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Relationship between Fusobacterium nucleatum,inflammatory mediators and microRNAs in colorectal carcinogenesis

World Journal of Gastroenterology 2018年第47期24卷 5351-5365页

作者： Marcela Alcantara Proenca Joice Matos Biselli maysa succi Fábio Eduardo Severino Gustavo Noriz Berardinelli Alaor Caetano Rui Manuel Reis David J Hughes Ana Elizabete Silva Department of Biology UNESPUniv. Estadual PaulistaCampus of Sao Jose do Rio PretoSao Jose do Rio PretoSao Paulo 15054-000Brazil Department of Surgery and Orthopedics Faculty of MedicineUNESPUniv. Estadual PaulistaCampus of BotucatuBotucatuSao Paulo 18618-687Brazil Endoscopy Center of Rio Preto Sao Jose do Rio PretoSao Paulo 15015-700Brazil Molecular Oncology Research Center Barretos Cancer HospitalBarretosSao Paulo 14784-400Brazil Life and Health Sciences Research Institute University of MinhoCampus GualtarBraga 4710-057Portugal ICVS/3B’s-PT Government Associate Laboratory Campus GualtarBraga 4710-057Portugal Cancer Biology and Therapeutics Group UCD Conway InstituteUniversity College DublinDublin D04 V1W8Ireland

AIM To examine the effect of Fusobacterium nucleatum(F. nucleatum) on the microenvironment of colonic neoplasms and the expression of inflammatory mediators and microRNAs(miRNAs).METHODS Levels of F. nucleatum DNA, cytokine gene mRNA(TLR2, TLR4, NFKB1, TNF, IL1 B, IL6 and IL8), and potentially interacting miRNAs(miR-21-3p, miR-22-3p, mi R-28-5p, miR-34a-5p, miR-135b-5p) were measured by quantitative polymerase chain reaction(qPCR) TaqMan? assays in DNA and/or RNA extracted from the disease and adjacent normal fresh tissues of 27 colorectal adenoma(CRA) and 43 colorectal cancer(CRC) patients. KRAS mutations were detected by direct sequencing and microsatellite instability(MSI) status by multiplex PCR. Cytoscape v3.1.1 was used to construct the postulated miRNA:mRNA interaction *** Overabundance of F. nucleatum in neoplastic tissue compared to matched normal tissue was detected in CRA(51.8%) and more markedly in CRC(72.1%). We observed significantly greater expression of TLR4, IL1 B, IL8, and miR-135 b in CRA lesions and TLR2, IL1 B, IL6, IL8, mi R-34 a and miR-135 b in CRC tumours compared to their respective normal tissues. Only two transcripts for miR-22 and miR-28 were exclusively downregulated in CRC tumour samples. The mRNA expression of IL1 B, IL6, IL8 and miR-22 was positively correlated with F. nucleatum quantification in CRC tumours. The mRNA expression of miR-135 b and TNF was inversely correlated. The miRNA:mRNA interaction network suggested that the upregulation of miR-34 a in CRC proceeds via a TLR2/TLR4-dependent response to F. nucleatum. Finally, KRAS mutations were more frequently observed in CRC samples infected with F. nucleatum and were associated with greater expression of miR-21 in CRA, while IL8 was upregulated in MSI-high *** Our findings indicate that F. nucleatum is a risk factor for CRC by increasing the expression of inflammatory mediators through a possible mi RNA-mediated activation of TLR2/TLR4.

关键词： Colorectal cancer Colorectal adenoma Fusobacterium nucleatum Inflammation Cytokines MicroRNAs

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TLR2 and TLR4 polymorphisms influence m RNA and protein expression in colorectal cancer

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World Journal of Gastroenterology 2015年第25期21卷 7730-7741页

作者： Marcela Alcantara Proenca Juliana Garcia de Oliveira Aline Cristina Targa Cadamuro maysa succi Joao Gomes Netinho Eny Maria Goloni-Bertolo érika Cristina Pavarino Ana Elizabete Silva Department of Biology UNESPSao Paulo State University USC-Sacred Heart University PróReitoria de Pesquisa e Pós Graduacao Department of Surgery School of MedicineFAMERPSao Josédo Rio Preto 15090-000SPBrazil UPGEM School of MedicineFAMERPSao Josédo Rio Preto 15090-000SPBrazil

AIM: To evaluate the effect of promoter region polymorphisms of toll-like receptor(TLR)2-196 to-174 del and TLR4-1607T/C(rs10759932) on m RNA and protein expression in tumor tissue and of TLR4+896A/G(rs4986790) on colorectal cancer(CRC) ***: The TLR2-196 to-174 del polymorphism was investigated using allele-specific polymerase chain reaction(PCR) and the TLR4-1607T/C and TLR4+896A/G by PCR-restriction fragment length p o l y m o r p h i s m( R F L P). W e g e n o t y p e d 4 3 4 D N A samples from 194 CRC patients and 240 healthy individuals. The m RNA relative quantification(RQ) was performed in 40 tumor tissue samples by quantitative PCR Taq Man assay, using specific probes for TLR2 and TLR4 genes, and ACTB and GAPDH reference geneswere used as endogenous controls. Protein expression was analyzed by immunohistochemistry with specific primary ***: No association was found for TLR4-1607T/C and TLR4+896A/G by three statistical models(logadditive, dominant and recessive). However, based on dominant and log-additive models, the polymorphic variant TLR2-196 to-174 del was associated with increased CRC risk [dominant: odds ratio(OR) = 1.72, 95%CI: 1.03-2.89; P = 0.038 and log-additive: OR =1.59, 95%CI: 1.02-2.48; P = 0.039]. TLR2 m RNA expression was increased in tumor tissue(RQ = 2.36) when compared to adjacent normal tissue(RQ = 1; P < 0.0001), whereas the TLR4 m RNA showed a basal expression(RQ = 0.74 vs RQ = 1, P = 0.452). Immunohistochemistry analysis of TLR2 and TLR4 protein expression was concordant with the findings of m RNA expression. In addition, the TLR2-196 to-174 del variant carriers showed m RNA relative expression 2.19 times higher than wild-genotype carriers. The TLR2 protein expression was also higher for the TLR2-196 to-174 del variant carriers [117 ± 10 arbitrary unit(a.u.) vs 95 ± 4 a.u., P = 0.03]. However, for the TLR4-1607T/C polymorphism no significant difference was found for both m RNA(P = 0.56) and protein expression(P

关键词： Toll-like receptor 2 Toll-like receptor 4 Colorectal cancer Protein expression Gene expression Genetic polymorphisms

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The Quantum Lattice Boltzmann Equation:Recent Developments

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Communications in Computational Physics 2008年第10期4卷 980-1007页

作者： Silvia Palpacelli Sauro succi Dipartimento di Matematica Universit`a Roma TreLargo San Leonardo Murialdo 100146RomaItaly Istituto Applicazioni del Calcolo Viale Policlinico 13700161 RomaItaly

The derivation of the quantum lattice Boltzmann model is reviewed with special emphasis on recent developments of the model,namely,the extension to a multi-dimensional formulation and the application to the computation of the ground state of the Gross-Pitaevskii equation(GPE).Numerical results for the linear and nonlinear Schr odinger equation and for the ground state solution of the GPE are also presented and validated against analytical results or other classical schemes such as Crank-Nicholson.

关键词： Quantum lattice Boltzmann multi-dimensions imaginary-time model linear and non-linear Schrodinger equation adiabatic limit

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Prospective Merger Between Car-Parrinello and Lattice Boltzmann Methods for Quantum Many-Body Simulations

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Communications in Computational Physics 2011年第5期9卷 1137-1151页

作者： Sauro succi Silvia Palpacelli Istituto Applicazioni Calcolo CNRvia dei Taurini 1900185 RomaItaly Freiburg Institute for Advanced Studies Albert-Ludwigs-Universität Freiburg Albertstraβe 19D-79104 Freiburg i.Br.Germany Numidia s.r.l. via Berna 3100144 RomaItaly

Formal analogies between the Car-Parrinello(CP)ab-initio molecular dynamics for quantum many-body systems,and the Lattice Boltzmann(LB)method for classical and quantum fluids,are pointed out.A theoretical scenario,whereby the quantum LB would be coupled to the CP framework to speed-up many-body quantum simulations,is also discussed,together with accompanying considerations on the computational efficiency of the prospective CP-LB scheme.

关键词： Quantum many-body problems Car-Parrinello ab-initio molecular dynamics lattice Boltzmann method

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In memory of Steven Alan Orszag(1943-2011)

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Communications in Computational Physics 2013年第3期13卷 I0001-I0002页

作者： Sauro succi Istituto Applicazioni Calcolo CNRvia dei Taurini 900185RomaItaly

I first met Steve in his Fine Hall office in Princeton,back in *** many years he had been one my biggest heroes and I was obviously very excited,and a bit tense at the prospect of meeting him in *** day it all went perfectly smoothly,and so too was the case on the very many occasions we had the chance to meet again during the next twenty years,in Princeton,Boston,Yale,Maine,and occasionally Rome.

关键词： smoothly Boston office

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A Generalised Lattice Boltzmann Equation on Unstructured Grids

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Communications in Computational Physics 2008年第2期3卷 342-356页

作者： Stefano Ubertini Sauro succi Universit`a degli Studi di Roma “Tor Vergata”Dip.Ingegneria MeccanicaVia del Politecnico10133 RomaItalia Istituto Applicazioni del Calcolo CNR Via del Policlinico13700161 RomaItalia.

This paper presents a new finite-volume discretization of a generalised LatticeBoltzmann equation (LBE) on unstructured grids. This equation is the continuumLBE, with the addition of a second order time derivative term (memory), and is derivedfrom a second-order differential form of the semi-discrete Boltzmann equationin its implicit form. The new scheme, named unstructured lattice Boltzmann equationwith memory (ULBEM), can be advanced in time with a larger time-step than the previousunstructured LB formulations, and a theoretical demonstration of the improvedstability is provided. Taylor vortex simulations show that the viscosity is the same aswith standard ULBE and demonstrates that the new scheme improves both stabilityand accuracy. Model validation is also demonstrated by simulating backward-facingstep flow at low and moderate Reynolds numbers, as well as by comparing the reattachmentlength of the recirculating eddy behind the step against experimental andnumerical data available in literature.

关键词： Lattice Boltzmann equation finite-volumes unstructured grids memory term.

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Bjorken Flow Revisited:Analytic and Numerical Solutions in Flat Space-Time Coordinates

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Communications in Computational Physics 2023年第1期33卷 174-188页

作者： Daniele Simeoni Alessandro Gabbana Sauro succi Universit`a di Ferrara and INFN-Ferrara I-44122 FerraraItaly Bergische UniversitatWuppertal D-42119WuppertalGermany University of Cyprus Physics departmentCY-1678 NicosiaCyprus Eindhoven University of Technology 5600MB EindhovenThe Netherlands Center for Life Nano Science@La Sapienza Italian Institute of TechnologyViale Regina Elena 295I-00161 RomaItaly Istituto Applicazioni del Calcolo National Research Council of ItalyVia dei Taurini 19I-00185 RomaItaly

In this work we provide analytic and numerical solutions for the Bjorken flow,a standard benchmark in relativistic hydrodynamics providing a simple model for the bulk evolution of matter created in collisions between heavy *** consider relativistic gases of both massive and massless particles,working in a(2+1)and(3+1)Minkowski space-time coordinate *** numerical results from a recently developed lattice kinetic scheme show excellent agreement with the analytic solutions.

关键词： Relativistic hydrodynamics heavy-ion collisions Bjorken flow lattice kinetic solvers

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A New Boundary Condition for Three-Dimensional Lattice Boltzmann Simulations of Capillary Filling in Rough Micro-Channels

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Communications in Computational Physics 2011年第5期9卷 1284-1292页

作者： Alessandro De Maio Silvia Palpacelli Sauro succi Numidia s.r.l. via Berna 3100144 RomaItaly Istituto Applicazioni Calcolo CNRvia dei Taurini 1900185 RomaItaly Freiburg Institute for Advanced Studies School of Soft Matter ResearchAlbertstr.1979104 Freiburg im BreisgauFreiburgGermany

A new boundary condition,aimed at inhibiting near-wall condensation effects in lattice Boltzmann simulations of capillary flows in micro-corrugated channels,is *** new boundary condition is validated against analytical solutions for smooth channels and demonstrated for the case of three-dimensional microflows over randomly corrugated walls.

关键词： Microfluidics capillary flows lattice Boltzmann simulation

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Lattice Boltzmann Simulation of Cavitating Flows

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Communications in Computational Physics 2013年第3期13卷 685-695页

作者： Giacomo Falcucci Stefano Ubertini Gino Bella Sauro succi Department of Technologies University of Naples“Parthenope”Centro Direzionale-Isola C480143 NaplesItaly DEIM-Industrial Engineering School University of TusciaLargo dell’Universita s.n.c.01100ViterboItaly Department of Mechanical Engineering University of“Tor Vergata”Viale PolitecnicoRomeItaly Istituto per le Applicazioni del Calcolo-CNR Via dei Taurini00100 RomaItaly

The onset of cavitating conditions inside the nozzle of liquid injectors is known to play a major role on spray characteristics,especially on jet penetration and *** this work,we present a Direct Numerical Simulation(DNS)based on the Lattice Boltzmann Method(LBM)to study the fluid dynamic field inside the nozzle of a cavitating *** formation of the cavitating region is determined via a multi-phase approach based on the Shan-Chen equation of *** results obtained by the LBM simulation show satisfactory agreement with both numerical and experimental *** addition,numerical evidence of bubble break-up,following upon flow-induced cavitation,is also reported.

关键词： Lattice Boltzmann multiphase flows cavitation liquid spray nozzle

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Lattice Boltzmann Simulation of Mixed Convection Heat Transfer in a Driven Cavity with Non-uniform Heating of the Bottom Wall

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Communications in Theoretical Physics 2015年第1期63卷 91-100页

作者： Soufiene Bettaibi Ezeddine Sediki Frdric Kuznik Sauro succi UR: Rayonnement Thermique Facult des Sciences de Tunis Universit de Tunis El Manar 2092 Tunis Tunisia INSA-Lyon CETHIL F-69621 Villeurbanne France Universit de Lyon CNRS UMR5008 F-69622 Villeurbanne France Research Director IAC-CNR Rome Via dei Taurini 19 00185 Roma

The goal of this article is to study numerically the mixed convection in a differentially heated rid-driven cavity with non-uniform heating of the bottom wall. The velocity field is solved by a hybrid scheme with multiple relaxation time Lattice Boltzmann （MRT-LBM） model, while the temperature field is obtained by resolution of the energy balance equation using the finite difference method （FDM）. First, the model is checked and validated using data from the riterature. Validation of the present resuJts with those available in the literature shows a good agreement. A good efficiency in time simulation is confirmed. Thereafter, the model has been applied to mixed convection in a driven cavity with non-uniform heating wall at the fixed Grashof number Gr = 106. It is found that, the heat transfer is weakened as the Richardson number is augmented. For Gr = 106, we note the appearance of secondary vortices at different positions of the cavity corners.

关键词： lattice Boltzmann method (LBM) finite difference method (FDM) heated Lid-driven cavity mixed convection non-uniform heating wall

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