Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions

This work was supported in part by the European Union, Area NMP.2013.1.1–2: Self-assembly of naturally occurring nanosystems: CellulosomePlus Project number: 604530, and by the EU Seventh Framework Programme (FP7 2007–2013) under the WallTraC project (Grant Agreement no 263916), and BioStruct-X (grant agreement no 283570). This paper reflects the author’s views only. The European Community is not liable for any use that may be made of the information contained herein. CMGAF is also supported by Fundação para a Ciência e a Tecnologia (Lisbon, Portugal) through grants PTDC/BIA-PRO/103980/2008 and EXPL/BIA-MIC/1176/2012. EAB is also funded by a grant (No. 1349/13) from the Israel Science Foundation (ISF), Jerusalem, Israel and by a grant (No. 2013284) from the U.S.-Israel Binational Science Foundation (BSF). E.A.B. is the incumbent of The Maynard I. and Elaine Wishner Chair of Bio-organic Chemistry.Peer reviewedPublisher PD

Interaction Gardens and Butterfly Catalogues: a Joint Strategy to Promote Capacity Development in Protected Areas and Reduce the Extinction of Experience in Cities

More than half of the world’s population live in cities. Increasing numbers of generations are now born and raised in urban landscapes with decreasing opportunities towards interacting with natural environments. This extinction of experience leads to environmental apathy and lack of bioliteracy, which is a central aspect to be tackled in conservation strategies. At the same time, people who live near or at non-urban settings are closer to natural habitats but do not have similar access to concepts of environmentalism and may lack incentives to lean towards nature conservation, instead of its exploitation or even illegal activities. We here propose that interaction gardens, that is, gardens with multiple trophic levels (primary producers, herbivores, predators, and parasitoids), can tackle these issues, especially if planned with incentives, such as butterfly catalogues, aimed as a common goal of the garden community. It can also bring benefits to human health and well-being, increase the survival chances of local biodiversity, and strengthen the front line of conservation by promoting income strategies to people who live near protected areas. Our specific aims are to 1) share a case study of capacity development at the Intervales State Park in the Atlantic Forest, Southeast Brazil; 2) present the butterfly catalogue of this protected area; 3) present guidelines for interaction gardens at both urban and non-urban settings; and 4) discuss alternative perspectives about Neotropical conservation. We provide a translated version of the text in Portuguese to encourage students, educators, NGOs and local communities of other protected areas to venture in our proposed joint strategy of interaction gardens with butterfly catalogues

ALTERAÇÃO DE PARÂMETROS RELACIONADOS AO RISCO CARDIOVASCULAR EM ADOLESCENTES OBESOS

Introdução: A obesidade juvenil é considerada um problema de saúde pública e o aumento de sobrepeso e obesidade nesta fase está associado a complicações metabólicas e cardiovasculares na idade adulta1. Objetivo: Identificar alterações nos parâmetros antropométricos e bioquímicas em adolescentes obesos. Metodologia: Adolescentes (14-18 anos), de ambos os sexos, matriculados em escolas de Ensino Médio de Barra do Garças – MT foram divididos em grupos experimentais de acordo com o Índice de Massa corporal (IMC): eutróficos (IMC ˃18 e ˂25) e obesos (IMC˂25)2. O IMC, circunferência abdominal, porcentagem de gordura corporal, pressão arterial, dosagens de colesterol total, triglicérides e glicemia foram avaliados em ambos grupos. Diferenças estatísticas foram calculadas através do teste T Student, (p˂0,05). Resultados e discussões: Foram avaliados 89 adolescentes, sendo 74 eutróficos e 15 obesos. Os adolescentes obesos apresentaram aumento dos valores de pressão sistólica [(mmHg) 126 ± 3,7 vs. 116±1,7], circunferência abdominal [(cm) 87± 1,9 vs. 72 ± 0,6], porcentagem de gordura corporal [(%) 27±1,8 vs. 18 ± 0,7], IMC (27,1±0,7 vs. 21.0±0,2), quando comparados ao grupo eutrófico. Adicionalmente, os adolescentes obesos apresentaram aumento nos índices de colesterol total [(mg/dL) 160 ± 7,4 vs. 140 ± 3,8], triglicérides [(mg/dL) 106,6±14,4 vs. 64,0±3,8], se comparados ao grupo eutrófico. Tanto a pressão diastólica quanto os níveis glicêmicos não apresentaram alteração entre os grupos. Conclusões: As alterações de parâmetros antropométricos e bioquímicos observados em adolescentes obesos demonstram que fatores de risco para doenças cardiovasculares estão alterados nessa população jovem, favorecendo o surgimento precoce de doenças crônicas como Diabetes Mellitus e da hipertensão arterial

Structure-function studies can improve binding affinity of cohesin-dockerin interactions for multi-protein assemblies

the Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS) grant LA/P/0059/2020. LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy - i4HB. National Institutes of Health R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases. Publisher Copyright: © 2022 The Author(s)The cellulosome is an elaborate multi-enzyme structure secreted by many anaerobic microorganisms for the efficient degradation of lignocellulosic substrates. It is composed of multiple catalytic and non-catalytic components that are assembled through high-affinity protein-protein interactions between the enzyme-borne dockerin (Doc) modules and the repeated cohesin (Coh) modules present in primary scaffoldins. In some cellulosomes, primary scaffoldins can interact with adaptor and cell-anchoring scaffoldins to create structures of increasing complexity. The cellulosomal system of the ruminal bacterium, Ruminococcus flavefaciens, is one of the most intricate described to date. An unprecedent number of different Doc specificities results in an elaborate architecture, assembled exclusively through single-binding-mode type-III Coh-Doc interactions. However, a set of type-III Docs exhibits certain features associated with the classic dual-binding mode Coh-Doc interaction. Here, the structure of the adaptor scaffoldin-borne ScaH Doc in complex with the Coh from anchoring scaffoldin ScaE is described. This complex, unlike previously described type-III interactions in R. flavefaciens, was found to interact in a dual-binding mode. The key residues determining Coh recognition were also identified. This information was used to perform structure-informed protein engineering to change the electrostatic profile of the binding surface and to improve the affinity between the two modules. The results show that the nature of the residues in the ligand-binding surface plays a major role in Coh recognition and that Coh-Doc affinity can be manipulated through rational design, a key feature for the creation of designer cellulosomes or other affinity-based technologies using tailored Coh-Doc interactions.publishersversionepub_ahead_of_prin

A dual cohesin-dockerin complex binding mode in Bacteroides cellulosolvens contributes to the size and complexity of its cellulosome

The Cellulosome is an intricate macromolecular protein complex that centralizes the cellulolytic efforts of many anaerobic microorganisms through the promotion of enzyme synergy and protein stability. The assembly of numerous carbohydrate processing enzymes into a macromolecular multiprotein structure results from the interaction of enzyme-borne dockerin modules with repeated cohesin modules present in noncatalytic scaffold proteins, termed scaffoldins. Cohesin- dockerin (Coh-Doc) modules are typically classified into different types, depending on structural conformation and cellulosome role. Thus, type I Coh-Doc complexes are usually responsible for enzyme integration into the cellulosome, while type II Coh-Doc complexes tether the cellulosome to the bacterial wall. In contrast to other known cellulosomes, cohesin types from Bacteroides cellulosolvens, a cellulosome-producing bacterium capable of utilizing cellulose and cellobiose as carbon sources, are reversed for all scaffoldins, i.e., the type II cohesins are located on the enzyme-integrating primary scaffoldin, whereas the type I cohesins are located on the anchoring scaffoldins. It has been previously shown that type I B. cellulosolvens interactions possess a dual-binding mode that adds flexibility to scaffoldin assembly. Herein, we report the structural mechanism of enzyme recruitment into B. cellulosolvens cellulosome and the identification of the molecular determinants of its type II cohesin-dockerin interactions. The results indicate that, unlike other type II complexes, these possess a dual-binding mode of interaction, akin to type I complexes. Therefore, the plasticity of dualbinding mode interactions seems to play a pivotal role in the assembly of B. cellulosolvens cellulosome, which is consistent with its unmatched complexity and size.publishersversionpublishe

Inflammation and adipose tissue: effects of progressive load training in rats

<p>Abstract</p> <p>Introduction</p> <p>Cytokines (IL-6, IL-10 and TNF-α) are increased after exhaustive exercise in the rat retroperitoneal (RPAT) and mesenteric adipose tissue (MEAT) pads. On the other hand, these cytokines show decreased expression in these depots in response to a chronic exercise protocol. However, the effect of exercise with overload combined with a short recovery period on pro- and anti-inflammatory cytokine expression is unknown. In the present study, we investigated the regulation of cytokine production in the adipose tissue of rats after an overtraining-inducing exercise protocol.</p> <p>Methods</p> <p>Male Wistar rats were divided into four groups: Control (C), Trained (Tr), Overtrained (OT) and recovered overtrained (R). Cytokines (IL-6, TNF-α and IL-10) levels and Toll Like Receptor 4 (TLR4), Nuclear Factor kBp65 (NF-kBp65), Hormone Sensitive Lipase (HSL) and, Perilipin protein expression were assessed in the adipose tissue. Furthermore, we analysed plasma lipid profile, insulin, testosterone, corticosterone and endotoxin levels, and liver triacylglycerol, cytokine content, as well as apolipoprotein B (apoB) and TLR4 expression in the liver.</p> <p>Results</p> <p>OT and R groups exhibited reduced performance accompanied by lower testosterone and increased corticosterone and endotoxin levels when compared with the control and trained groups. IL-6 and IL-10 protein levels were increased in the adipose tissue of the group allowed to recover, in comparison with all the other studied groups. TLR-4 and NF-kBp65 were increased in this same group when compared with both control and trained groups. The protein expression of HSL was increased and that of Perilipin, decreased in the adipose in R in relation to the control. In addition, we found increased liver and serum TAG, along with reduced apoB protein expression and IL-6 and IL-10 levels in the of R in relation to the control and trained groups.</p> <p>Conclusion</p> <p>In conclusion, we have shown that increases in pro-inflammatory cytokines in the adipose tissue after an overtraining protocol may be mediated via TLR-4 and NF-kBp65 signalling, leading to an inflammatory state in this tissue.</p

Implementation and first results of the KM3NeT real-time core-collapse supernova neutrino search

The KM3NeT research infrastructure is unconstruction in the Mediterranean Sea. KM3NeT will study atmospheric and astrophysical neutrinos with two multi-purpose neutrino detectors, ARCA and ORCA, primarily aimed at GeV–PeV neutrinos. Thanks to the multi-photomultiplier tube design of the digital optical modules, KM3NeT is capable of detecting the neutrino burst from a Galactic or near-Galactic core-collapse supernova. This potential is already exploitable with the first detection units deployed in the sea. This paper describes the real-time implementation of the supernova neutrino search, operating on the two KM3NeT detectors since the first months of 2019. A quasi-online astronomy analysis is introduced to study the time profile of the detected neutrinos for especially significant events. The mechanism of generation and distribution of alerts, as well as the integration into the SNEWS and SNEWS 2.0 global alert systems, are described. The approach for the follow-up of external alerts with a search for a neutrino excess in the archival data is defined. Finally, an overview of the current detector capabilities and a report after the first two years of operation are given.Acknowledgements The authors acknowledge the financial support of the funding agencies: Agence Nationale de la Recherche (contract ANR-15-CE31-0020), Centre National de la Recherche Scientifique (CNRS), Commission Européenne (FEDER fund and Marie Curie Program), Institut Universitaire de France (IUF), LabEx UnivEarthS (ANR-10-LABX-0023 and ANR-18-IDEX-0001), Paris Île-de-France Region, France; Shota Rustaveli National Science Foundation of Georgia (SRNSFG, FR-18-1268), Georgia; Deutsche Forschungsgemeinschaft (DFG), Germany; The General Secretariat of Research and Technology (GSRT), Greece; Istituto Nazionale di Fisica Nucleare (INFN), Ministero dell’Università e della Ricerca (MIUR), PRIN 2017 program (Grant NAT-NET 2017W4HA7S) Italy; Ministry of Higher Education Scientific Research and Professional Training, ICTP through Grant AF-13, Morocco; Nederlandse organisatie voor Wetenschappelijk Onderzoek (NWO), the Netherlands; The National Science Centre, Poland (2015/18/E/ST2/00758); National Authority for Scientific Research (ANCS), Romania; Ministerio de Ciencia, Innovación, Investigación y Universidades (MCIU): Programa Estatal de Generación de Conocimiento (refs. PGC2018-096663-B-C41, -A-C42, -B-C43, -B-C44) (MCIU/FEDER), Generalitat Valenciana: Prometeo (PROMETEO/2020/019), Grisolía (ref. GRISOLIA/2018/119) and GenT (refs. CIDEGENT/2018/034, /2019/043, /2020/049) programs, Junta de Andalucía (ref. A-FQM-053-UGR18), La Caixa Foundation (ref. LCF/BQ/IN17/11620019), EU: MSC program (ref. 101025085), Spain

Spectrochemical analysis in blood plasma combined with subsequent chemometrics for fibromyalgia detection

Fibromyalgia is a rheumatologic condition characterized by multiple and chronic body pain, and other typical symptoms such as intense fatigue, anxiety and depression. It is a very complex disease where treatment is often made by non-medicated alternatives in order to alleviate symptoms and improve the patient’s quality of life. Herein, we propose a method to detect patients with fibromyalgia (n = 252, 126 controls and 126 patients with fibromyalgia) through the analysis of their blood plasma using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy in conjunction with chemometric techniques, hence, providing a low-cost, fast and accurate diagnostic approach. Different chemometric algorithms were tested to classify the spectral data; genetic algorithm with linear discriminant analysis (GA-LDA) achieved the best diagnostic results with a sensitivity of 89.5% in an external test set. The GA-LDA model identified 24 spectral wavenumbers responsible for class separation; amongst these, the Amide II (1,545 cm−1) and proteins (1,425 cm−1) were identified to be discriminant features. These results reinforce the potential of ATR-FTIR spectroscopy with multivariate analysis as a new tool to screen and detect patients with fibromyalgia in a fast, low-cost, non-destructive and minimally invasive fashion