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In silico analysis of lncRNA-miRNA-mRNA signatures related to Sorafenib effectiveness in liver cancer cells

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World Journal of Gastroenterology 2025年第3期31卷 84-102页

作者： Patricia de la cruz-Ojeda ester Parras-Martínez Raquel Rey-Pérez Jordi Muntané Functional Genomics of Solid Tumors laboratory Centre de Recherche des CordeliersParis 75006France department of Oncology Surgery Cell Therapy and Organ TransplantationInstitute of Biomedicine of SevilleVirgen del Rocio University HospitalSeville 41013Spain biomedical Research Center for Hepatic and Digestive Diseases CIBERehdMadrid 28029Spain department of Medical Physiology and biophysics University of SevilleSeville 41009Spain

bACKGROUND Hepatocellular carcinoma(HCC)is the most common subtype of primary liver cancer with varied incidence and epidemiology *** is still a recomme.ded treatment for a large proportion of patients with advanced *** patterns of treatment responsiveness have been identified in differentiated hepatoblastoma HepG2 cells and metastatic HCC SNU449 *** To define the long non-codingRNA-microRNA-mRNA(lncRNA-miRNA-mRNA)predicted signatures related to selected hallmarks of cancer(apoptosis,autophagy,cell stress,cell dedifferentiation and invasiveness)in RNAseq studies using Sorafenib-treated HepG2 and SNU449 *** available software analyses allowed us to establish the lncRNA-miRNA-mRNA regulatory axes following treatment in HepG2 and SNU449 *** HepG2 and SNU449 cells were treated with Sorafenib(10μmol/L)for 24 *** RNA,including small and long RNA,was extracted with a commercial miRNeasy *** was carried out for the identification of changes in lncRNA-miRNA-mRNA regulatory *** MAlaT,THAP9-AS1 and SNGH17 appeared to coordinately regulate miR-374b-3p and miR-769-5p that led to upregulation of SMAD7,TIRARP,TFAP4 and FAXDC2 in HepG2 ***12,ePb41 L4A-AS1,LINC01578,SNHG12 and GAS5 interacted with let-7b-3p,miR-195-5p and VeGFA in SNU449 *** axes MAlaT1/hsamir-374b-3p/SMAD7 and MAlaT1/hsa-mir-769-5p/TFAP4 were of high relevance for Sorafenib response in HepG2 cells,whereas PVT1/hsa-miR-195-5p/VeGFA was responsible for the differential response of SNU449 cells to Sorafenib *** Critical lncRNAs acting as sponges of miRNA were identified that regulated mRNA expression,whose proteins mainly increased the antitumor effectiveness of the treatment(SMAD7,TIRARP,TFAP4,FAXDC2 and ADRb2).However,the broad regulatory axis leading to increased VeGFA expression may be related to the side effect of Sorafenib in SNU449 cells.

关键词： Cell culture Hepatocellular carcinoma Non-coding RNA RNAseq Sorafenib

Sustainable transit vehicle tracking service,using intelligent transportation system services and emerging communication technologies:A review

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Journal of Traffic and Transportation engineering(english edition) 2020年第6期7卷 729-747页

作者： Ricardo Salazar-Cabrera álvaro Pachón de la cruz Juan Manuel Madrid Molina Telematics engineering Research Group(GIT) Telematics DepartmentUniversidad del CaucaPopayanColombia Information Technology and Telecommunications Research Group(I2T) ICT DepartmentUniuersidad IcesiCaliColombia

The most salient problems of transit vehicle service in latin American intermediate cities include:the high number of passengers involved in traffic accidents;traffic congestion caused by transit vehicles,and pollution generated by these vehicles,which increases in high congestion *** improve upon this situation,a research was conducted on the transit vehicle tracking service,which is a basic service for implementing mobility solutions for the aforementioned problems,the most relevant characteristics of this service for the context of latin American intermediate cities were identified,and an implementation was *** paper presents the four stages of the study:(a)a review of the state-of-the-art of services or systems related to vehicle tracking,including wireless communications technologies,implemented sustainability approaches,usage of special algorithms for efficiency improvement,and the intelligent transportation system(ITS)architecture used as a basis;(b)the process of identifying relevant characteristics of the service for a given context;(c)proposal of an ITS architecture for this service in an intermediate city,its requirements and the suggested technologies;and(d)development of experiments for validating usage of the key suggested *** review allowed to identify the main service characteristics,with regard to vehicle positioning technologies,the recomme.ded wireless communication technology(long range,LoRa),energy consumption considerations,and use of artificial intelligence(AI)to calculate waiting time of users at bus ***,an ITS architecture for the city of Popayan(Colombian city)considering the aforementioned characteristics is proposed,and the experiments related to the use of these technologies are.described in detail.

关键词： Transportation engineering Intelligent transportation systems Transit vehicle ITS architecture Tracking Long range

Nondestructive and Fast Vibration Phenotyping of Plants

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Plant Phenomics 2019年第1期1卷 152-161页

作者： e.de langre O.Penalver P.Hémon J.-M.Frachisse M.-b.bogeat-Triboulot b.Niez e.badel b.Moulia ladHyX CNRSEcole PolytechniqueInstitut Polytechnique de Paris91128 PalaiseauFrance Institute for Integrative biology of the Cell(I2bC) CEACNRSUniv.Paris-SudUniversit′e Paris-Saclay91198Gif-sur-Yvette cedexFrance Universit′e.de Lorraine INRAAgroParisTechUMR Silva54000 NancyFrance Universit′e Clermont Auvergne INRAPIAF63100 Clermont-FerrandFrance

The frequencies of free oscillations of plants,or plant parts,depend on their geometries,stiffnesses,and *** direct biomechanical interest,free frequencies also provide insights into plant properties that can usually only bemeasured destructively or with low-throughput techniques(e.g.,change inmass,tissue.density,or stiffness over development or with stresses).We propose here a new high-throughput method based on the noncontact measurements of the free frequencies of the standing *** plant is excited by short air pulses(typically 100ms).The resulting motion is recorded by a high speed video camera(100 fps)and processed using fast space and time correlation *** less than aminute the mechanical behavior of the plant is tested over several *** performance and versatility of this method has been tested in three contrasted species:tobacco(Nicotiana benthamian),wheat(Triticum aestivum L.),and poplar(Populus sp.),for a total ofmore than 4000 data *** tobaccowe show that water stress decreased the free frequency by 15%.In wheat we could detect variations of less than 1 g in the mass of *** poplar we could measure frequencies of both the whole stem and *** work provides insight into new potential directions for development of phenotyping.

关键词： directions Vibration insight

Optopharmacological control of TRPC channels by coumarin-caged lipids is associated with a phototoxic membrane effect

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Science China(Life Sciences) 2016年第8期59卷 802-810页

作者： Oleksandra Tiapko bernadett bacsa Gema Guedes de la cruz Toma Glasnov Klaus Groschner Institute of biophysics Medical University of GrazBio Tech Med-GrazHarrachgasse 21Graz 8010Austria Institute of Chemistry University of GrazNAWI GrazBio Tech Med-GrazHeinrichstrasse 28Graz 8010Austria

Photouncaging of second messengers has been successfully employed to gain mechanistic insight of cellular signaling path- ways. One of the most enigmatic processes of ion channel regulation is lipid recognition and lipid-gating of TRPC channels, which represents pivotal mechanisms of cellular Ca2＋ homeostasis. Recently, optopharmacological tools including caged lipid mediators became available, enabling an unprecedented level of temporal and spatial control of the activating lipid species within a cellular environment. Here we tested a commonly used caged ligand approach for suitability to investigate TRPC sig- naling at the level of membrane conductance and cellular Ca2＋ handling. We report a specific photouncaging artifact that is triggered by the cage structure coumarin at UV illumination. electrophysiological characterization identified a light-depe.dent membrane effect of coumarin. UV light （340 nm） as used for photouncaging, initiated a membrane conductance specifically in the presence of coumarin as low as 30 pmol L-1 concentrations. This conductance masked the TRPC3 conductance evoked by photouncaging, while TRPC-mediated cellular Ca2＋ responses were largely preserved. The observed light-induced membrane effects of the released caging moiety may well interfere with certain cellular functions, and prompt caution in using couma- fin-caged second messengers in cellular studies.

关键词： caged diacylglycerols TRPC channels Ca2+ signaling optopharmacology

Climate change,thermal niches,extinction risk and maternal-effect rescue of toad-he.ded lizards,Phrynocephalus,in thermal extremes of the Arabian Peninsula to the Qinghai-Tibetan Plateau

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Integrative Zoology 2018年第4期13卷 450-470页

作者： barry SINeRVO Donald b.MILeS Yayong WU Fausto R.MÉNdeZ-de la cruz Sebastian KIRCHHOF Yin QI The Institute for the Study of the ecological and evolutionary Climate Impacts University of Californiaand Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA department of biological Sciences Ohio UniversityAthensOhioUSA Chengdu Institute of biology Chinese Academy of SciencesChengduSichuanChina laboratory of Herpetology Institute of BiologyUniversidad Nacional Autónoma de MéxicoMexico CityMexico Museum of Natural History Leibniz-Institute for Evolution and Biodiversity Scienceand Berlin-Brandenburg Institute of Advanced Biodiversity Research(BBIB)BerlinGermany

determining the susceptibility of species to changing thermal niches is a major goal for *** this paper we.develop an eco-physiological model of extinction risk under climate change premised on behavioral *** method downscales operative environmental temperatures,which restrict hours of activity of lizards,hr,for present-day climate(1975)and future climate scenarios(2070).We apply our model using occurrence records of 20 Phrynocephalus lizards(or taxa in species complexes)drawn from literature and museum *** analysis is phylogenetically informed,because some clades may be more sensitive to rising *** limits for computed hr predict local extirpations among Phrynocephalus lizards at continental scales and delineate upper boundaries of thermal niches as defined by extreme Value *** the 8.5 Representative Concentration Pathway scenario,we predict extirpation of 64%of local populations by 2070 across 20 Phrynocephalus species,and 12 are at high risk of total extinction due to thermal limits being *** tandem with global strategies of lower CO_(2) emissions,we propose regional strategies for establishing new national parks to protect extinction-prone taxa by preserving high-elevation climate refugia within existing sites of species *** propose that evolved acclimatization–maternal plasticity–may ameliorate risk,but is poorly *** studies revealed that adaptive maternal plasticity by thermoregulating gravid females alter progeny thermal preferences by±1℃.We.describe plasticity studies for extinction-prone species that could assess whether they might be buffered from climate warming–a *** discuss an epigenetic framework for studying such maternal-effect evolution.

关键词： climate change eco-physiology extinction model maternal effect lizards

Vascular endothelial growth factor：an essential neurotrophic factor for motoneurons？

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Neural Regeneration Research 2018年第7期13卷 1181-1182页

作者： Paula M.Calvo Angel M.Pastor Rosa R.de la cruz departamento de Fisiologia Facultad de Biologia Universidad de Sevilla Sevilla Spain

Vascular endothelial growth factor（VeGF）,an angiogenic factor with neuroprotective effects：The VeGF was initially characterized by its vasculogenic and angiogenic activities and its capacity to promote vascular permeability（Yancopoulos et al.,2000）.VeGF is also known as VeGF-A and is the prototype member of a related group of five trophic factors,VeGF-b,VeGF-C,VeGF-D and placental growth factor（Pl GF;lange et al.,2016）.

关键词： VeGFR Vascular endothelial growth factor:an essential neurotrophic factor for motoneurons

Role of vascular endothelial growth factor as a critical neurotrophic factor for the survival and physiology of motoneurons

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Neural Regeneration Research 2023年第8期18卷 1691-1696页

作者： Paula M.Calvo Rosendo G.Hernández Rosa R.de la cruz Angel M.Pastor departamento de Fisiología Facultad de BiologíaUniversidad de SevillaSevillaSpain

Vascular endothelial growth factor(VeGF)was discovered by its angiogenic ***,during evolution,it appeared earlier as a neurotrophic factor required for the.development of the nervous system in invertebrates lacking a circulatory *** aimed at reviewing recent evidence indicating that VeGF has neuroprotective effects in neurons exposed to a variety of *** particular interest is the link established between VeGF and motoneurons,especially after the.design of the VeGFδ/δmutant *** mice are characterized by low levels of VeGF and develop muscle weakness and motoneuron degeneration resembling amyotrophic lateral *** administration of VeGF through several routes to animal models of amyotrophic lateral sclerosis delays motor impairment and motoneuron degeneration and increases life *** are new recent advances in the role of VeGF in the physiology of *** experimental aims use the extraocular(abducens)motoneurons lesioned by axotomy as a model for studying VeGF *** abducens motoneurons exhibit severe alterations in their discharge activity and a loss of synaptic *** exogenous administration of VeGF to axotomized abducens motoneurons,either from the transected nerve or intraventricularly,fully restores the synaptic and discharge properties of abducens motoneurons,despite being *** addition,when an anti-VeGF neutralizing antibody is delivered from the muscle to intact,uninjured abducens motoneurons,these cells display alterations in their discharge pattern and a loss of synaptic boutons that resemble the state of *** these data indicate that VeGF is an essential neurotrophic factor for motoneurons.

关键词： abducens nucleus amyotrophic lateral sclerosis cell death extracellular single-unit recordings eye movements neurodegeneration oculomotor trophic factors

A review of recent research progress on the effect of external influences on tropical cyclone intensity change

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Tropical Cyclone Research and Review 2023年第3期12卷 200-215页

作者： Joshua b.Wadler Johna e.Rudzin benjamin Jaimes de la cruz Jie Chen Michael Fischer Guanghua Chen Nannan Qin brian Tang Qingqing Li embry-Riddle Aeronautical University Department of Applied Aviation SciencesDaytona BeachFLUSA Mississippi State University Department of GeosciencesStarkvilleMSUSA University of Miami Department of Ocean SciencesMiamiFLUSA Princeton University Atmospheric and Oceanic Sciences ProgramPrincetonNJUSA University of Miami Cooperative Institute for Marine and Atmospheric Studies and NOAAAtlantic Oceanographic and Meteorological LaboratoryHurricane Research DivisionMiamiFLUSA Institute of Atmospheric Physics of the Chinese Academy of Sciences BeijingChina Key laboratory of Transportation Meteorology of China Meteorological Administration Nanjing Joint Institute for Atmospheric SciencesNanjingChina University at Albany State University of New YorkDepartment of Atmospheric and Environmental SciencesAlbanyNYUSA Nanjing University of Information and Science Technology NanjingChina

Over the past four years,signiﬁcant research has advanced our understanding of how external factors inﬂuence tropical cyclone(TC)intensity *** on air-sea interactions shows that increasing the moisture disequilibrium is a very effective way to increase surface heatﬂuxes and that ocean salinity-stratiﬁcation plays a non-negligible part in TC intensity *** wind shear from the environment induces vortex misalignment,which controls the onset of signiﬁcant TC intensiﬁ*** due to upper-level outﬂow from TCs can reduce the magnitude of vertical wind shear,making for TC intensiﬁ*** TC-trough interactions are vital for rapid intensiﬁcation in some TC cases because of strengthened warm air advection,but upper-level troughs are found to limit TC intensiﬁcation in other cases due to dry midlevel air intrusions and increased *** effects on TCs can be divided into direct effects involving aerosol-radiation interactions and indirect effects involving aerosol-cloud *** radiation absorption by the aerosols can change the temperature proﬁle and affect outer rainbands through changes in stability and *** spray and sea salt aerosols are more important in the inner region,where the aerosols increase precipitation and latent heating,promoting more intensiﬁ*** landfalling TCs,the intensity decay is initially more sensitive to surface roughness than soil moisture,and the subsequent decay is mainly due to the rapid reduction in surface moistureﬂ*** new insights further sharpen our understanding of the mechanisms by which external factors inﬂuence TC intensity changes.

关键词： Tropical cyclone external inﬂuence Intensity change Review

A functional variant in the CD209 promoter is associated with DQ2-negative celiac disease in the Spanish population

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World Journal of Gastroenterology 2006年第27期12卷 4397-4400页

作者： C Nú■ez b Rueda A Martínez C Maluenda I Polanco MA López-Nevot e Ortega e Sierra e Gómez de la Concha e Urcelay J Martín Servicio de Inmunología Clínica Hospital Clínico San CarlosMadridSpain Instituto de Parasitología y biomedicina "López Neyra" CSICGranadaSpain Servicio de Pediatría Hospital Clínico San CarlosMadrid Spain Servicio de Gastroenterología y Nutrición Pediátrica Hospital La PazMadridSpain Servicio de Inmunología Hospital Virgen de las NievesGranadaSpain Servicio de Pediatría Hospital Virgen de las NievesGranadaSpain Centro de Investigaciones biológicas CISCMadridSpain

AIM： To address the role of CD209 in celiac disease （CD） patients. Non-human leukocyte antigen （Hla） genetic factors in CD predisposition are poorly understood, and environmental factors like infectious pathogens may play a role. CD209 is a dendritic and macrophage surface molecule involved in pathogen recognition and immune activation. Recently, a functional variant in the promoter of the CD209 gene （-336A/G） has been shown to affect the transcriptional CD209 activity in vitro and it has been associated with a higher susceptibility to/or severity of infection. MeTHODS： The study population was composed of two case-control cohorts of 103 and 386 CD patients and 312 y 419 healthy controls as well as a panel of 257 celiac families. Genotyping for the -336A/G CD209 promoter polymorphism was performed using a TaqMan 5＇ allelic discrimination assay. Hla-DQ was determined by hybridization with allele specific probes. ReSULTS： Initially, the case-control and familial studies did not find any association of the -336 A/G CD209 genetic variant with CD susceptibility. However, the stratification by Hla-DQ2 did reveal a significant association of CD209 promoter polymorphism in the Hla-DQ2 （-） group （carrier A vs GG in DQ2 （-） vs DQ2 （＋） patients （P = 0.026, OR = 3.71）. CONCLUSION： The -336G CD209 allele seems to be involved in CD susceptibility in Hla-DQ2 （-） patients. Our results might suggest a possible role of pathogens in the onset of a minor group of CD patients.

关键词： CD209 Hla-DQ2 Celiac disease Single nucleotide polymorphism Susceptibility