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Multi-omics Analysis of Young Portulaca oleracea ***’Responses to High NaCl Doses Reveals Insights into Pathways and Genes Responsive to Salinity Stress in this Halophyte Species

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Phenomics 2023年第1期3卷 1-21页

作者： Vivianny Nayse Belo Silva Thalliton Luiz Carvalho da Silva Thalita Massaro Malheiros Ferreira jorge Candido Rodrigues neto AndréPereira Leão JoséAntônio de Aquino Ribeiro Patrícia Verardi Abdelnur Leonardo Fonseca Valadares Carlos Antônio Ferreira de Sousa Manoel Teixeira Souza Júnior Graduate Program of Plant Biotechnology Federal University of LavrasCP 3037LavrasMG 37200-000Brazil Institute of Chemistry Federal University of GoiásCampus SamambaiaGoiâniaGO 74690‐900Brazil Brazilian Agricultural Research Corporation Embrapa Mid-NorthTeresinaPI 64008-780Brazil Brazilian Agricultural Research Corporation Embrapa AgroenergyBrasíliaDF 70770‐901Brazil

Soil salinity is among the abiotic stressors that threaten agriculture the most,and purslane(Portulaca oleracea L.)is a dicot species adapted to inland salt desert and saline habitats that hyper accumulates salt and has high phytoremediation *** researchers consider purslane a suitable model species to study the mechanisms of plant tolerance to drought and salt ***,a robust salinity stress protocol was developed and used to characterize the morphophysiological responses of young purslane plants to salinity stress;then,leaf tissue underwent characterization by distinct omics platforms to gain further insights into its response to very high salinity *** salinity stress protocol did generate different levels of stress by gradients of electrical conductivity at field capacity and water potential in the saturation extract of the substrate,and the morphological parameters indicated three distinct stress *** expected from a halophyte species,these plants remained alive under very high levels of salinity stress,showing salt crystal-like structures constituted mainly by Na^(+),Cl^(−),and K^(+)on and around closed stomata.A comprehensive and large-scale metabolome and transcriptome single and integrated analyses were then employed using leaf *** multi-omics integration(MOI)system analysis led to a data-set of 51 metabolic pathways with at least one enzyme and one metabolite differentially expressed due to salinity *** data sets(of genes and metabolites)are valuable for future studies aimed to deepen our knowledge on the mechanisms behind the high tolerance of this species to salinity *** conclusion,besides showing that this species applies salt exclusion already in young plants to support very high levels of salinity stress,the initial analysis of metabolites and transcripts data sets already give some insights into other salt tolerance mechanisms used by this species to support high levels of salinity stress.

关键词： Purslane RNA-Seq Chemometrics High-resolution mass spectrometry Abiotic stress Multi-omics integration

Calculations of Optical Rotation from Density Functional Theory

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Chinese Physics Letters 2007年第5期24卷 1207-1209页

作者： Antǒnio Canal neto Francisco Elias jorge Departamento de Fisica Universidade Federal do Espírito Santo 29060-900 Vitória ES Brazil

Density function theory calculations of frequency-dependent optical rotations [α]ω for three rigid chiral molecules are reported. Calculations have been carried out at the sodium D line frequency, using the ADZP basis set and a wide variety of functionals. Gauge-invariant atomic orbitals are used to guarantee origin-independent values of [ω]D. In addition, study of geometry dependence of [ω]D is reported. Using the geometries optimized at the B3LYP/ADZP level, the mean absolute deviation of B3LYP/ADZP and experimental laiD values yields 60.1°/（dm g/cm^3）. According to our knowledge, this value has not been achieved until now with any other model.

关键词： MOLECULAR WAVE-FUNCTIONS BASIS-SETS MP2 HF

All-electron basis sets for H to Xe specific for ZORA calculations:Applications in atoms and molecules

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Chinese Physics B 2024年第8期33卷 238-246页

作者： C.S.Gomes F.E.jorge A.Canal neto Departamento de Fisica Universidade Federal do Espirito Santo29075-910 VitoriaESBrazil Departamento de Fisica Instituto de Ciencias Exatas e BiologicasUniversidade Federal de Ouro Preto Campus Universitario Morro do Cruzeiro35402-136 Ouro PretoMGBrazil

A segmented basis set of quadruple zeta valence quality plus polarization functions(QZP)for H through Xe was developed to be used in conjunction with the ZORA *** set was augmented with diffuse functions to describe electrons farther away from the nuclei *** the ZORA-CCSD(T)/QZP-ZORA theoretical model,atomic ionization energies and bond lengths,harmonic vibrational frequencies,and atomization energies of some molecules were *** addition of core-valence corrections has been shown to improve the agreement between theoretical and experimental results for molecular *** atomization energies,a similar observation emerges when considering spin-orbit *** the augmented QZP-ZORA set,static mean dipole polarizabilities of a set of atoms were calculated and compared with previously published recommended and experimental *** evaluations of the ZORA and Douglas–Kroll–Hess Hamiltonians were made for each property studied.

关键词： QZP-ZORA and AQZP-ZORA basis sets elements from H to Xe CCSD(T)method atomic and molecular properties

All-electron ZORA triple zeta basis sets for the elements Cs-La and Hf-Rn

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Chinese Physics B 2023年第9期32卷 242-249页

作者： Antônio Canal neto Francisco E.jorge Henrique R.Cda Cruz Departamento de Física Universidade Federal do Espírito Santo29075-910 VitóriaESBrazil

Segmented all-electron basis set of triple zeta valence quality plus polarization functions(TZP)for the elements of the fifth row to be used together with the zero-order regular approximation(ZORA)is carefully *** correctly describe electrons distant from atomic nuclei,the basis set is augmented with diffuse functions giving rise to a set designated as *** the ZORA-B3LYP theoretical level,these sets are used to calculate the ionization energy and mean dipole polarizability of some atoms,bond length,dissociation energy,and harmonic vibrational frequency of diatomic ***,these results are compared with the theoretical and experimental data found in the *** considering that our sets are relatively compact,they are sufficiently accurate and reliable to perform property calculations involving simultaneously electrons from the inner shell and outer *** performances of the ZORA and second-order Douglas-Kroll-Hess Hamiltonians are evaluated and the results are also discussed.

关键词： TZP-ZORA and ATZP-ZORA basis sets ZORA-B3LYP method Cs-La and Hf-Rn elements atomic and molecular properties

Diversity of the Formicidae (Hymenoptera) carrion communities in Lisbon (Portugal): preliminary approach as seasonal and geographic indicators

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Forensic Sciences Research 2018年第1期3卷 65-73页

作者： António neto-Silva Ricardo jorge Dinis-Oliveira Catarina Prado e Castro Department of Public Health Forensic Sciences and Medical EducationFaculty of MedicineUniversity of PortoPortoPortugal Department of Sciences IINFACTS-Institute of Research and Advanced Training in Health Sciences and TechnologiesUniversity Institute of Health Sciences(IUCS)CESPUCRLGandraPortugal UCIBIO REQUIMTE-Laboratory of ToxicologyDepartment of Biological SciencesFaculty of PharmacyUniversity of PortoPortoPortugal Department of Life Sciences Centre for Functional EcologyUniversity of CoimbraCoimbraPortugal

The value of the Formicidae (Insecta,Hymenoptera) community in forensic investigations is poorly studied in *** order to better understand the structure and dynamics of this group of insects in cadavers and their putative value in forensic investigations,studies were carried out in Lisbon area during one *** carcasses were used as a model of human *** entomofauna attracted to the carcasses was collected over a period of about 2 months in each season of the *** collection of ants was performed at regular intervals,daily in the first 23 days and then with intervals of 2,3 or 5 days until the end of the *** stages of cadaveric decomposition were recognized with the ants being present in all of *** hundred and nine specimens were captured: 7 in autumn,6 in winter,90 in spring and 206 in *** specimens belong to three subfamilies and seven different *** of them had never been mentioned before as being associated to cadavers in this geographical *** and summer had the greater diversity of species and a larger number of *** luteus was the dominant species in spring and Tapinoma nigerrimum in *** the information of other similar studies carried out in the Iberian Peninsula,the sarcosaprophagous Formicidae community found in Lisbon is unique and different from other studied locations,which supports the need to perform regional *** results shown that ants do not present a definite pattern of succession,but some species have the potential to be seasonal or geographic indicators.

关键词： Forensic science forensic entomology Formicidae sarcosaprophagous community decomposition process postmortem interval seasonal study

Viral infections and implications for male reproductive health

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Asian Journal of Andrology 2021年第4期23卷 335-347页

作者： Thiago A Teixeira Yasmin C Oliveira Felipe S Bernardes Esper G Kallas Amaro N Duarte-neto Sandro C Esteves Joël R Drevet jorge Hallak Androscience Science and Innovation Center in Andrology and High-Complex Clinical and Research Andrology LaboratorySão Paulo 04534-011SPBrazil Division of Urology University of São PauloSão Paulo 05403-000SPBrazil Men's Health Study Group Institute for Advanced StudiesUniversity of São PauloSão Paulo 05508-060SPBrazil Division of Urology School of MedicineFederal University of AmapaMacapa 68903-419APBrazil Department of Infectious and Parasitic Diseases University of São PauloSão Paulo 05403-000SPBrazil BIAS–Brazilian Image Autopsy Study Group Department of PathologyUniversity of São PauloSão Paulo 05403-000SPBrazil ANDROFERT Andrology and Human Reproduction ClinicCampinas 13075-460SPBrazil Department of Surgery(Division of Urology) University of Campinas(UNICAMP)Campinas 13083-968SPBrazil Department of Clinical Medicine Faculty of HealthAarhus UniversityAarhus 8000Denmark GReD Institute CNRS-INSERM-UniversitéClermont AuvergneFaculty of MedicineClermont-Ferrand 63000France Reproductive Toxicology Unit Department of PathologyUniversity of São PauloSão Paulo 05403-000SPBrazil

Viral infections have haunted humankind since times ***,globalization,and extensive deforestation have created an ideal environment for a viral spread with unknown and multiple shedding *** viruses can infect the male reproductive tract,with potential adverse consequences to male reproductive health,including infertility and ***,some genital tract viral infections can be sexually transmitted,potentially impacting the resulting offspring's *** have summarized the evidence concerning the presence and adverse effects of the relevant viruses on the reproductive tract(mumps virus,human immunodeficiency virus,herpes virus,human papillomavirus,hepatitis B and C viruses,Ebola virus,Zika virus,influenza virus,and coronaviruses),their routes of infection,target organs and cells,prevalence and pattern of virus shedding in semen,as well as diagnosis/testing and treatment *** pathophysiological understanding in the male genital tract is essential to assess its clinical impact on male reproductive health and guide future research.

关键词： male genital tract reproduction semen sexual transmission sperm testis viral persistence viruses

New Insights into Aluminum Tolerance in Rice： The ASR5 Protein Binds the STAR1 Promoter and Other Aluminum-Responsive Genes

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Molecular Plant 2014年第4期7卷 709-721页

作者： Rafael Augusto Arenhart Yang Bai Luiz Felipe Valter de Oliveira Lauro Bucker neto Mariana Schunemann Felipe dos Santos Maraschin jorge Mariath Adriano Silverio Gilberto Sachetto-Martins Rogerio Margis Zhi-Yong Wang Marcia Margis-Pinheiro Programa de Pos-Graduacao em Genetica e Biologia Molecular Avenida Bento Goncalves 9500 Departamento de Genetica sala 207 predio 43312 Universidade Federal do Rio Grande do Sul 91501-970 Porto Alegre Brasil Department of Plant Biology Carnegie Institution for Science Stanford CA 94305 USA School of Computer Science and Technology Harbin Institute of Technology Harbin 150001 China Departamento de Botanica Universidade Federal do Rio Grande do Sul Porto Alegre Brasil Departamento de Genetica Universidade Federal do Rio de Janeiro Porto Alegre Brasil Centro de Biotecnologia Universidade Federal do Rio Grande do Sul Porto Alegre Brasil

Aluminum （AI） toxicity in plants is one of the primary constraints in crop production. Al3＋, the most toxic form of Al, is released into soil under acidic conditions and causes extensive damage to plants, especially in the roots. In rice, Al tolerance requires the ASR5 gene, but the molecular function of ASR5 has remained unknown. Here, we perform genome-wide analyses to identify ASR5-dependent Al-responsive genes in rice. Based on ASRS_RNAi silencing in plants, a global transcriptome analysis identified a total of 961 genes that were responsive to Al treatment in wildtype rice roots. Of these genes, 909 did not respond to Al in the ASR5_RNAi plants, indicating a central role for ASR5 in Al-responsive gene expression. Under normal conditions, without Al treatment, the ASR5 RNAi plants expressed 1.756 genes differentially compared to the wild-type plants, and 446 of these genes responded to AI treatment in the wild-type plants. Chromatin immunoprecipitation followed by deep sequencing identified 104 putative target genes that were directly regulated by ASR5 binding to their promoters, including the STAR1 gene, which encodes an ABC transporter required for AI tolerance. Motif analysis of the binding peak sequences revealed the binding motif for ASR5, which was confirmed via in vitro DNA-binding assays using the STAR1 promoter. These results demonstrate that ASR5 acts as a key transcription factor that is essential for AI-responsive gene expression and Al tolerance in rice.

关键词： Aluminum ChlP-Seq RNA-Seq rice ASR.

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镧系离子间无辐射能量传递速率的教程综述

发光学报 2022年第12期43卷 1871-1891页

作者： Albano N Carneiro neto Renaldo T Moura Jr jorge A A Coelho Mauro E Silva-Junior Janderson L Costa Oscar L Malta Ricardo L Longo 阿威罗大学物理系和CICECO-阿威罗材料研究所阿威罗葡萄牙3810-193 南卫理公会大学化学系达拉斯美国75275-0314 帕拉伊巴联邦大学化学与物理系阿雷亚巴西58397-000 伯南布哥联邦大学基础化学系累西腓巴西50740-560 伯南布哥联邦大学材料科学研究生院累西腓巴西50670-901

在本教程综述中,我们重新阐述和表达了镧系离子间无辐射能量传递(ET)速率的理论形式,并且强调了考虑镧系离子本身特异性所引发的与Förster和Dexter理论不同之处。所给出的表达式遵循了Judd-Ofelt的4f-4f跃迁理论框架之下的Kushida方法,... 详细信息

在本教程综述中,我们重新阐述和表达了镧系离子间无辐射能量传递(ET)速率的理论形式,并且强调了考虑镧系离子本身特异性所引发的与Förster和Dexter理论不同之处。所给出的表达式遵循了Judd-Ofelt的4f-4f跃迁理论框架之下的Kushida方法,并计入了如下电多极机制:偶极-偶极(W_(d-d))、偶极-四极(W_(d-q))和四极-四极(W_(q-q))。更为重要的是,当前的机制也扩展包括了交换(W_(ex))和磁偶极子-磁偶极子(W_(md-md))作用,并经过改进进一步包含了屏蔽效应以及给出了F因子(费米黄金规则中的态密度)的解析表达式。与Kushida的原始方法类似,我们只考虑了强制电偶极子(FED)对Judd-Ofelt强度参数的贡献,并细节性地讨论了磁偶极-磁偶极相互作用的选择定则以及相关矩阵元的计算。此外,我们还以Tb(Ⅲ)-Eu(Ⅲ)和Yb(Ⅲ)-Er(Ⅲ)的能量传递速率计算为例,逐步展示了计算过程、主要的计算支撑信息以及所使用的计算脚本。

关键词：无辐射能量传递镧系理论计算 Ln-Ln能量传递速率选择定则

Pathogenesis of Chagas disease cardiomyopathy

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World Journal of Clinical Infectious Diseases 2012年第3期2卷 39-53页

作者： Priscila Camillo Teixeira Amanda Farrage Frade Luciana Gabriel Nogueira jorge Kalil Christophe Chevillard Edecio Cunha-neto Labora-tory of Immunology Heart Institute (Incor) School of Medicine University of Sao Paulo Institute for Investigation in Immunology (III) INCT Division of Clinical Immunol-ogy and Allergy School of Medicine University of Sao Paulo INSERM Aix-Marseille University

Chagas disease, or American trypanosomiasis, is a parasitic infection caused by the flagellate protozoanTrypanosoma cruzi. Chagas disease is mainly affecting rural populations in Mexico and Central and South America. The World Health Organization estimates that 300 000 new cases of Chagas disease occur every year and approximately 20 000 deaths are attributable to Chagas. However, this organisation classified Chagas disease as a neglected tropical disease. The economic burden of this disease is significant. In many Latin American countries, the direct and indirect costs, including the cost of health care in dollars and loss of productivity, attributable to Chagas disease ranges from $40 million to in excess of $800 million per nation per annum. So, it remains a contemporary public health concern. In chronic phase, mortality is primarily due to the rhythm disturbances and congestive heart failure that result from the chronic inflammatory cardiomyopathy(CCC) due to the persistence presence of parasites in the heart tissue. Mechanisms underlying differential progression to CCC are still incompletely understood. In the last decades immunological proteomic genetic approaches lead to significant results which help to disperse the veil covering the knowledge of the pathogenic process. Here, we reported these significant progresses.

关键词： Chagas Pathogenesis Cardiomyopathy Susceptibility Parasitic