Bacillus extracellular matrix modulates Botrytis metabolism and growth

In nature, bacteria often form communities known as biofilms, where cells are embedded in a self-produced extracellular matrix (ECM) that provides protection against external aggressions or facilitates efficient use of resources. Interactions with other microbes can significantly alter the structure of the community and thus the type of relationship with the environment. Here, we study the role of different components of Bacillus ECM in the adhesion to Botrytis hyphae, which could facilitate the efficient release of antifungal metabolites. We also describe how the different purified components of the ECM and certain Bacillus secondary metabolites (TasA, TapA, EPS, Fengycin) modulate the chemical communication between Bacillus and Botrytis, altering the physiology and ultrastructure of Botrytis.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Deletion of transketolase triggers a stringent metabolic response in promastigotes and loss of virulence in amastigotes of Leishmania mexicana

Transketolase (TKT) is part of the non-oxidative branch of the pentose phosphate pathway (PPP). Here we describe the impact of removing this enzyme from the pathogenic protozoan Leishmania mexicana. Whereas the deletion had no obvious effect on cultured promastigote forms of the parasite, the Δtkt cells were not infective to mice. Δtkt promastigotes were more susceptible to oxidative stress and various leishmanicidal drugs than wild-type, and metabolomics analysis revealed profound changes to metabolism in these cells. In addition to changes consistent with those directly related to the role of TKT in the PPP, central carbon metabolism was substantially decreased, the cells consumed significantly less glucose, flux through glycolysis diminished, and production of the main end products of metabolism was decreased. Only minor changes in RNA abundance from genes encoding enzymes in central carbon metabolism, however, were detected although fructose-1,6-bisphosphate aldolase activity was decreased two-fold in the knock-out cell line. We also showed that the dual localisation of TKT between cytosol and glycosomes is determined by the C-terminus of the enzyme and by engineering different variants of the enzyme we could alter its sub-cellular localisation. However, no effect on the overall flux of glucose was noted irrespective of whether the enzyme was found uniquely in either compartment, or in both

Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters

Members of the candidate phylum Hyd24-12 are globally distributed, but no genomic information or knowledge about their morphology, physiology or ecology is available. In this study, members of the Hyd24-12 lineage were shown to be present and abundant in full-scale mesophilic anaerobic digesters at Danish wastewater treatment facilities. In some samples, a member of the Hyd24-12 lineage was one of the most abundant genus-level bacterial taxa, accounting for up to 8% of the bacterial biomass. Three closely related and near-complete genomes were retrieved using metagenome sequencing of full-scale anaerobic digesters. Genome annotation and metabolic reconstruction showed that they are Gram-negative bacteria likely involved in acidogenesis, producing acetate and hydrogen from fermentation of sugars, and may play a role in the cycling of sulphur in the digesters. Fluorescence in situ hybridization revealed single rod-shaped cells dispersed within the flocs. The genomic information forms a foundation for a more detailed understanding of their role in anaerobic digestion and provides the first insight into a hitherto undescribed branch in the tree of life

A Systems Biology Approach Identifies Molecular Networks Defining Skeletal Muscle Abnormalities in Chronic Obstructive Pulmonary Disease

Chronic Obstructive Pulmonary Disease (COPD) is an inflammatory process of the lung inducing persistent airflow limitation. Extensive systemic effects, such as skeletal muscle dysfunction, often characterize these patients and severely limit life expectancy. Despite considerable research efforts, the molecular basis of muscle degeneration in COPD is still a matter of intense debate. In this study, we have applied a network biology approach to model the relationship between muscle molecular and physiological response to training and systemic inflammatory mediators. Our model shows that failure to co-ordinately activate expression of several tissue remodelling and bioenergetics pathways is a specific landmark of COPD diseased muscles. Our findings also suggest that this phenomenon may be linked to an abnormal expression of a number of histone modifiers, which we discovered correlate with oxygen utilization. These observations raised the interesting possibility that cell hypoxia may be a key factor driving skeletal muscle degeneration in COPD patients

Engraulis encrasicolus larvae from two different environmental spawning areas of the Central Mediterranean Sea: first data on amino acid profiles and biochemical evaluations

Early life stages of marine fish populations may be strongly affected by environmental factors. Changes in the physical environment or the availability of food resources could lead to stress-related physiological responses affecting larval fitness, growth and survival. In the present study, we determined, for the first time, amino acid composition (AAC), lipid, and carbohydrate content, as well as alkaline phosphatase and peroxidase activities in larvae from the European anchovy Engraulis encrasicolus. Fishes were caught in two different spawning areas of the Strait of Sicily, characterized by different environmental conditions, including a coastal upwelling with a lower temperature (Adventure Bank; 20.22 ± 0.38°C) and a thermohaline front with a higher temperature (Maltese Bank 23.10 ± 0.25°C). The results showed that the two groups of larvae, in their early life, had similar nutritional status. However, compared with the samples from the Maltese Bank, the specimens collected in the Adventure Bank area exhibited higher alkaline phosphatase activity, lower concentrations of aspartate plus asparagine, threonine, and arginine but a higher concentration of leucine, highlighting different patterns of amino acid metabolism. Collectively, these results indicated that AAC analysis could represent an additional valid tool to evaluate the link between physiological responses and environmental conditions at early life stages

Evaluation of Data Dependent MS/MS Acquisition Parameters for Non-targeted Metabolomics and Molecular Networking of Environmental Samples - Focus on the Q Exactive Platform

Non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) is a widely used tool for the detection and annotation of small molecules in complex environmental samples. Data Dependent Acquisition (DDA) of product ion spectra is thereby currently one of the most frequently applied data acquisition strategies. The optimization of DDA parameters is central to ensuring high spectral quality, coverage and number of compound annotations. Here, we evaluated the influence of 10 central DDA settings of the Q Exactive mass spectrometer on natural organic matter samples from ocean, river, and soil environments. After data analysis with Classical and Feature-based Molecular Networking using MZmine and GNPS, we compared the total number of network nodes, multivariate clustering, and spectrum quality related metrics such as annotation and singleton rates, MS/MS placement and coverage. Our results show that Automatic Gain Control, Microscans, Mass Resolution, and Dynamic Exclusion are the most critical parameters, whereas Collision Energy, TopN, and Isolation Width had moderate and Apex Trigger, Monoisotopic Selection, and Isotopic Exclusion minor effects. The insights into the data acquisition ergonomics of the Orbitrap platform presented here can guide new users and provide them with initial method parameters, some of which may also be transferable to other sample types and MS platforms

Protocolli di pretrattamento sul prodotto agroalimentare fresco o minimamente processato e individuazione del processo ottimale

L’obiettivo di questo studio è la messa a punto dei protocolli di conservazione per le diverse tipologie di prodotti ittici mediante lo studio delle variazioni del profilo nutrizionale di questi ultimi forniti in relazione al tipo di trattamento subito nell’immediato post raccolta con lo scopo di acquisire informazioni utili sul prolungamento della shelf life del prodotto