Correction: Population dynamics of a salmonella lytic phage and its host: implications of the host bacterial growth rate in modelling

Correction.The Fig 1 Figure Legend is incorrect. The authors have provided a corrected version here

Development of a predictive model for phage-bacteria interaction

The prevalence and impact of bacteriophages in the ecology of bacterial communities coupled with their ability to control pathogens turns essential to understand and predict the existing dynamics between phage and bacteria populations. The success of phage therapy is dependent on the knowledge of the phage replication kinetic properties in the presence of the host as well as on the prediction, controlling and optimization of phage production for future application. To achieve this knowledge it is important to develop mathematical models able to explain and simulate the population dynamics of phage and bacteria. We have developed a mathematical model using delay-differential equations to predict the interaction between a broad-host-range Salmonella phage and its pathogenic host. The model takes into consideration the main biological parameters that rule phagebacteria interactions likewise the latent period. burst size, bacterial growth rate, substrate uptake rate among others. The experimental validation of the model was performed in a bioreactor and it was found that the bacterial growth rate is critical to understand and predict the phage growth and bacterial control. By modelling the adsorption rate as a function of the bacterial growth rate it was possible to accurately predict the behaviour of the phage-bacteria population. The model generates data with a good agreement with the experimental observations and explains how a lytic phage and its host bacteria are able to coexist. Consequently, the model can be used to explain the structure of ecological communities of phages and bacteria and also to optimize phage production and guide the experimental studies of population dynamics by identifying and evaluating the relative contribution of phage and bacteria in the course and outcome of an infection

Identification of lignocellulose-degrading enzymes using metagenomic approaches

Composting units which handle lignocellulosic residues are suitable sources of novel and promising lignocellulose-degrading enzymes such as cellulases, xylanases and amylases. These enzymes have practical application in many industries where lignocellulose is converted into several added-value bioproducts. However, the effective conversion of lignocellulose by a sustainable process is currently incomplete. Therefore, there is a need to find novel and robust catalysts to overcome this fact. Function- and sequence-based metagenomic approaches were used to identify novel lignocellulose-degrading enzymes with interesting industrial applications.info:eu-repo/semantics/publishedVersio

A Rapidly Incremented Tethered-Swimming Maximal Protocol for Cardiorespiratory Assessment of Swimmers

Incremental exercise testing is the standard means of assessing cardiorespiratory capacity of endurance athletes. While the maximal rate of oxygen consumption is typically used as the criterion measurement in this regard, two metabolic breakpoints that reflect changes in the dynamics of lactate production/consumption as the work rate is increased are perhaps more relevant for endurance athletes from a functional standpoint. Exercise economy, which represents the rate of oxygen consumption relative to performance of submaximal work, is also an important parameter to measure for endurance-athlete assessment. Ramp incremental tests comprising a gradual but rapid increase in work rate until the limit of exercise tolerance is reached are useful for determining these parameters. This type of test is typically performed on a cycle ergometer or treadmill because there is a need for precision with respect to work-rate incrementation. However, athletes should be tested while performing the mode of exercise required for their sport. Consequently, swimmers are typically assessed during free-swimming incremental tests where such precision is difficult to achieve. We have recently suggested that stationary swimming against a load that is progressively increased (incremental tethered swimming) can serve as a "swim ergometer" by allowing sufficient precision to accommodate a gradual but rapid loading pattern that reveals the aforementioned metabolic breakpoints and exercise economy. However, the degree to which the peak rate of oxygen consumption achieved during such a protocol approximates the maximal rate that is measured during free swimming remains to be determined. In the present article, we explain how this rapidly incremented tethered-swimming protocol can be employed to assess the cardiorespiratory capacity of a swimmer. Specifically, we explain how assessment of a short-distance competitive swimmer using this protocol revealed that his rate of oxygen uptake was 30.3 and 34.8 mL∙min 1∙kg-1BM at his gas-exchange threshold and respiratory compensation point, respectively.info:eu-repo/semantics/publishedVersio

Covalent organic frameworks as catalyst support: A case study of thermal, hydrothermal, and mechanical pressure stability of β-ketoenamine-linked TpBD-Me2

Covalent organic frameworks (COFs) are crystalline, ordered networks, that, due to their high surface areas and the opportunity for periodic placement of catalytically active sites, are interesting materials for catalysis. Despite the great interest in the use of COFs for this application, there is currently a lack of fundamental understanding on how catalytically relevant conditions affect the integrity of the materials. To gain insight into the stability of COFs as catalyst supports, we herein subjected a β-ketoenamine-linked COF to thermal treatment at high temperatures, to autogenous pressure in water at different temperatures, and to mechanical pressure during pelletizing, after which the materials were thoroughly characterized to gain insight into the structural changes occurring during these catalytically relevant treatments. The COF was largely stable under all hydrothermal conditions studied, highlighting the applicability of β-ketoenamine-linked COFs under aqueous and vapor conditions. On the other hand, thermal and pressure treatments led to a rapid decline in the surface area already at the lowest temperatures and pressures studied. Theoretical calculations indicated this loss to stem from interlayer rearrangement or buckling of the COF layers induced by the applied conditions. This study demonstrates the suitability of β-ketoenamine-linked COFs for use under hydrothermal conditions, and sheds light on the degradation pathways under thermal and pressure treatments, opening the path to the design of COFs with increased stability under such conditions.Fundação para a Ciência e a Tecnologia | Ref. UTA-EXPL/NPN/0055/2019Fundação para a Ciência e a Tecnologia | Ref. PTDC/QUI-OUT/2095/2021Fundação para a Ciência e a Tecnologia | Ref. PTDC/EQU-EQU/1707/2020Agencia Estatal de Investigación | Ref. RYC2020-030414-IUniversidade de Vigo/CISU

Microglia dysfunction caused by the loss of Rhoa disrupts neuronal physiology and leads to neurodegeneration

© 2020 The Author(s). Creative Commons Attribution (CC BY 4.0)Nervous tissue homeostasis requires the regulation of microglia activity. Using conditional gene targeting in mice, we demonstrate that genetic ablation of the small GTPase Rhoa in adult microglia is sufficient to trigger spontaneous microglia activation, producing a neurological phenotype (including synapse and neuron loss, impairment of long-term potentiation [LTP], formation of β-amyloid plaques, and memory deficits). Mechanistically, loss of Rhoa in microglia triggers Src activation and Src-mediated tumor necrosis factor (TNF) production, leading to excitotoxic glutamate secretion. Inhibiting Src in microglia Rhoa-deficient mice attenuates microglia dysregulation and the ensuing neurological phenotype. We also find that the Rhoa/Src signaling pathway is disrupted in microglia of the APP/PS1 mouse model of Alzheimer disease and that low doses of Aβ oligomers trigger microglia neurotoxic polarization through the disruption of Rhoa-to-Src signaling. Overall, our results indicate that disturbing Rho GTPase signaling in microglia can directly cause neurodegeneration.The authors acknowledge the support of the following i3S Scientific Platforms: Animal Facility, Translational Cytometry Unit (TraCy), BioSciences Screening (BS) and Advanced Light Microscopy (ALM), and members of the national infrastructure PPBI-Portuguese Platform of BioImaging (supported by POCI-01–0145-FEDER-022122). FCT Portugal ( PTDC/MED-NEU/31318/2017-031318 ) supported work in the J.B.R. lab. FCT Portugal , PEst ( UID/NEU/04539/2013 ), COMPETE-FEDER ( POCI-01-0145-FEDER-007440 ), Centro 2020 Regional Operational Programme ( CENTRO-01-0145-FEDER-000008 : BrainHealth 2020), and Strategic Project UIDB/04539/2020 and UIDP/04539/2020 (CIBB) supported work in the A.F.A. lab. C.C.P. and R.S. hold employment contracts financed by national funds through FCT (Fundação para a Ciência e a Tecnologia, I.P.) in the context of the program contract described in paragraphs 4, 5, and 6 of article 23 of law no. 57/2016, of August 29th, as amended by law no. 57/2017 of July 19th.info:eu-repo/semantics/publishedVersio

Chromosome copy number changes carry prognostic information independent of KIT/PDGFRA point mutations in gastrointestinal stromal tumors

<p>Abstract</p> <p>Background</p> <p>Oncogenic point mutations in <it>KIT </it>or <it>PDGFRA </it>are recognized as the primary events responsible for the pathogenesis of most gastrointestinal stromal tumors (GIST), but additional genomic alterations are frequent and presumably required for tumor progression. The relative contribution of such alterations for the biology and clinical behavior of GIST, however, remains elusive.</p> <p>Methods</p> <p>In the present study, somatic mutations in <it>KIT </it>and <it>PDGFRA </it>were evaluated by direct sequencing analysis in a consecutive series of 80 GIST patients. For a subset of 29 tumors, comparative genomic hybridization was additionally used to screen for chromosome copy number aberrations. Genotype and genomic findings were cross-tabulated and compared with available clinical and follow-up data.</p> <p>Results</p> <p>We report an overall mutation frequency of 87.5%, with 76.25% of the tumors showing alterations in <it>KIT </it>and 11.25% in <it>PDGFRA</it>. Secondary <it>KIT </it>mutations were additionally found in two of four samples obtained after imatinib treatment. Chromosomal imbalances were detected in 25 out of 29 tumors (86%), namely losses at 14q (88% of abnormal cases), 22q (44%), 1p (44%), and 15q (36%), and gains at 1q (16%) and 12q (20%). In addition to clinico-pathological high-risk groups, patients with <it>KIT </it>mutations, genomic complexity, genomic gains and deletions at either 1p or 22q showed a significantly shorter disease-free survival. Furthermore, genomic complexity was the best predictor of disease progression in multivariate analysis.</p> <p>Conclusions</p> <p>In addition to <it>KIT/PDGFRA </it>mutational status, our findings indicate that secondary chromosomal changes contribute significantly to tumor development and progression of GIST and that genomic complexity carries independent prognostic value that complements clinico-pathological and genotype information.</p