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Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots

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Molecular Plant 2019年第12期12卷 1545-1560页

作者： Jose M.Alvarez Tomas C.Moyano Tao Zhang Diana E.Gras Francisco J.Herrera Viviana Araus Jose AQ'Brien Laura Carrillo Joaquin Medina Jesus Vicente-Carbajosa Jiming Jiang rodrigo a.gutierrez Pontificia Universidad Catolica de Chile SantiagoChile Yangzhou University YangzhouChina Instituto de Agrobiotecnologia del Litoral CONICETSanta FeArgentina University of California BerkeleyCAUSA Trancura Biosciences Inc.San FranciscoCA 94158USA Centro de Biotecnología y Genómica de Plantas(CBGP UPM-INIA)Universidad Politecnica de Madrid(UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria(INIA)Campus de Montegancedo28223-Pozuelo de AlarcóMadridSpain Department of Horticulture University of Wisconsin-MadisonMadisonWI 53706USA Department of Plant Biology and Horticulture Michigan State UniversityMI 48824USA

Transcriptional regulation,determined by the chromatin structure and regulatory elements interacting at pro-moter regions,is a key step in plant responses to environmental ***(NO3-)is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis ***,we integrate mRNA sequencing,genome-wide RNA polymeraseⅡ(RNPⅡ),chromatin immunoprecipitation sequencing,and DNase Sequencing datasets to establish the relationship between RNPⅡoccupancy and chromatin accessibility in response to NO3-treatments in Arabidopsis *** footprinting allowed us to identify in vivo regula-tory elements controlling gene expression in response to ***3--modulated transcription factor(TF)footprints are important for a rapid increase in RNPⅡoccupancy and transcript accumulation over *** mapped key TF regulatory interactions and functionally validated the role of NAP,an NAC-domain containing TF,as a new regulatory factor in *** together,our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.

关键词： nitrate transcriptional regulation footprinting RNA polymeraseⅡ regulatory networks

Emerging Players in the Nitrate Signaling Pathway

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Molecular Plant 2017年第8期10卷 1019-1022页

作者： Grace Armijo rodrigo A. gutierrez Departamento de Genetica Molecular y Microbiologia Facultad de Ciencias Biologicas FONDAP Center for Genome Regulation Pontificia Universidad Cat61ica de Chile Santiago 8331150 Chile Departamento de Genetica Molecular y Microbiologia Facultad de Ciencias Biologicas Millennium Nucleus Center for Plant Functional Genomics Pontificia Universidad Catolica de Chile Santiago 8331150 Chile

Nitrogen （N）-based fertilizers are routinely used to increase agricultural productivity for both food and non-food uses of crops. Unfortunately, excess N fertilizers escape to the environment, leading to detrimental effects on the ecosystem and human health. Understanding how plants sense and respond to different N nutrients or metabolites to regulate metabolism, physiology, growth, and development is essential for sustained yields while reducing agriculture＇s environmental and economic costs.

关键词： ARABIDOPSIS NETWORKS RESPONSES PLANTS CHL1

Molecular overview of progressive familial intrahepatic cholestasis

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World Journal of Gastroenterology 2020年第47期26卷 7470-7484页

作者： Sriram Amirneni Nils Haep Mohammad A Gad Alejandro Soto-gutierrez James E Squires rodrigo MFlorentino Department of Pathology University of PittsburghPittsburghPA 15213United States Pittsburgh Liver Research Center University of PittsburghPittsburghPA 15213United States Division of Gastroenterology Hepatologyand NutritionUPMC Children's Hospital of PittsburghPittsburghPA 15224United States

Cholestasis is a clinical condition resulting from the imapairment of bile *** condition could be caused by defects of the hepatocytes,which are responsible for the complex process of bile formation and secretion,and/or caused by defects in the secretory machinery of *** mutations and pathways that lead to cholestasis have been *** familial intrahepatic cholestasis(PFIC)is a group of rare diseases caused by autosomal recessive mutations in the genes that encode proteins expressed mainly in the apical membrane of the *** 1,also known as Byler’s disease,is caused by mutations of the ATP8B1 gene,which encodes the familial intrahepatic cholestasis 1 *** 2 is characterized by the downregulation or absence of functional bile salt export pump(BSEP)expression via variations in the ABCB11 *** of the ABCB4 gene result in lower expression of the multidrug resistance class 3 glycoprotein,leading to the third type of *** variations of this disease have been *** of function of the tight junction protein 2 protein results in PFIC 4,while mutations of the NR1H4 gene,which encodes farnesoid X receptor,an important transcription factor for bile formation,cause PFIC 5.A recently described type of PFIC is associated with a mutation in the MYO5B gene,important for the trafficking of BSEP and hepatocyte membrane *** this review,we provide a brief overview of the molecular mechanisms and clinical features associated with each type of PFIC based on peer reviewed journals published between 1993 and 2020.

关键词： Progressive familial intrahepatic cholestasis ATP8B1/familial intrahepatic cholestasis 1 ABCB11/bile salt export pump ABCB4/multidrug resistance class 3 Intrahepatic cholestasis Bile

Nitrate Transport, Sensing, and Responses in Plants

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Molecular Plant 2016年第6期9卷 837-856页

作者： Jose A. O'Brien Andrea Vega Eleonore Bouguyon Gabriel Krouk Alain Gojon Gloria Coruzzi rodrigo A. gutierrez Departamento de Genetica Molecular y Microbiologia FONDAP Center for Genome Regulation Millennium Nucleus Center for Plant Systems and Synthetic Biology Pontificia Universidad Cat61ica de Chile 8331150 Chile Departamento de Fruticultura y Enologia Pontificia Universidad Catolica de Chile Santiago 7820436 Chile Departamento de Ciencias Vegetales Pontificia Universidad Catolica de Chile Santiago 7820436 Chile Department of Biology Center for Genomics and Systems Biology New York University New York NY 10003 USA SLaboratoire de Biochimie et Physiologie Moleculaire des Plantes Institut de Biologie Integrative des Plantes 'Claude Grignon' UMR CNRS INRA SupAgro UM 2 Place Viala 34060 Montpellier Cedex France

Nitrogen （N） is an essential macronutrient that affects plant growth and development. N is an important component of chlorophyll, amino acids, nucleic acids, and secondary metabolites. Nitrate is one of the most abundant N sources in the soil. Because nitrate and other N nutrients are often limiting, plants have developed sophisticated mechanisms to ensure adequate supply of nutrients in a variable environment. Nitrate is absorbed in the root and mobilized to other organs by nitrate transporters. Nitrate sensing activates signaling pathways that impinge upon molecular, metabolic, physiological, and developmental responses locally and at the whole plant level. With the advent of genomics technologies and genetic tools, important advances in our understanding of nitrate and other N nutrient responses have been achieved in the past decade. Furthermore, techniques that take advantage of natural polymor- phisms present in divergent individuals from a single species have been essential in uncovering new components. However, there are still gaps in our understanding of how nitrate signaling affects biolog- ical processes in plants. Moreover, we still lack an integrated view of how all the regulatory factors iden- tified interact or crosstalk to orchestrate the myriad N responses plants typically exhibit. In this review, we provide an updated overview of mechanisms by which nitrate is sensed and transported throughout the plant. We discuss signaling components and how nitrate sensing crosstalks with hormonal pathways for developmental responses locally and globally in the plant. Understanding how nitrate impacts on plant metabolism, physiology, and growth and development in plants is key to improving crops for sustainable agriculture.

关键词： nitrate nitrate transporters hormones N-foraging

Sweet Potato Leaf Curl Virus: Coat Protein Gene Expression in <i>Escherichia coli</i>and Product Identification by Mass Spectrometry

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American Journal of Plant Sciences 2015年第19期6卷 3013-3024页

作者： Dina Lida.gutierrez Reynoso rodrigo A. Valverde Norimoto Murai Department of Plant Pathology & Crop Physiology College of Agriculture and LSU Agricultural Center Louisiana State University Baton Rouge USA

Sweet potato is one of the first natural GMOs, genetically modified 8000 years ago by Agrobacterium rhizogenes as reported recently by Kyndt et al. A section of 10 kbp long DNA (Transferred- DNA or T-DNA) of the Ri (Root-inducing) plasmid was transferred to the plant genome by A. rhizo-genes and has been maintained in all 291 hexaploid sweet potato cultivars of the world. The maintenance in the sweet potato genome and expression of two T-DNA genes for tryptophan-2-monooxygenease (iaaM) and for indole-3-acetamide hydrolase (iaaH) are likely to be physiologically significant since these enzymes convert tryptophan to indole-3-acetic acid, a major plant growth hormone auxin. Sweet potato (Ipomoea batatas (L.) Lam) is ranked the third most important root crop after potato and cassava, and the seventh in global food crop production with more than 126 million metric tons. Although sweet potato originated in Central or South America, China currently produces over 86% of world production with 109 million metric tons. In the United States, North Carolina is the leading producer with 38.5% of the 2007 sweet potato production, followed by California, Mississippi, and Louisiana with 23%, 19%, and 15.9%, respectively. Leaf curl virus diseases have been reported in sweet potato throughout the world. One of the causal agents is Sweet potato leaf curl virus (SPLCV) belonging to the genus Begomovirus (family Geminiviridae). Although SPLCV does not cause symptoms on Beauregard, one of the most predominant sweet potato cultivars in the US, it can reduce the yield up to 26%. Serological detection of SPLCV is not currently available due to the difficulties in obtaining purified virions that can be used as antigen for antiserum production. In attempts to obtain the coat protein (CP) of SPLCV for antibody production, primers were designed to amplify the CP gene. This gene was cloned into the expression vector pMAL-c2E as a fusion protein with maltose-binding protein, and transformed into E

关键词： Affinity Chromatography Purification Coat Protein Escherichia coli Mass Spectrometry Maltose Binding Protein Sweet Potato Leaf Curl Virus

Interfacial Strategies for Smart Slippery Surfaces

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Journal of Bionic Engineering 2020年第4期17卷 633-643页

作者： Glen McHale rodrigo Ledesma-Aguilar Gary George Wells Smart Materials&Surfaces Laboratory Faculty of Engineering and EnvironmentNorthumbria UniversityNewcastle upon TyneNE18STUK

The problem of contact line pinning on surfaces is pervasive and contributes to problems from ring stains to ice *** we provide a single conceptual framework for interfacial strategies encompassing five strategies for modifying the solid-liquid interface to remove pinning and increase droplet *** biomimetic strategies are included,(i)reducing the liquid-solid interfacial area inspired by the Lotus effect,(ii)converting the liquid-solid contact to a solid-solid contact by the formation of a liquid marble inspired by how galling aphids remove honeydew,and(iii)converting the liquid-solid interface to a liquid-lubricant contact by the use of a lubricant impregnated surface inspired by the Nepenthes Pitcher *** further strategies are,(iv)converting the liquid-solid contact to a liquid-vapor contact by using the Leidenfrost effect,and(v)converting the contact to a liquid-liquid-like contact using slippery omniphobic covalent attachment of a liquid-like coating(SOCAL).Using these approaches,we explain how surfaces can be designed to have smart functionality whilst retaining the mobility of contact lines and ***,we show how droplets can evaporate at constant contact angle,be positioned using a Cheerios effect,transported by boundary reconfiguration in an energy invariant manner,and drive the rotation of solid components in a Leidenfrost heat *** conceptual framework enables the rationale design of surfaces which are slippery to liquids and is relevant to a diverse range of applications.

关键词： superhydrophobicity SLIPS liquid marbles leidenfrost SOCAL

Manipulation of parasite load induces significant changes in the structural-based throat color of male iberian green lizards

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Current Zoology 2018年第3期64卷 293-302页

作者： rodrigo MEGiA-PALMA Javier MARTiNEZ Santiago MERINO Dept Ecologia Evolutiva Museo Nacional de Ciencias Naturales-CSIC J. Gutierrez Abascal 2 E-28006 Madrid Spain Area Parasitologia Dept Biomedicina y Biotecnologia Area de Parasitologia. Facultad de Farmacia Universidad de Alcala de Henares Alcala de Henares E-28871 Madrid Spain

The honesty of structural-based ornaments is controversial. Sexual selection theory predicts that the honesty of a sexual signal relies on its cost of production or maintenance. Therefore, environmental factors with negative impact on individuals could generate high costs and affect the expres- sion of these sexual signals. In this sense, parasites are a main cost for their hosts. To probe the effect of parasites on the structural-based coloration of a lacertid species Lacerta schreiberi, we have experimentally removed ticks from a group of male Iberian green lizards using an acaricide treatment （i.e., the broad-use insecticide fipronil）. All individuals were radio-tracked and recaptured after 15 days to study changes in coloration in both the ultraviolet （UV）-blue （structural-based） and UV-yellow （structural and pigment-based） ornamentations after manipulation, as well as changes in endoand ectoparasitic load and body condition. Additionally, after the experiment, we measured the skin inflammatory response to a mitogen. The fipronil treatment was effective in reducing ticks and it was associated with a significant reduction of hemoparasite load. Throughout the season, individuals treated with fipronil tended to maintain the brightness of the UV-blue throat coloration while control lizards tended to increase it. However, individuals treated with fipronil that were not infected with hemoparasites significantly reduced the brightness of the UV-blue throat color ation. Individuals with a higher initial tick load exhibited a lower UV saturation increment （UV-blue） and a higher brightness increment （UV-yellow） during the experiment. Overall these results experimentally support the idea that parasites adversely influence the expression of the structural-based coloration of male Iberian green lizards. This adds evidence to the hypothesis that sexual ornaments in lizards function as honest signals.

关键词： animal communication ectoparasites Hamilton & Zuk structural-coloration.

Evaluation of VEGF gene polymorphisms and proliferative diabetic retinopathy in Mexican population

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International Journal of Ophthalmology(English edition) 2017年第1期10卷 135-139页

作者： Roberto Gonzalez-Salinas Maria C Garcia.gutierrez Gerardo Garcia-Aguirre Virgilio Morales-Canton Raul Velez-Montoya Vidal R Soberon-Ventura Victoria Gonzalez rodrigo Lechuga Pablo Garcia-Solis David G Garcia.gutierrez Marco Vinicio Garcia-Solis Manuel Saenz de Viteri Juan C Solis-S Biomedical Research Department Autonomous University of QueretaroQueretaro 76170Mexico Retina Department Asociation to Prevent Blindness in MexicoMexico City 04030Mexico Research Department Asociation to Prevent Blindness in MexicoMexico City 04030Mexico Retina Department General Hospital of Queretaro(ISSSTE)Queretaro 76000Mexico Universidad La Salle School of Medicine Mexico City 06140Mexico

AIM： To assess if the included vascular endothelial growth factor （VEGF） polymorphisms rs3025035, rs3025021 and rs2010963 are associated to proliferative retinopathy in a Mexican population with type 2 diabetes mellitus （T2DM）. METHODS： A case-control study was conducted in adult individuals with T2DM associated to proliferative retinopathy or non-proliferative retinopathy from Oct. 2014 to Jun. 2015 from the Retina Department of the Asociation to Prevent Blindness in Mexico. The selected patients were adults with a diagnosis of T2DM ≥5y. All subjects had a comprehensive ocular examination and the classification of the retinopathy severity was made considering the Early Treatment Diabetic Retinopathy Study （ETDRS） standardization protocols. Genomic DNA was extracted from whole fresh blood. All samples were genotyped by qPCR for selected VEGF polymorphisms. Hardy-Weinberg equilibrium was calculated by comparing Chi-square values between the expected and the observed values for genotype ***： In total 142 individuals were enrolled, 71 individuals with T2DM and associated proliferative retinopathy and 71 individuals with non-proliferative retinopathy. One-sided Fisher’s exact test was performed for rs3025021 [OR （95% CI）=0.44（0.08-2.2）; P=0.25] and rs2010963 [OR （95% CI）=0.63（0.25-1.6）; P=0.23]. The minor allelic frequencies obtained were 26% for rs3025021, 10% for rs3025035 and 61% for rs2010963. The pairwise linkage disequilibrium between the three SNP was assessed, and was as follows： rs3025021 vs rs3025035： D’=1.0, r2=0.1043, P≤0.0001; rs3025021 vs rs2010963： D’=0.442, r2=0.0446, P=0.149; rs3025035 vs rs2010963： D’=0.505, r2=0.0214, P=***： This is the first analysis involving VEGF polymorphisms and proliferative diabetic retinopathy in a Mexican population. A major finding of the present study is that none of the polymorphisms studied was significantly associated with proliferative retinopathy. Based on these results, we can infer that differ

关键词： vascular endothelial growth factor polymor-phism proliferative diabetic retinopathy non-proliferative diabetic retinopathy rs3025021 rs3025035 rs2010963

Granulomatous Mastitis: Incidence and Experience in a Mexican Institute

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Journal of Biosciences and Medicines 2019年第6期7卷 24-32页

作者： Arnoldo Topete Olin Carrasco Gabriel Barrera Juan Garzón Eduardo gutierrez Cuahutémoc Márquez rodrigo Dávila Marco Cuervo María Irene Rivera Department of Plastic and Reconstructive Surgery Pemex Hospital Mexico City Mexico Department of Pathological Anatomy Pemex Hospital Mexico City Mexico

The significance of this work is that chronic granulomatous disease can mimic two common breast diseases;breast cancer and breast abscess;so it is mandatory that the diagnosis is made in order to avoid mistaken carcinoma diagnosis. On the other hand, the current treatment of this particular disease still remains controversial. Objectives: The aim of this study is to expose and describe the chronicity and the impact in a patient’s quality of life with Granulomatous Mastitis diagnosis. We describe the evolution of the disease and the treatment of the disease in a Mexican Institution. Material and methods: In a descriptive retrospective study we identified 9 patients with idiopathic granulomatous mastitis (IMG), all of them were diagnosed with histopathological findings. Results: In a period of time between January 2005 and December 2017, we included a total of 9 female patients. All of them have had histopathological findings consistent with granulomatous mastitis. The age range was 25 - 83 years old (mean 50.8 yrs). In 4 patients (44.4%) had the right side affected, three patients (33.3%) had the left side affected and 2 patients (22.2%) had a bilateral presentation. In 3 patients (33.3%) we observed more than one affected quadrant and 4 patients (44.4%) had a diffuse presentation on image. The most common symptom was breast pain in 9 patients (100%) and the most common sign was the presence of a nodule, 8 patients (88.8%). We observed erythema in 7 cases (77.7%) followed by abscess, edema and pus secretion in 6 patients (66.6%). The most frequent treatment was the use of a combination of NAIDs and antibiotic in 8 patients (88.8%). Six patients were incised with scalp and drained. Six patients underwent mastectomy.

关键词： Idiopathic Granulomatous Mastitis Incidence and Experience Descriptive Retrospective Study