph Curve Analysis

A regression model composed of two sigmoid functions with variable asymptotes was developed and used to analyse the dietary fibre supplement behaviour during bread dough mixing. Using eight commercial dietary fibres of different botanical origin and model wheat starch-gluten flour, farinograph curves for fibre-flour blends and for the flour only were performed. After smoothing of the curves with the regression model, difference farinograms as the fibre supplementation effects were determined. The results showed that the difference farinograms had two peaks, whose shape was strongly differentiated by the studied supplements. The presence of both peaks allowed distinguishing two kinds of the rheological activity of each fibre supplement: weakening and strengthening of the consistency of bread dough during its development. The carrot, oat, cranberry, and cacao fibres exhibited dominance of strengthening over weakening action. While chokeberry, carob, apple, and flax fibres were characterised by dominance of weakening over strengthening action. The analysis of both position and height of the peaks in the difference farinogram can be also helpful for determination of hydration kinetics of the fibres used for bread supplementation.     

Optimal sensor placement for joint parameter and state estimation problems in large-scale dynamical systems with applications to thermo-mechanics

We consider large-scale dynamical systems in which both the initial state and some parameters are unknown. These unknown quantities must be estimated from partial state observations over a time window. A data assimilation framework is applied for this purpose. Specifically, we focus on large-scale linear systems with multiplicative parameter-state coupling as they arise in the discretization of parametric linear time-dependent partial differential equations. Another feature of our work is the presence of a quantity of interest different from the unknown parameters, which is to be estimated based on the available data. In this setting, we employ a simplicial decomposition algorithm for an optimal sensor placement and set forth formulae for the efficient evaluation of all required quantities. As a guiding example, we consider a thermo-mechanical PDE system with the temperature constituting the system state and the induced displacement at a certain reference point as the quantity of interest.     

Node discovery in networks

This paper abstracts the problem of network nodes discovering one another in a network of unknown size using all-to-all gossip. The problem is studied in terms of evolving directed graphs where each vertex represents a participating node and each edge represents one node’s knowledge about another. Ideally, such a graph has diameter one, i.e., each node knows all others. Nodes share their knowledge by sending gossip messages. Gossip among the nodes allows them to discover one another, decreasing the diameter of the graph. Here this problem is considered in several synchronous settings under different assumptions about the ability of the participating nodes to communicate. Specifically, the following aspects of communication are considered: (1) the ability of the nodes to multicast gossip messages, and (2) the size of the messages. The results describe the lower and upper bounds on the number of synchronous rounds required for the participants to discover each other. A particular question of interest is: if the network size is unknown, how does a node know that it has discovered all other nodes? Given a weakly-connected graph describing the initial knowledge of the nodes, every node in our algorithm can stop the discovery process knowing that there are no unknown nodes—this is done without any prior knowledge of the total number of nodes participating in the computation.     

New insights into the mechanism of H2 generation through NaBH4 hydrolysis on Co-based nanocatalysts studied by differential reaction calorimetry

To our knowledge, the present study is the first investigation by liquid-phase calorimetry of the mechanism of hydrogen generation by hydrolysis of sodium borohydride catalyzed by Co₂B nanoparticles generated in situ. The differential reaction calorimeter was coupled with a volumetric hydrogen measurement, allowing a simultaneous thermodynamic and kinetic study of the reaction. At the end of the reaction, the catalyst was characterized ex situ by TEM, XRD, magnetism, N₂ adsorption, TGA–DTA, and the liquid hydrolysis products were analyzed by Wet-STEM and ¹¹B-NMR. The in situ preparation method made it possible to form nanoparticles (<12 nm) of Co₂B which are the active phase for the hydrolysis reaction. In semi-batch conditions, the Co₂B catalyst formed in situ is subsequently reduced by each borohydride addition and oxidized at the end of the hydrolysis reaction by OH⁻ in the presence of metaborate. A coating of the nanoparticles has been observed by calorimetry and physico-chemical characterization, corresponding to the formation of a 2–3 nm layer of cobalt oxide or hydroxide species.