90 results on '"Rumen Ivanov"'
Search Results
2. SEC14-GOLD protein PATELLIN2 binds IRON-REGULATED TRANSPORTER1 linking root iron uptake to vitamin E
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Jannik Hornbergs, Karolin Montag, Jennifer Loschwitz, Inga Mohr, Gereon Poschmann, Anika Schnake, Regina Gratz, Tzvetina Brumbarova, Monique Eutebach, Kalina Angrand, Claudia Fink-Straube, Kai Stühler, Jürgen Zeier, Laura Hartmann, Birgit Strodel, Rumen Ivanov, and Petra Bauer
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ddc:580 ,Physiology ,Biochemistry and Molecular Biology ,Genetics ,Plant Science - Abstract
Organisms require micronutrients, and Arabidopsis (Arabidopsis thaliana) IRON-REGULATED TRANSPORTER1 (IRT1) is essential for iron (Fe2+) acquisition into root cells. Uptake of reactive Fe2+ exposes cells to the risk of membrane lipid peroxidation. Surprisingly little is known about how this is avoided. IRT1 activity is controlled by an intracellular variable region (IRT1vr) that acts as a regulatory protein interaction platform. Here, we describe that IRT1vr interacted with peripheral plasma membrane SEC14-Golgi dynamics (SEC14-GOLD) protein PATELLIN2 (PATL2). SEC14 proteins bind lipophilic substrates and transport or present them at the membrane. To date, no direct roles have been attributed to SEC14 proteins in Fe import. PATL2 affected root Fe acquisition responses, interacted with ROS response proteins in roots, and alleviated root lipid peroxidation. PATL2 had high affinity in vitro for the major lipophilic antioxidant vitamin E compound α-tocopherol. Molecular dynamics simulations provided insight into energetic constraints and the orientation and stability of the PATL2-ligand interaction in atomic detail. Hence, this work highlights a compelling mechanism connecting vitamin E with root metal ion transport at the plasma membrane with the participation of an IRT1-interacting and α-tocopherol-binding SEC14 protein.
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- 2022
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3. the Transdisciplinarity for Sustainable Development: Incorporating Organic Waste into Bread-Making
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Claudia Hernandez-Aguilar, David Abraham Saucedo-Alfonzo, Arturo Dominguez-Pacheco, Maria del Carmen Valderrama-Bravo, Otoniel Igno Rosario, Joel Eduardo Valencia-Hernandez, Zayra Mundo-Franco, Rumen Ivanov Tsonchev, and Efrain Jose Martinez-Ortiz
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Multidisciplinary - Abstract
This research proposes to take advantage of waste generated in the kitchen to be added into bread-making. The main findings were as follows: 1) family members of the population studied (more than 80%) had diabetes or cancer, their diet is based on high glycemic index foods, including bread. It is necessary to modify its characteristics through fiber and bioactive compounds. 2) Bread added with wastes showed changes in the color (L*a*b*). Those that presented the highest difference with respect to (control) were coriander (30.5), cabbage (30.8) and parsley (22.1) breads; followed by tomato bread (19.6). The porosity increased with the addition of waste, presenting the highest in the breads added with parsley and coffee grain. The bread with lowest hardness after control was the tomato bread, and this was also the of highest sensory acceptance. 3) Bronfenbrenner model was proposed for the evaluation of impacts and self-change to use waste.
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- 2023
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4. Characterization of the smallArabidopsis thalianaGTPase and ADP-ribosylation factor-like 2 protein TITAN5
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Inga Mohr, Amin Mirzaiebadizi, Sibaji K. Sanyal, Pichaporn Chuenban, Mohammad R. Ahmadian, Rumen Ivanov, and Petra Bauer
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Small GTPases comprise key proteins in signal transduction that function by conformational switching ability between GDP- and GTP-bound states. The ADP-ribosylation factor (ARF) family is involved in vesicle trafficking and cellular functions. Though evolutionarily well conserved, little is known about ARF and ARF-like GTPases in plants. Here, we characterized functional properties and cellular localization of the essential small ARF-like GTPase TITAN5/HALLIMASCH/ARL2/ARLC1 (hereafter termed TTN5) fromArabidopsis thaliana. TTN5 showed rapid guanine nucleotide exchange capacity comparable to that of human counterparts, but a remarkably low GTP hydrolysis reaction. A TTN5Q70Lmutant had enhanced nucleotide exchange activity, indicative of intracellular activation, while TTN5T30Nwith fast nucleotide dissociation can be considered a dominant-negative form. This suggests that TTN5 is present in GTP-loaded active form in the cells. YFP-tagged TTN5 and the two derived mutant variants were located at multiple sites of the endomembrane system in the epidermis of Arabidopsis seedlings andNicotiana benthamianaleaves. While YFP-TTN5 and YFP-TTN5Q70Lwere highly mobile in the cells, mobility was reduced for TTN5T30N. Colocalization with endomembrane markers in combination with pharmacological treatments resolved localization at membrane sites and showed that YFP-TTN5 and YFP-TTN5Q70Lwere located in Golgi stacks, multivesicular bodies, while this was less the case for YFP-TTN5T30N. On the other hand, all three TTN5 forms were located at the plasma membrane. Hence, the unusual capacity of rapid nucleotide exchange activity of the small ARF-like GTPase TTN5 is linked with cell membrane dynamics, likely associated with vesicle transport pathways in the endomembrane system.HighlightsThe small ARF-like GTPase TTN5 has a very rapid intrinsic nucleotide exchange capacity with a conserved nucleotide switching mechanismBiochemical data classified TTN5 as a non-classical small GTPase, likely present in GTP-loaded active form in the cellYFP-TTN5 is dynamically associated with vesicle transport and different processes of the endomembrane system, requiring the active form of TTN5
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- 2023
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5. Small ADP-ribosylation factor-like GTPase TITAN5 (TTN5/ARL2) is linked with the dynamic regulation of IRON-REGULATED TRANSPORTER1
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Inga Mohr, Monique Eutebach, Naima Schommen, Regina Gratz, Kalina Angrand, Lara Genders, Tzvetina Brumbarova, Petra Bauer, and Rumen Ivanov
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The endomembrane system is the central sorting machinery for membrane proteins where signals can be integrated to control plant nutritional responses. IRON-REGULATED TRANSPORTER1 (IRT1) is tightly controlled through trafficking between the endomembrane system and the plasma membrane to balance the demands for iron (Fe) and toxic effects that may arise from excess of this micronutrient in roots. Small GTPases of the Ras superfamily regulate signaling inputs in endomembrane trafficking, but their functions and activities are poorly known in plants. One plant endomembrane system-associated regulatory component is the small ARF-like GTPase TITAN 5/ARL2/ARLC1/HALLIMASCH (hereafter termed TTN5). TTN5 is required during early embryo development but many open questions remain with regard to its physiological function during the later life cycle or in response to environmental cues. Here, we demonstrate that TTN5 interacts with IRT1vr, the large cytoplasmic variable region and protein-regulatory platform of IRT1. TTN5 also interacts with peripheral membrane proteins that are components of the IRT1 regulation machinery and can be involved in protein trafficking, like SNX1, the C2 domain protein EHB1 and the SEC14-GOLD domain-containing PATL2. We show that heterozygousttn5-1+/-plants have a Fe reduction phenotype. Fluorescent fusion proteins of TTN5 and IRT1 colocalize at the plasma membrane and in endosomes/multivesicular bodies, where IRT1 sorting and cycling between the plasma membrane and the vacuole are coordinated. Hence, this work links IRT1 and iron nutritional regulation with a small GTPase. This opens up the possibility that iron nutrient levels are controlledviathe cellular regulation of the endomembrane system.HighlightsThe small GTPase TITAN 5 (TTN5/ARL2) is linked to iron homeostasisTTN5 interacts with the large intracellular loop and variable region of IRON-REGULATED TRANSPORTER 1 (IRT1) and has a positive effect on root iron (Fe) reductionTTN5 interacts with peripheral membrane proteins of the IRT1 interactome, EHB1, PATL2 and SNX1 suggesting a coordinating role in IRT1 regulationTTN5 and IRT1 colocalize at the plasma membrane and the endomembrane system related to vesicle transportOne-sentence summaryADP-ribosylation factor-like small GTPase TITAN 5 (TTN5/ARL2) links vesicle transport and iron homeostasis by binding the intracellular regulatory protein interaction region of IRON-REGULATED TRANSPORTER 1 (IRT1).
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- 2023
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6. Biophysical methods used to generate tolerance to drought stress in seeds and plants: a review
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Raul Romero-Galindo, Claudia Hernandez-Aguilar, Arturo Dominguez-Pacheco, Juan Godina-Nava, and Rumen Ivanov Tsonchev
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Fluid Flow and Transfer Processes ,Soil Science ,General Agricultural and Biological Sciences ,Water Science and Technology - Published
- 2022
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7. Role of SEC14-like phosphatidylinositol transfer proteins in membrane identity and dynamics
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Karolin Montag, Rumen Ivanov, and Petra Bauer
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Plant Science - Abstract
The identity of membranes and dynamic processes acting at membrane sites provide important cues to regulate transport and signal transduction and communicate information across membranes. There are still numerous open questions as to how membrane identity changes and the dynamic processes acting at the surface of membranes are regulated in diverse eukaryotes in particular plants and which roles are being played by protein interaction complexes composed of peripheral and integral membrane proteins. One class of peripheral membrane proteins conserved across eukaryotes comprises the SEC14-like phosphatidylinositol transfer proteins (SEC14L-PITPs). These proteins share a SEC14 domain that contributes to membrane identity and fulfills regulatory functions in membrane trafficking by its ability to sense, bind, transport and exchange lipophilic substances between membranes, such as phosphatidylinositol, phosphoinositides and diverse other lipophilic substances. SEC14L-PITPs can occur as single-domain SEC14-only proteins in all investigated organisms or with a modular domain structure as multi-domain proteins in animals, green algae II and land plants. Here, we present an overview on the functional roles of SEC14L-PITPs, with a special focus on the multi-domain SEC14L-PITPs of the SEC14-nodulin and SEC14-GOLD group (in plants SEC14-GOLD proteins are termed PATELLINs, PATLs), which indicates that SEC14L-PITPs play diverse roles from membrane trafficking to organism fitness in plants. We concentrate on the structure of SEC14L-PITPs, their ability to not only bind phospholipids but also other lipophilic ligands, and their ability to regulate complex cellular responses through interacting with proteins at membrane sites.
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- 2023
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8. Induced changes of phenolic compounds in turmeric bread by UV-C radiation
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María del Carmen Valderrama Bravo, Rubén San Miguel-Chávez, Claudia Hernández-Aguilar, Jose Ordonez-Miranda, Marcos Soto-Hernández, A. Dominguez-Pacheco, Mariana Palma-Tenango, and Rumen Ivanov
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UV-C radiation ,Original Paper ,Chemistry ,Secondary metabolites ,General Chemical Engineering ,Uv c radiation ,Turmeric ,Bread ,Safety, Risk, Reliability and Quality ,Industrial and Manufacturing Engineering ,Food Science ,Nuclear chemistry - Abstract
Phenolic compounds of breads added with turmeric at different concentrations (A: 0, B: 1.25, C: 2.5, D: 5 and E:10%) and radiated by UV-C (I. 0, II. 15, III. 30 and IV. 60 s), have been evaluated by HPLC (High-performance liquid chromatography). It is shown that: (i) UV-C radiation modifies the content of phenolic compounds as a function of the percentage of addition of turmeric and the exposure time. There were significant differences (ρ ≤ 0.05) in the concentration of phenolic acids of the turmeric bread (TB): 0 s (sinapic, chlorogenic, protocatechuic), 15 s (chlorogenic, ferulic, protocatechuic, p-hydroxybenzoic, gallic), 30 s (chlorogenic and gallic) and 60 s (chlorogenic). (ii) In TB without radiation appeared, the sinapic, beta resorcylic, syringic and ferulic acids. In the radiation of bread at 15 s, the phenolic acids chlorogenic, ferulic, protocatechuic, p-hydroxybenzoic, gallic, had the highest concentration in the breads added with turmeric at 10% (0.02 μg mL−1), 10% (0.38 μg mL−1), 1.25, 2.5, 5% (0.39 μg mL−1), 10% (1.06 μg mL −1) and 0% (1.10 μg mL−1). (iii) There was a degradation of phenolic acids due to UV-C radiation at 30 and 60 s. At 15 s radiation, sinapic, beta resorcylic, syringic and ferulic acids were not detected in turmeric breads from breads added with turmeric at (1.25, 1.25, 0 and 0%). In radiation at 60 s, beta resorcylic, syringic and ferulic acids were not detected in any bread added with turmeric. In addition, measurements of proximate chemistry, color, sensory analysis, and number of fungal colonies were performed. It is important to mention that the sanitary quality is improved by both UV-C radiation and turmeric. However, the highest results in sanitary quality improvement were due to turmeric.
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- 2021
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9. The Multiple Sclerosis Data Alliance Catalogue
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Lotte Geys, Tina Parciak, Ashkan Pirmani, Robert McBurney, Hollie Schmidt, Tanja Malbaša, Tjalf Ziemssen, Arnfin Bergmann, Juan I. Rojas, Edgardo Cristiano, Juan Antonio García-Merino, Óscar Fernández, Jens Kuhle, Claudio Gobbi, Amber Delmas, Steve Simpson-Yap, Nupur Nag, Bassem Yamout, Nina Steinemann, Pierrette Seeldrayers, Bénédicte Dubois, Ingrid van der Mei, Alexander Stahmann, Jelena Drulovic, Tatjana Pekmezovic, Waldemar Brola, Mar Tintore, Nynke Kalkers, Rumen Ivanov, Magd Zakaria, Maged Abdel Naseer, Wim Van Hecke, Nikolaos Grigoriadis, Marina Boziki, Adriana Carra, Mikolaj A. Pawlak, Ruth Dobson, Kerstin Hellwig, Arlene Gallagher, Letizia Leocani, Gloria Dalla Costa, Nise Alessandra de Carvalho Sousa, Bart Van Wijmeersch, and Liesbet M. Peeters
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Advanced and Specialized Nursing ,Neurology (clinical) - Abstract
Background: One of the major objectives of the Multiple Sclerosis Data Alliance (MSDA) is to enable better discovery of multiple sclerosis (MS) real-world data (RWD). Methods: We implemented the MSDA Catalogue, which is available worldwide. The current version of the MSDA Catalogue collects descriptive information on governance, purpose, inclusion criteria, procedures for data quality control, and how and which data are collected, including the use of e-health technologies and data on collection of COVID-19 variables. The current cataloguing procedure is performed in several manual steps, securing an effective catalogue. Results: Herein we summarize the status of the MSDA Catalogue as of January 6, 2021. To date, 38 data sources across five continents are included in the MSDA Catalogue. These data sources differ in purpose, maturity, and variables collected, but this landscaping effort shows that there is substantial alignment on some domains. The MSDA Catalogue shows that personal data and basic disease data are the most collected categories of variables, whereas data on fatigue measurements and cognition scales are the least collected in MS registries/cohorts. Conclusions: The Web-based MSDA Catalogue provides strategic overview and allows authorized end users to browse metadata profiles of data cohorts and data sources. There are many existing and arising RWD sources in MS. Detailed cataloguing of MS RWD is a first and useful step toward reducing the time needed to discover MS RWD sets and promoting collaboration.
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- 2021
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10. Associations of Disease-Modifying Therapies With COVID-19 Severity in Multiple Sclerosis
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Georgina Arrambide, Ingrid van der Mei, Raed Alroughani, Lars Forsberg, Rodden M. Middleton, Guilherme Sciascia do Olival, Nikola Lazovski, Rumen Ivanov, Alexander Stahmann, Tomas Kalincik, Helmut Butzkueven, Richard S. Nicholas, J. Hillert, Alice Estavo Dias, Edward De Brouwer, Amber Salter, Serkan Ozakbas, Nupur Nag, Doralina Guimarães Brum, Alexander Fidao, Anna Zabalza, Yves Moreau, Ricardo Alonso, Anneke Van Der Walt, Nick Rijke, Lotte Geys, Anibal Chertcoff, Arnfin Bergmann, Robert N. McBurney, Clare Walton, Anna Glaser, Tina Parciak, Gilles Edan, Clément Gautrais, Ashkan Pirmani, Maria Fernanda Mendes, Juan Ignacio Rojas, Melinda Magyari, Liesbet M. Peeters, Robert J. Fox, Hollie Schmidt, Amin Ardeshirdavanai, Steve Simpson-Yap, Stefan Braune, Giancarlo Comi, Johana Bauer, Tim Spelman, Zabalza, Ana/0000-0003-3860-5251, Simpson, Jr., Steve/0000-0001-6521-3056, Kalincik, Tomas/0000-0003-3778-1376, Simpson-Yap, Steve, DE BROUWER, Edward, Kalincik, Tomas, Rijke, Nick, Hillert, Jan A., Walton, Clare, Edan, Gilles, Moreau, Yves, Spelman, Tim, GEYS, Lotte, PARCIAK, Tina, Gautrais, Clement, Lazovski, Nikola, PIRMANI, Ashkan, Ardeshirdavanai, Amin, Forsberg, Lars, Glaser, Anna, McBurney, Robert, Schmidt, Hollie, Bergmann, Arnfin B., Braune, Stefan, Stahmann, Alexander, Middleton, Rodden, Salter, Amber, Fox, Robert J., van der Walt, Anneke, Butzkueven, Helmut, Alroughani, Raed, Ozakbas, Serkan, Rojas, Juan, I, van der Mei, Ingrid, Nag, Nupur, Ivanov, Rumen, do Olival, Guilherme Sciascia, Dias, Alice Estavo, Magyari, Melinda, Brum, Doralina, Mendes, Maria Fernanda, Alonso, Ricardo N., Nicholas, Richard S., Bauer, Johana, Chertcoff, Anibal Sebastian, Zabalza, Anna, Arrambide, Georgina, Fidao, Alexander, Comi, Giancarlo, PEETERS, Liesbet, Institut Català de la Salut, [Simpson-Yap S] Department of Medicine, and Neuroepidemiology Unit, Melbourne School of Population & Global Health, University of Melbourne, Parkville, Australia. Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia [De Brouwer E] University of Tasmania, Hobart, Australia. ESAT-STADIUS, KU Leuven, Belgium. [Kalincik T] Department of Neurology, Melbourne MS Centre, Royal Melbourne Hospital, Parkville, Australia. [Rijke N, Walton C] MS International Federation, London, UK. [Hillert JA] Department of Clinical Neuroscience, Swedish MS Registry, Stockholm, Sweden. [Zabalza A, Arrambide G] Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (CEMCAT), Barcelona, Spain. Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Vall d’Hebron Hospital Universitari, Barcelona, Spain. Universitat Autònoma de Barcelona, Bellaterra, Spain, Vall d'Hebron Barcelona Hospital Campus, and Neuroepidemiology Unit, Melbourne School of Population and Global Health, University of Tasmania, KU Leuven, Royal Melbourne Hospital, MS International Federation, Swedish MS Registry, CHU Pontchaillou, Karolinska Institutet, Hasselt University, University Medical Center, QMENTA, Molecular Unit, Accelerated Cure Project for MS, NeuroTransData, MS Forschungs- und Projektentwicklungs-gGmbH, Swansea University, COViMS, Washington University in St. Louis, Cleveland Clinic, Monash University, Kuwait City, Dokuz Eylul University, Hospital Universitario de CEMIC, RELACOEM, Bulgarian SmartMS COVID-19 Dataset, ABEM-Brazilian MS Patients Association, University Hospital Rigshospitalet, Universidade Estadual Paulista (UNESP), REDONE.br-Brazilian Registry of Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorders, Irmandade da Santa Casa de Misericórdia de São Paulo, Ramos Mejia Hospital-EMA, Imperial College, Mental Health Area, EMA, Cemcat, Vall d'Hebron Hospital Universitari, Universitat Autònoma de Barcelona, and Ospedale San Raffaele
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Male ,Dimethyl Fumarate ,Other subheadings::Other subheadings::/drug therapy [Other subheadings] ,Otros calificadores::Otros calificadores::/complicaciones [Otros calificadores] ,chemistry.chemical_compound ,0302 clinical medicine ,Natalizumab ,virosis::infecciones por virus ARN::infecciones por Nidovirales::infecciones por Coronaviridae::infecciones por Coronavirus [ENFERMEDADES] ,Medicine ,10. No inequality ,COVID-19 (Malaltia) - Complicacions ,B-Lymphocytes ,Nervous System Diseases::Autoimmune Diseases of the Nervous System::Demyelinating Autoimmune Diseases, CNS::Multiple Sclerosis [DISEASES] ,Virus Diseases::RNA Virus Infections::Nidovirales Infections::Coronaviridae Infections::Coronavirus Infections [DISEASES] ,Middle Aged ,3. Good health ,Hospitalization ,enfermedades del sistema nervioso::enfermedades autoinmunitarias del sistema nervioso::enfermedades autoinmunes desmielinizantes del SNC::esclerosis múltiple [ENFERMEDADES] ,Cohort ,Female ,Rituximab ,Life Sciences & Biomedicine ,Research Article ,medicine.drug ,Adult ,medicine.medical_specialty ,Multiple Sclerosis ,Adolescent ,Clinical Neurology ,Otros calificadores::Otros calificadores::/farmacoterapia [Otros calificadores] ,Antibodies, Monoclonal, Humanized ,Young Adult ,03 medical and health sciences ,Internal medicine ,Humans ,Risk factor ,Aged ,030203 arthritis & rheumatology ,Science & Technology ,Expanded Disability Status Scale ,SARS-CoV-2 ,business.industry ,COVID-19 ,Odds ratio ,Respiration, Artificial ,Cross-Sectional Studies ,Siponimod ,chemistry ,Ocrelizumab ,Neurosciences & Neurology ,Neurology (clinical) ,business ,Esclerosi múltiple - Tractament ,030217 neurology & neurosurgery ,Other subheadings::Other subheadings::/complications [Other subheadings] - Abstract
Made available in DSpace on 2022-04-28T19:46:29Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-11-09 Background and ObjectivesPeople with multiple sclerosis MS are a vulnerable group for severe coronavirus disease 2019 COVID-19, particularly those taking immunosuppressive disease-modifying therapies DMTs. We examined the characteristics of COVID-19 severity in an international sample of people with MS.MethodsData from 12 data sources in 28 countries were aggregated sources could include patients from 1-12 countries. Demographic age, sex, clinical MS phenotype, disability, and DMT untreated, alemtuzumab, cladribine, dimethyl fumarate, glatiramer acetate, interferon, natalizumab, ocrelizumab, rituximab, siponimod, other DMTs covariates were queried, along with COVID-19 severity outcomes, hospitalization, intensive care unit ICU admission, need for artificial ventilation, and death. Characteristics of outcomes were assessed in patients with suspected/confirmed COVID-19 using multilevel mixed-effects logistic regression adjusted for age, sex, MS phenotype, and Expanded Disability Status Scale EDSS score.ResultsSix hundred fifty-seven 28.1% with suspected and 1,683 61.9% with confirmed COVID-19 were analyzed. Among suspected plus confirmed and confirmed-only COVID-19, 20.9% and 26.9% were hospitalized, 5.4% and 7.2% were admitted to ICU, 4.1% and 5.4% required artificial ventilation, and 3.2% and 3.9% died. Older age, progressive MS phenotype, and higher disability were associated with worse COVID-19 outcomes. Compared to dimethyl fumarate, ocrelizumab and rituximab were associated with hospitalization adjusted odds ratio [aOR] 1.56, 95% confidence interval [CI] 1.01-2.41; aOR 2.43, 95% CI 1.48-4.02 and ICU admission aOR 2.30, 95% CI 0.98-5.39; aOR 3.93, 95% CI 1.56-9.89, although only rituximab was associated with higher risk of artificial ventilation aOR 4.00, 95% CI 1.54-10.39. Compared to pooled other DMTs, ocrelizumab and rituximab were associated with hospitalization aOR 1.75, 95% CI 1.29-2.38; aOR 2.76, 95% CI 1.87-4.07 and ICU admission aOR 2.55, 95% CI 1.49-4.36; aOR 4.32, 95% CI 2.27-8.23, but only rituximab was associated with artificial ventilation aOR 6.15, 95% CI 3.09-12.27. Compared to natalizumab, ocrelizumab and rituximab were associated with hospitalization aOR 1.86, 95% CI 1.13-3.07; aOR 2.88, 95% CI 1.68-4.92 and ICU admission aOR 2.13, 95% CI 0.85-5.35; aOR 3.23, 95% CI 1.17-8.91, but only rituximab was associated with ventilation aOR 5.52, 95% CI 1.71-17.84. Associations persisted on restriction to confirmed COVID-19 cases. No associations were observed between DMTs and death. Stratification by age, MS phenotype, and EDSS score found no indications that DMT associations with COVID-19 severity reflected differential DMT allocation by underlying COVID-19 severity.DiscussionUsing the largest cohort of people with MS and COVID-19 available, we demonstrated consistent associations of rituximab with increased risk of hospitalization, ICU admission, and need for artificial ventilation and of ocrelizumab with hospitalization and ICU admission. Despite the cross-sectional design of the study, the internal and external consistency of these results with prior studies suggests that rituximab/ocrelizumab use may be a risk factor for more severe COVID-19. CORe Department of Medicine and Neuroepidemiology Unit Melbourne School of Population and Global Health Menzies Institute for Medical Research University of Tasmania ESAT-STADIUS KU Leuven Department of Neurology Melbourne MS Centre Royal Melbourne Hospital MS International Federation Department of Clinical Neuroscience Swedish MS Registry Department of Neurology CHU Pontchaillou Karolinska Institutet Biomedical Research Institute-Data Science Institute Hasselt University Department of Medical Informatics University Medical Center Department of Computer Science and AI KU Leuven QMENTA Medpace Reference Laboratories Molecular Unit IConquerMS People-Powered Research Network Accelerated Cure Project for MS NeuroTransData Study Group NeuroTransData German MS-Register by the National MS Society MS Forschungs- und Projektentwicklungs-gGmbH MS Register Swansea University COViMS Division of Biostatistics Washington University in St. Louis Mellen Center for Multiple Sclerosis Cleveland Clinic Department of Neuroscience Central Clinical School Monash University Al-Amiri Hospital Kuwait City Dokuz Eylul University Neurology Department Hospital Universitario de CEMIC RELACOEM Australian MS Longitudinal Study Menzies Institute for Medical Research University of Tasmania Bulgarian SmartMS COVID-19 Dataset ABEM-Brazilian MS Patients Association Danish Multiple Sclerosis Registry Department of Neurology University Hospital Rigshospitalet Universidade Estadual Paulista Unesp Faculdade de Medicina REDONE.br-Brazilian Registry of Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorders Irmandade da Santa Casa de Misericórdia de São Paulo Multiple Sclerosis University Center Ramos Mejia Hospital-EMA Imperial College Swansea University Mental Health Area MS and Demyelinating Diseases Hospital Británico de Buenos Aires EMA Servei de Neurologia-Neuroimmunologia Centre d'Esclerosi Múltiple de Catalunya Cemcat Vall d'Hebron Institut de Recerca Vall d'Hebron Hospital Universitari Universitat Autònoma de Barcelona Institute of Experimental Neurology Ospedale San Raffaele Universidade Estadual Paulista Unesp Faculdade de Medicina
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- 2021
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11. FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) accumulates in homo- and heterodimeric complexes in dynamic and inducible nuclear condensates associated with speckle components
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Ksenia Trofimov, Regina Gratz, Rumen Ivanov, Yvonne Stahl, Petra Bauer, and Tzvetina Brumbarova
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Some nuclear proteins undergo condensation, but the functional importance remains often unclear. The basic helix-loop-helix (bHLH) FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) integrates internal and external signals to control iron acquisition and growth. The previously described C-terminal residues Ser271/272 allow FIT to form active complexes with subgroup Ib bHLH factors such as bHLH039. FIT has lower nuclear mobility than mutant FITmSS271AA. Here, we show that FIT undergoes a light-inducible subnuclear partitioning into nuclear condensates that we termed FIT nuclear bodies (NBs). FIT NB characteristics were examined using a standardized FIT NB analysis procedure coupled with different types of quantitative and qualitative microscopy-based approaches. FIT condensates were reversible and likely formed by liquid-liquid phase separation. FIT accumulated preferentially in FIT NBs versus nucleoplasm when engaged in protein complexes with itself and with bHLH039. FITmSS271AA, instead, localized to NBs with different dynamics. FIT colocalized with splicing and light signaling NB markers. The light conditions inducing NBs were linked with active FIT and elevated FIT target gene expression in roots. Hence, the inducible highly dynamic FIT condensates link active transcription factor complexes with posttranscriptional regulation processes and light. Inducible FIT nuclear condensates may affect nuclear mobility and integrate environmental and Fe nutrition signals.HighlightsFIT undergoes light-induced, reversible condensation and localizes to nuclear bodies (NBs), likely via liquid-liquid phase separationFunctionally relevant Ser271/272 defines an intrinsically disordered region and influences NB formation dynamicsNBs are preferential sites for FIT dimerization with FIT and bHLH039, dependent on Ser271/272FIT NBs colocalize with NB markers related to splicing and light signalingLight conditions inducing NBs are linked with active FIT, in agreement with elevated FIT target gene expression in roots
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- 2022
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12. Organic nitrogen nutrition: LHT1.2 protein from hybrid aspen (Populus tremula L. x tremuloides Michx) is a functional amino acid transporter and a homolog of Arabidopsis LHT1
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Henrik Svennerstam, Ulrika Ganeteg, Mattias Holmlund, Iftikhar Ahmad, Sandra Jämtgård, Jonathan Love, Rumen Ivanov, and Regina Gratz
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0106 biological sciences ,0301 basic medicine ,nitrogen nutrition ,Amino Acid Transport Systems ,Nitrogen ,Physiology ,amino acid uptake ,Populus tremula L. x tremuloides Michx ,Mutant ,Lysine ,organic nitrogen ,Arabidopsis ,lysine histidine transporter (LHT) ,Plant Science ,01 natural sciences ,03 medical and health sciences ,hybrid aspen ,Arabidopsis thaliana ,early senescence-like phenotype ,Amino acid transporter ,Ecosystem ,chemistry.chemical_classification ,amino acid transport ,biology ,AcademicSubjects/SCI01210 ,Chemistry ,Transporter ,biology.organism_classification ,Amino acid ,Complementation ,Populus ,030104 developmental biology ,Biochemistry ,Research Paper ,010606 plant biology & botany - Abstract
The contribution of amino acids (AAs) to soil nitrogen (N) fluxes is higher than previously thought. The fact that AA uptake is pivotal for N nutrition in boreal ecosystems highlights plant AA transporters as key components of the N cycle. At the same time, very little is known about AA transport and respective transporters in trees. Tree genomes may contain 13 or more genes encoding the lysine histidine transporter (LHT) family proteins, and this complicates the study of their significance for tree N-use efficiency. With the strategy of obtaining a tool to study N-use efficiency, our aim was to identify and characterize a relevant AA transporter in hybrid aspen (Populus tremula L. x tremuloides Michx.). We identified PtrLHT1.2, the closest homolog of Arabidopsis thaliana (L.) Heynh AtLHT1, which is expressed in leaves, stems and roots. Complementation of a yeast AA uptake mutant verified the function of PtrLHT1.2 as an AA transporter. Furthermore, PtrLHT1.2 was able to fully complement the phenotypes of the Arabidopsis AA uptake mutant lht1 aap5, including early leaf senescence-like phenotype, reduced growth, decreased plant N levels and reduced root AA uptake. Amino acid uptake studies finally showed that PtrLHT1.2 is a high affinity transporter for neutral and acidic AAs. Thus, we identified a functional AtLHT1 homolog in hybrid aspen, which harbors the potential to enhance overall plant N levels and hence increase biomass production. This finding provides a valuable tool for N nutrition studies in trees and opens new avenues to optimizing tree N-use efficiency.
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- 2021
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13. Caracterización colorimétrica, textura y calidad sanitaria de panes adicionados con maíces criollos y Curcuma longa
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Claudia Hernandez-Aguilar, Maria del Carmen Valderrama-Bravo, Arturo Dominguez-Pacheco, Raul Romero-Galindo, Otoniel Igno-Rosario, Eder Contreras-Gallegos, Rumen Ivanov Tsonchev, and Alfredo Cruz-Orea
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Surfaces, Coatings and Films - Abstract
En esta investigación se planteó como objetivo caracterizar color, textura y calidad sanitaria de pan adicionado con maíz criollo y cúrcuma. Se realizaron 14 diferentes panes empleando seis tipos de maíces (M1, M2, M3, M4, M5 y M6). Los principales hallazgos fueron a) El color de los maíces, harinas nixtamalizada y masas tuvieron diferencia significativa (p < 0.05) al comparar valores medios de parámetros de Luminosidad, a* y b*. Los maíces azules y rojizo M2 (37.01), M3 (44.06) y M6 (41.07) y, amarillos y amarillo-naranja M1 (21.26), M4 (15.92) y M5 (26.01) presentaron los valores inferiores en L* y superiores en b*, respectivamente. La menor diferencia en color ?E encontrada en el proceso de transformación de maíz a harina y masa, fue para maíces amarillos. b) En el pan de maíz se encontraron diferencias significativas en variable a* al compararse el mismo tipo de pan durante tres días consecutivos, en los panes BM1, BM5 y BM6, con una disminución de 7.5, 2.6 y 16.9%, con respecto al primer día. c) La calidad sanitaria del pan de trigo mejora con la adición de maíz nixtamalizado y cúrcuma. En los panes adicionados de maíz los que presentaron menor cantidad de colonias de hongos fueron los maíces azules y rojo (M2, M3 y M6). d) La dureza del pan de maíz criollo y cúrcuma no presentó diferencias durante tres días consecutivos beneficiando su conservación. El pan de maíz amarillo y cúrcuma BM1-C mostró incrementos en la dureza en los días 2 y 3.
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- 2022
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14. Phylogenetic analysis of plant multi-domain SEC14-like phosphatidylinositol transfer proteins and structure–function properties of PATELLIN2
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Petra Bauer, Karolin Montag, Jannik Hornbergs, and Rumen Ivanov
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Cell division ,Lineage (evolution) ,Plant Science ,SEC14 ,Phosphatidylinositols ,Article ,Structure-Activity Relationship ,Protein Domains ,Arabidopsis ,Genetics ,Phospholipid Transfer Proteins ,PATELLIN ,Phylogeny ,Phosphatidylinositol transfer protein ,Chara ,biology ,Phylogenetic tree ,Arabidopsis Proteins ,Gene Expression Profiling ,Cell Membrane ,Membrane ,General Medicine ,biology.organism_classification ,Plant cell ,Biological Evolution ,Cell biology ,Liposome ,GOLD domain ,Phosphatidylinositides ,Agronomy and Crop Science - Abstract
Key message SEC14L-PITPs guide membrane recognition and signaling. An increasingly complex modular structure of SEC14L-PITPs evolved in land plants compared to green algae. SEC14/CRAL-TRIO and GOLD domains govern membrane binding specificity. Abstract SEC14-like phosphatidylinositol transfer proteins (SEC14L-PITPs) provide cues for membrane identity by exchanging lipophilic substrates, ultimately governing membrane signaling. Flowering plant SEC14L-PITPs often have modular structure and are associated with cell division, development, and stress responses. Yet, structure–function relationships for biochemical–cellular interactions of SEC14L-PITPs are rather enigmatic. Here, we evaluate the phylogenetic relationships of the SEC14L-PITP superfamily in the green lineage. Compared to green algae, land plants have an extended set of SEC14L-PITPs with increasingly complex modular structure. SEC14-GOLD PITPs, present in land plants but not Chara, diverged to three functional subgroups, represented by the six PATELLIN (PATL) proteins in Arabidopsis. Based on the example of Arabidopsis PATL2, we dissect the functional domains for in vitro binding to phosphoinositides and liposomes and for plant cell membrane association. While the SEC14 domain and its CRAL-TRIO-N-terminal extension serve general membrane attachment of the protein, the C-terminal GOLD domain directs it to the plasma membrane by recognizing specific phosphoinositides. We discuss that the different domains of SEC14L-PITPs integrate developmental and environmental signals to control SEC14L-PITP-mediated membrane identity, important to initiate dynamic membrane events. Electronic supplementary material The online version of this article (10.1007/s11103-020-01067-y) contains supplementary material, which is available to authorized users.
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- 2020
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15. EMAC, Retromer, and VSRs: do they connect?
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David Robinson and Rumen Ivanov
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0106 biological sciences ,0301 basic medicine ,Retromer ,Sorting Nexins ,Golgi Apparatus ,Plant Science ,Biology ,Endomembrane trafficking ,Sorting nexin ,01 natural sciences ,Vesicle tethering ,SNX ,03 medical and health sciences ,New Ideas in Cell Biology ,Compartment (development) ,Endomembrane system ,Subcellular localization ,VPS26-VPS35-VPS29 ,Biological Transport ,Cell Biology ,General Medicine ,Cell biology ,030104 developmental biology ,Vacuoles ,Function (biology) ,010606 plant biology & botany - Abstract
Eukaryotic organisms share many common features in terms of endomembrane trafficking. This fact has helped plant scientists to propose testable hypotheses on how plant intracellular membrane trafficking is achieved and regulated based on knowledge from yeast and mammals. However, when a new compartment has been identified in a plant cell that has a vesicle tethering complex located at a position which is completely different to its counterpart in yeast and mammalian cells, caution is demanded when interpreting possible interactions with other trafficking elements. This is exemplified by the recently discovered EMAC (ER and microtubule-associated compartment). It has been postulated that this compartment is the recipient of vacuolar sorting receptors (VSRs) transported retrogradely via “retromer vesicles” from a post-Golgi location. Unfortunately, this suggestion was based entirely on our knowledge of retromer from yeast and mammalian cells, and did not take into account the available literature on the composition, localization, and function of the plant retromer. It also lacked reference to recent contradictory findings on VSR trafficking. In this short article, we have tried to rectify this situation, pointing out that plant retromer may not function as a pentameric complex of two subunits: the retromer core and the sorting nexins.
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- 2020
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16. 1298Associations of DMT therapies with COVID-19 severity in multiple sclerosis
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Lotte Geyes, Nikola Lazovski, Ingrid van der Mei, Ricardo Alonso, Anna Glaser, Tomas Kalincik, Tina Parciak, Rumen Ivanov, Richard Nicholas, Arnfin Bergmann, Gilles Edan, Ashkan Pirmani, Hollie Schmidt, Amber Salter, Robert J. Fox, Steve Simpson-Yap, Johana Bauer, Jan Hillert, Liesbet Peeters, Giancarlo Comi, Amin Ardeshirdavani, Helmut Butzkueven, Alexander Fidao, Anibal Chertcoff, Alice Estavo Dias, Robert N. McBurney, Melinda Magyari, Lars Forsberg, Ana Zabalza, Georgina Arrambide, Alexander Stahmann, Rodden M. Middleton, Nupur Nag, Doralina Guimarães Brum, Nick Rijke, Guilherme Sciascia do Olival, Tim Spelman, Juan Ignacio Rojas, Edward De Brouwer, Clare Walton, Anneke van der Walt, Clément Gautrais, Maria Fernandes Mendes, and Stefan Braune
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medicine.medical_specialty ,Epidemiology ,business.industry ,Multiple sclerosis ,General Medicine ,medicine.disease ,Intensive care unit ,law.invention ,chemistry.chemical_compound ,Siponimod ,Natalizumab ,chemistry ,law ,Internal medicine ,medicine ,Alemtuzumab ,Ocrelizumab ,Rituximab ,Risk factor ,business ,medicine.drug - Abstract
Background People with multiple sclerosis (MS) are a vulnerable group for severe COVID-19, particularly those taking immunosuppressive disease-modifying therapies (DMTs). We examined the characteristics of COVID-19 severity in an international sample of people with MS. Methods Data from 12 data-sources in 28 countries were aggregated (sources could include patients from 1-12 countries). Demographic (age, sex), clinical (MS phenotype, disability), and DMT (untreated, alemtuzumab, cladribine, dimethyl-fumarate, glatiramer-acetate, interferon, natalizumab, ocrelizumab, rituximab, siponimod, other) covariates were queried, alongside COVID-19 hospitalisation, admission to ICU, requiring artificial ventilation, and death. Characteristics of outcomes were assessed in patients with suspected/confirmed COVID-19 using multilevel mixed-effects logistic regression, adjusted for age, sex, MS phenotype, and EDSS. Results 657 (28.1%) with suspected and 1,683 (61.9%) with confirmed COVID-19 were analysed. Among suspected+confirmed/confirmed-only COVID-19, 20.9%/26.9% were hospitalised, 5.4%/7.2% were admitted to ICU, 4.1%/5.4% required artificial ventilation, and 3.2%/3.9% died. Older age, progressive MS-phenotype, and higher disability were associated with worse COVID-19 outcomes. Compared to dimethyl-fumarate, ocrelizumab and rituximab were associated with hospitalisation (aOR=1.56,95%CI=1.01-2.41; aOR=2.43,95%CI=1.48-4.02) and ICU admission (aOR=2.30,95%CI=0.98-5.39; aOR=3.93,95%CI=1.56-9.89), though only rituximab was associated with higher risk of artificial ventilation (aOR=4.00,95%CI=1.54-10.39). Importantly, associations persisted on restriction to confirmed COVID-19 cases. No associations were observed between DMTs and death. Conclusions Despite the cross-sectional design of this study, the internal and external consistency of these results with prior studies suggests their use may be a risk factor for more severe COVID-19. Key messages Anti-CD20 DMTs may be associated with worse COVID-19 severity amongst people with multiple sclerosis.
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- 2021
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17. Modeling of active thermography through uncertainty quantifi cation of parameters of the heat transfer equation
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Tapia Arturo Ortiz, Tsonchev Rumen Ivanov, Mart´ın A D´ıaz Viera, Hern Marlen, and Marlen Hern andez Ortiz
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Materials science ,Thermography ,Heat transfer ,Mechanics ,Laser beams ,Power (physics) - Abstract
Active thermography is an experimental technique used to analyze samples of materials or entire structures without destroying them, by means of a heat source, such as a laser beam of a given power.
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- 2019
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18. The Nutrient Response Transcriptional Regulome of Arabidopsis
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Tzvetina Brumbarova and Rumen Ivanov
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0301 basic medicine ,Plant Nutrition ,Omics ,Plant Biology ,Regulome ,02 engineering and technology ,Computational biology ,Article ,Transcriptome ,03 medical and health sciences ,Nutrient ,Arabidopsis ,Transcriptional regulation ,lcsh:Science ,Transcriptomics ,Multidisciplinary ,biology ,Nutrient stress ,Biological Sciences ,021001 nanoscience & nanotechnology ,Gene coexpression ,biology.organism_classification ,030104 developmental biology ,lcsh:Q ,0210 nano-technology ,Reprogramming - Abstract
Summary Plants respond actively to changes in their environment. Variations in nutrient availability elicit substantial transcriptional reprogramming, and we aimed to systematically describe these adjustments and identify the regulators responsible. Using gene coexpression analysis based on 13 different nutrient availability anomalies, we defined and analyzed nutrient stress response signatures. We identified known regulators and could predict functions in nutrient responses for transcriptional regulators previously associated with other processes, thus linking development and environmental interaction. Three of the identified transcriptional regulators, PIF4, HY5, and NF-Y, known from their role in light signaling, targeted a substantial part of the network and may participate in remodeling the global Arabidopsis transcriptome in response to variations of nutrient availability. We present gene coexpression and transcriptional regulation networks, which can be used as tools to further explore regulatory events and dependencies even by users with basic informatics skills., Graphical Abstract, Highlights • Gene coexpression analysis is a powerful tool for elucidating nutrient stress • Nutrient stress elicits unique signatures of modular transcriptional response • Master transcriptional regulators coordinate plant growth and nutrient utilization • Analysis suggests PIF4, HY5, and the NF-Y to be master regulators, Biological Sciences; Omics; Plant Biology; Plant Nutrition; Transcriptomics
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- 2019
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19. Orphan crops at the food for future conference
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Rumen Ivanov, Richard P. Jacoby, Mara Schuler-Bermann, Stanislav Kopriva, Antonella Succurro, and Timothy O. Jobe
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Crops, Agricultural ,0106 biological sciences ,0301 basic medicine ,Novel food ,Context (language use) ,Plant Science ,01 natural sciences ,Food Supply ,03 medical and health sciences ,Global population ,Functional food ,Political science ,Genetics ,Vision ,Food security ,business.industry ,Congresses as Topic ,Public relations ,Crop Production ,030104 developmental biology ,Food ,Agriculture ,Food processing ,business ,Forecasting ,010606 plant biology & botany - Abstract
In her 1929 essay A Room of One's Own, Virginia Wolf famously wrote, "One cannot think well, love well, sleep well, if one has not dined well." While this popular quote is perhaps not the most inspiring, it is an elegant reminder that food and the cultural practices surrounding food are paramount for our wellbeing. However, in our quest to feed a growing global population, we have become focused on increasing the production of a few staple crops and overlooked hundreds or thousands of locally and regionally important crops that may represent the future of agriculture. The growing interest in identifying and developing promising new crops and novel food sources prompted the 1st Cologne Conference on Food for Future, which took place between the 5 and 7th of September 2018 at the Rautenstrauch-Joest museum in Cologne, Germany. It offered a unique platform for researchers, journalists, politicians, and entrepreneurs to present and discuss their views, visions, and concerns on the topics of Food Security. This interdisciplinary meeting acted as a stage to cover diverse aspects of crop science, food research, and food production in the context of global food and nutrition security. Three sessions accommodated scientific contributions on the topics of "Orphan Crops", "Functional food", and "Innovative food sources and production systems", and two public events (a public lecture and a plenary discussion) engaged the citizens with informative discussions on relevant and mediatic topics. With delegates from Africa, Europe, and the United States of America, the conference aimed at building bridges between different communities through scientific exchange.
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- 2019
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20. Calcium-Promoted Interaction between the C2-Domain Protein EHB1 and Metal Transporter IRT1 Inhibits Arabidopsis Iron Acquisition
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Holger Gohlke, Rubek Merina Basgaran, Kalina Angrand, Stephan Schott-Verdugo, Claudia Fink-Straube, Lara Genders, Imran Khan, Tzvetina Brumbarova, Petra Bauer, Polina Denezhkin, Regina Gratz, and Rumen Ivanov
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0106 biological sciences ,Physiology ,Iron ,Saccharomyces cerevisiae ,Arabidopsis ,chemistry.chemical_element ,Plant Science ,Calcium ,01 natural sciences ,Membrane Lipids ,Gene Expression Regulation, Plant ,Genetics ,Arabidopsis thaliana ,Cation Transport Proteins ,Ecosystem ,C2 domain ,biology ,Arabidopsis Proteins ,Chemistry ,Cell Membrane ,Genetic Complementation Test ,Peripheral membrane protein ,Biological Transport ,Transporter ,Plants, Genetically Modified ,biology.organism_classification ,Cell biology ,Complementation ,C2 Domains ,Research Article ,Protein Binding ,010606 plant biology & botany - Abstract
Iron is a key transition element in the biosphere and is crucial for living organisms, although its cellular excess can be deleterious. Maintaining the balance of optimal iron availability in the model plant Arabidopsis (Arabidopsis thaliana) requires the precise operation of iron import through the principal iron transporter IRON-REGULATED TRANSPORTER1 (IRT1). Targeted inhibition of IRT1 can prevent oxidative stress, thus promoting plant survival. Here, we report the identification of an IRT1 inhibitor, namely the C2 domain-containing peripheral membrane protein ENHANCED BENDING1 (EHB1). EHB1 interacts with the cytoplasmically exposed variable region of IRT1, and we demonstrate that this interaction is greatly promoted by the presence of calcium. We found that EHB1 binds lipids characteristic of the plasma membrane, and the interaction between EHB1 and plant membranes is calcium-dependent. Molecular simulations showed that EHB1 membrane binding is a two-step process that precedes the interaction between EHB1 and IRT1. Genetic and physiological analyses indicated that EHB1 acts as a negative regulator of iron acquisition. The presence of EHB1 prevented the IRT1-mediated complementation of iron-deficient fet3fet4 yeast (Saccharomyces cerevisiae). Our data suggest that EHB1 acts as a direct inhibitor of IRT1-mediated iron import into the cell. These findings represent a major step in understanding plant iron acquisition, a process that underlies the primary production of bioavailable iron for land ecosystems.
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- 2019
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21. Bironchigram processing method for quantitative evaluation of optical focusing mirrors
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Jorge L. Flores, Rumen Ivanov, Ismael de la Rosa, Gustavo Rodríguez, and Jesús Villa
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Wavefront ,Iterative method ,Computer science ,Mechanical Engineering ,Image processing ,02 engineering and technology ,021001 nanoscience & nanotechnology ,Grid ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,Ronchi test ,Field (computer science) ,Electronic, Optical and Magnetic Materials ,010309 optics ,Interferometry ,Schlieren ,0103 physical sciences ,Electrical and Electronic Engineering ,0210 nano-technology ,Algorithm - Abstract
Since its proposal the Ronchi “ruling” test has been considered as the most remarkable technique of the Schlieren family. Despite being based on fringe pattern generation and commonly interpreted in a qualitative way, it was capable of achieving outstanding results in the detection of aberrations in optical surfaces. Given its theoretical straightforwardness, experimental simplicity and economic affordability in comparison to other methodologies in the field, in the present work is addressed the lingering issue of how to extract quantitative information from digital captures of this test. Such task was accomplished taking advantage of the improved Ronchi test with a square grid, from which it was possible to develop a mathematical model with foundation in the Fourier theory to describe its observations. Thereupon, it was devised a novel iterative algorithm grounded in Fourier phase measuring able to compute fairly accurate wavefront gradient estimations from a single “bironchigram” sample with grid defocus. This procedure is complemented by a mandatory integration algorithm that is based on the regularization theory. The overall proposed methodology was put to test in a large aspherical mirror, estimating a surface aberration profile with a P–V (peak to valley) ratio of 155 nm, value well in accord with the one reported by the commercial interferometric system used for validation.
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- 2019
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22. Photoacoustic Spectroscopy in the Optical Characterization of Foodstuff: A Review
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Claudia Hernández-Aguilar, Rumen Ivanov, A. Dominguez-Pacheco, and Alfredo Cruz-Orea
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Materials science ,Food industry ,business.industry ,010401 analytical chemistry ,food and beverages ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Analytical Chemistry ,Characterization (materials science) ,lcsh:QC350-467 ,Food science ,0210 nano-technology ,Food quality ,business ,Photoacoustic spectroscopy ,lcsh:Optics. Light ,Spectroscopy ,Contaminated food - Abstract
In this review, the application of the photoacustic spectroscopy (PAS) is presented as an option to evaluate the quality of food. This technique is a type of spectroscopy based on photothermal phenomena, which allow spectroscopic studies. According to the literature review, it was found that its application is increasing in several countries. Spectroscopic studies carried out by employing PAS in the food industry include, among others, fruit, vegetables, condiments, grains, legumes, flours, “tortillas,” milk, water, eggs, etc. Additionally, this technique has been used to evaluate adulterated, irradiated, and contaminated food and so on. The literature review has shown the applicability of PAS to one of the problems of the real world, i.e., food quality assessment. Therefore, PAS can contribute in the future with a wide potential for new applications in the food agroindustry.
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- 2019
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23. Associations of DMT therapies with COVID-19 severity in multiple sclerosis
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Tomas Kalincik, Nick Rijke, Ingrid van der Mei, Clare Walton, Clément Gautrais, Stefan Braune, Yves Moreau, Tim Spelman, Robert McBurney, Georgina Arrambide, Guilherme Sciascia do Olival, Juan Ignacio Rojas, Edward De Brouwer, Jan Hillert, Amin Ardeshirdavani, Ashkan Pirmani, Giancarlo Comi, Lotte Geys, Anna Glaser, Alice Estavo Dias, Alexander Stahmann, Doralina Guimarães Brum, Alexander Fidao, Melinda Magyari, Rumen Ivanov, Lars Forsberg, Amber Salter, Rodden M. Middleton, Nikola Lazovski, Anneke van der Walt, R. Alroughani, Serkan Ozakbas, Liesbet M. Peeters, Helmut Butzkueven, Maria Fernanda Mendes, Anibal Chertcoff, Arnfin Bergmann, Hollie Schmidt, Nupur Nag, Tina Parciak, Richard Nicholas, Gilles Edan, Steve Simpson-Yap, Robert J. Fox, Johana Bauer, Ricardo Alonso, and Anna Zabalza
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Artificial ventilation ,medicine.medical_specialty ,business.industry ,medicine.medical_treatment ,Multiple sclerosis ,Logistic regression ,medicine.disease ,3. Good health ,03 medical and health sciences ,0302 clinical medicine ,Natalizumab ,Internal medicine ,Cohort ,Medicine ,Ocrelizumab ,Rituximab ,030212 general & internal medicine ,Risk factor ,business ,030217 neurology & neurosurgery ,medicine.drug - Abstract
BackgroundPeople with multiple sclerosis (MS) are a vulnerable group for severe COVID-19, particularly those taking immunosuppressive disease-modifying therapies (DMTs). We examined the characteristics of COVID-19 severity in an international sample of people with MS.MethodsData from 12 data-sources in 28 countries were aggregated. Demographic and clinical covariates were queried, alongside COVID-19 clinical severity outcomes, hospitalisation, admission to ICU, requiring artificial ventilation, and death. Characteristics of outcomes were assessed in patients with suspected/confirmed COVID-19 using multilevel mixed-effects logistic regression.Results657 (28.1%) with suspected and 1,683 (61.9%) with confirmed COVID-19 were analysed. Older age, progressive MS-phenotype, and higher disability were associated with worse COVID-19 outcomes. Compared to dimethyl fumarate, ocrelizumab and rituximab were associated with hospitalisation (aOR=1.56,95%CI=1.01-2.41; aOR=2.43,95%CI=1.48-4.02) and ICU admission (aOR=2.30,95%CI=0.98-5.39; aOR=3.93,95%CI=1.56-9.89), though only rituximab was associated with higher risk of artificial ventilation (aOR=4.00,95%CI=1.54-10.39). Compared to pooled other DMTs, ocrelizumab and rituximab were associated with hospitalisation (aOR=1.75,95%CI=1.29-2.38; aOR=2.76,95%CI=1.87-4.07) and ICU admission (aOR=2.55,95%CI=1.49-4.36; aOR=4.32,95%CI=2.27-8.23) but only rituximab with artificial ventilation (aOR=6.15,95%CI=3.09-12.27). Compared to natalizumab, ocrelizumab and rituximab were associated with hospitalisation (aOR=1.86,95%CI=1.13-3.07; aOR=2.88,95%CI=1.68-4.92) and ICU admission (aOR=2.13,95%CI=0.85-5.35; aOR=3.23,95%CI=1.17-8.91), but only rituximab with ventilation (aOR=5.52,95%CI=1.71-17.84). Importantly, associations persisted on restriction to confirmed COVID-19 cases. No associations were observed between DMTs and death.ConclusionsUsing the largest cohort of people with MS and COVID-19 available, we demonstrated consistent associations of rituximab with increased risk of hospitalisation, ICU admission, and requiring artificial ventilation, and ocrelizumab with hospitalisation and ICU admission, suggesting their use may be a risk factor for more severe COVID-19.
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- 2021
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24. Photoacoustic characterization of wheat bread mixed with
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C, Hernandez-Aguilar, A, Dominguez-Pacheco, C, Valderrama-Bravo, A, Cruz-Orea, E, Martínez Ortiz, Rumen, Ivanov, and J, Ordonez-Miranda
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Moringa oleifera ,Wheat flour ,digestive, oral, and skin physiology ,food and beverages ,Antifungal activity ,Bread photoacoustic spectrum ,Research Article - Abstract
Photoacoustic spectroscopy is applied to evaluate the impact of Moringa at different concentrations (0, 1.25, 2.5, 5 and 10%) on the elaboration, sanity, texture, and color of wheat bread. It was found that: i) Photoacoustic signal amplitude values of bread significantly increase from 37 to 90% when moringa powder concentration raises from 1.25% to 10%, at 300 nm wavelength. ii) Comparing the photoacoustic signal values at 300, 330, and 370 nm wavelengths, produced by the different bread types, there were statistically significant differences. iii) The sanitary quality of bread mixed with a 2.5% of moringa is relatively higher than the ones obtained for other concentrations, such that the number of fungal colonies were reduced by 99% in comparison with the control bread without moringa, after six days of storage. Moringa at 2.5% of concentration could thus improve the sanitary quality of wheat bread. iv) The addition of moringa for making bread slows down its textural changes (hardness, elasticity, cohesiveness, resilience, and chewiness) during storage. v) Finally, the highest correlation between the photoacoustic amplitude and the moringa concentration occurs at the wavelengths of 300 and 330 nm, which could be related to significant changes in the content of flavonoids and phenolic acids., Graphical abstract The PAS technique allows characterizing the different concentrations of Moringa oleifera in bread and analyzing the data through various mathematical models., Highlights • Fortified foods with vitamin and mineral content •Non-destructive technique for the characterization of foods •Moringa added to white bread modifies its textural quality.
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- 2021
25. Growth Sphere for Optical Measurements in Plants
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Efrén González, Daniel Alaniz, Noel Mijares, Ismael de la Rosa, Ernesto Olvera, and Rumen Ivanov
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Surface (mathematics) ,0303 health sciences ,030303 biophysics ,Optical measurements ,04 agricultural and veterinary sciences ,Geometric shape ,engineering.material ,Ray ,03 medical and health sciences ,Variable (computer science) ,Coating ,040103 agronomy & agriculture ,engineering ,0401 agriculture, forestry, and fisheries ,Stage (hydrology) ,Biological system ,Absorption (electromagnetic radiation) ,Mathematics - Abstract
A precise measurement in plants is necessary to know in detail the functions and processes of these living beings, which are a fundamental part for the development of life on the planet. The optimal growth conditions for any plant generated in a controlled atmosphere are very helpful to make measurements of the variable that may be the highest hierarchy: light. This paper describes the design of a growth sphere for optical measurements in plants (GSOMP), which fulfills two primary functions; generate the optimal conditions for the growth of the plant during its whole life cycle and perform incident light absorption measurements taking advantage of the geometric shape (spherical) and the coating of the device surface, so it is possible to obtain the light absorption spectrum in each phenological stage of any plant. Due to the aforementioned, this device is unique and represents a very useful option for research and experimentation in vegetables.
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- 2020
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26. Associations of DMT Therapies with COVID-19 Severity in Multiple Sclerosis: An International Cohort Study
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Liesbet Peeters, Lotte Geys, Anna Glaser, Nupur Nag, Welt Avd, Lars Forsberg, Ashkan Pirmani, Juan Ignacio Rojas, Alexander Stahmann, Tina Parciak, Ricardo Alonso, Amin Ardeshirdavani, Gilles Edan, Maria Fernanda Mendes, Alice Estavo Dias, Helmut Butzkueven, Doralina Guimarães Brum, Hollie Schmidt, J. Hillert, Mei Ivd, Yves Moreau, Rod Middleton, Anibal Chertcoff, Amber Salter, Arnfin Bergmann, Robert McBurney, Georgina Arrambide, Edward De Brouwer, Tim Spelman, Rumen Ivanov, Melinda Magyari, Clare Walton, Steve Simpson-Yap, Clément Gautrais, Nikola Lazovski, Stefan Braune, Olival GSd, Tomas Kalincik, Nick Rijke, Giancarlo Comi, Alexander Fidao, Anna Zabalza, Richard Nicholas, Robert J. Fox, and Johana Bauer
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Oncology ,medicine.medical_specialty ,Text mining ,Coronavirus disease 2019 (COVID-19) ,business.industry ,Internal medicine ,Multiple sclerosis ,medicine ,medicine.disease ,business ,Cohort study - Published
- 2020
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27. Fe acquisition at the crossroad of calcium and reactive oxygen species signaling
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Claudia von der Mark, Regina Gratz, Tzvetina Brumbarova, and Rumen Ivanov
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0106 biological sciences ,0301 basic medicine ,Arabidopsis ,chemistry.chemical_element ,Plant Science ,Biology ,Calcium ,01 natural sciences ,Redox ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Iron deficiency (plant disorder) ,Transcription factor ,chemistry.chemical_classification ,Reactive oxygen species ,Arabidopsis Proteins ,Effector ,030104 developmental biology ,chemistry ,Catalase ,Biophysics ,biology.protein ,Reactive Oxygen Species ,Function (biology) ,010606 plant biology & botany - Abstract
Due to its redox properties, iron is both essential and toxic. Therefore, soil iron availability variations pose a significant problem for plants. Recent evidence suggests that calcium and reactive oxygen species coordinate signaling events related to soil iron acquisition. Calcium was found to affect directly IRT1-mediated iron import through the lipid-binding protein EHB1 and to trigger a CBL-CIPK-mediated signaling influencing the activity of the key iron-acquisition transcription factor FIT. In parallel, under prolonged iron deficiency, reactive oxygen species both inhibit FIT function and depend on FIT through the function of the catalase CAT2. We discuss the role of calcium and reactive oxygen species signaling in iron acquisition, with post-translational mechanisms influencing the localization and activity of iron-acquisition regulators and effectors.
- Published
- 2021
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28. Correction to: EMAC, Retromer, and VSRs: do they connect?
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David Robinson and Rumen Ivanov
- Subjects
Retromer ,Cell Biology ,Plant Science ,General Medicine ,Computational biology ,Biology - Published
- 2021
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29. Self-normalized inverse photopyroelectric technique with viscous front window for thermal effusivity measurements in liquids
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Ernesto Olvera, Ernesto Marín, Jesús Villa, Daniel Alaniz, and Rumen Ivanov
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Materials science ,business.industry ,Detector ,02 engineering and technology ,Viscous liquid ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,Signal ,Piezoelectricity ,Pyroelectricity ,Physics::Fluid Dynamics ,Thermoelastic damping ,Optics ,0103 physical sciences ,Light beam ,Physical and Theoretical Chemistry ,010306 general physics ,0210 nano-technology ,business ,Instrumentation ,Thermal effusivity - Abstract
In this paper, the front detection (also called inverse configuration) photopyroelectric method for thermal effusivity measurement in liquids is improved by adding a viscous liquid to the front face of the pyroelectric sensor, on which the intensity modulated excitation light beam impinges, while the sample is attached to the rear side of the sensor. This viscous liquid will act as an optical transparent window. This configuration avoids problems related with the piezoelectric contribution to the photopyroelectric signal at high modulation frequencies that can be present in conventional approaches due to thermoelastic waves generated in the heated sample or by thermally induced deformations of the detector material itself. The theoretical and experimental principles behind the proposed method are presented and its usefulness is demonstrated with measurements on test samples.
- Published
- 2017
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30. Mobility and localization of the iron deficiency‐induced transcription factor bHLH039 change in the presence of FIT
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Rumen Ivanov, Tzvetina Brumbarova, Petra Bauer, Ksenia Trofimov, Inga Mohr, Büsra Acaroglu, and Monique Eutebach
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Mutant ,Plant Science ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,iron deficiency ,Arabidopsis ,medicine ,Transcription factor ,Ecology, Evolution, Behavior and Systematics ,Original Research ,Ecology ,biology ,Chemistry ,Botany ,bHLH039 ,Subcellular localization ,biology.organism_classification ,Cell biology ,medicine.anatomical_structure ,transcription factor regulation ,Cytoplasm ,QK1-989 ,Fer‐like iron deficiency‐induced transcription factor ,Nucleus ,Nuclear localization sequence ,Intracellular ,nucleocytoplasmic partitioning - Abstract
Regulation of iron (Fe) acquisition and homeostasis is critical for plant survival. In Arabidopsis, Fe deficiency‐induced bHLH039 forms a complex with the master regulator FIT and activates it to upregulate Fe acquisition genes. FIT is partitioned between cytoplasm and nucleus, whereby active FIT accumulates more in the nucleus than inactive FIT. At the same time, there is so far no information on the subcellular localization of bHLH039 protein and how it is controlled. We report here that the bHLH039 localization pattern changes depending on the presence of FIT in the cell. When expressed in cells lacking FIT, bHLH039 localizes predominantly in the cytoplasm, including cytoplasmic foci in close proximity to the plasma membrane. The presence of FIT enhances the mobility of bHLH039 and redirects the protein toward primarily nuclear localization, abolishing its accumulation in cytoplasmic foci. This FIT‐dependent change in localization of bHLH039 found in transient fluorescent protein expression experiments was confirmed in both leaves and roots of Arabidopsis transgenic plants, stably expressing hemagglutinin‐tagged bHLH039 in wild‐type or fit mutant background. This posttranslational mechanism for intracellular partitioning of Fe‐responsive transcription factors suggests a signaling cascade that translates Fe sensing at the plasma membrane to nuclear accumulation of the transcriptional regulators.
- Published
- 2019
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31. Phospho-mutant activity assays provide evidence for alternative phospho-regulation pathways of the transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR
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Rumen Ivanov, Matias D. Zurbriggen, Johannes Meiser, Ksenia Trofimov, Tim Blomeier, Stefanie Weidtkamp-Peters, Regina Gratz, Rocio Ochoa-Fernandez, Laura Tünnermann, Tzvetina Brumbarova, and Petra Bauer
- Subjects
Transcriptional Activation ,Physiology ,Mutant ,Arabidopsis ,Plant Science ,CHO Cells ,Models, Biological ,serine phosphorylation ,chemistry.chemical_compound ,Transactivation ,Cricetulus ,Cricetinae ,Basic Helix-Loop-Helix Transcription Factors ,Animals ,Amino Acid Sequence ,Phosphorylation ,Phosphotyrosine ,Transcription factor ,Cellular localization ,transcription factor ,Full Paper ,Chemistry ,Arabidopsis Proteins ,Protein Stability ,Research ,iron uptake ,tyrosine phosphorylation ,Tyrosine phosphorylation ,bHLH039 ,Full Papers ,FIT ,Cell biology ,Complementation ,Mutation ,Biological Assay ,Signal transduction ,Protein Multimerization ,IRT1 - Abstract
Summary The key basic helix–loop–helix (bHLH) transcription factor in iron (Fe) uptake, FER‐LIKE IRON DEFICIENCY‐INDUCED TRANSCRIPTION FACTOR (FIT), is controlled by multiple signaling pathways, important to adjust Fe acquisition to growth and environmental constraints. FIT protein exists in active and inactive protein pools, and phosphorylation of serine Ser272 in the C‐terminus, a regulatory domain of FIT, provides a trigger for FIT activation.Here, we use phospho‐mutant activity assays and study phospho‐mimicking and phospho‐dead mutations of three additional predicted phosphorylation sites, namely at Ser221 and at tyrosines Tyr238 and Tyr278, besides Ser 272.Phospho‐mutations at these sites affect FIT activities in yeast, plant, and mammalian cells. The diverse array of cellular phenotypes is seen at the level of cellular localization, nuclear mobility, homodimerization, and dimerization with the FIT‐activating partner bHLH039, promoter transactivation, and protein stability. Phospho‐mimicking Tyr mutations of FIT disturb fit mutant plant complementation.Taken together, we provide evidence that FIT is activated through Ser and deactivated through Tyr site phosphorylation. We therefore propose that FIT activity is regulated by alternative phosphorylation pathways.
- Published
- 2019
32. Sequence and coexpression analysis of iron-regulated ZIP transporter genes reveals crossing points between iron acquisition strategies in green algae and land plants
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Rumen Ivanov and Petra Bauer
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0106 biological sciences ,0301 basic medicine ,Lineage (genetic) ,biology ,Mechanism (biology) ,Chlamydomonas ,Soil Science ,Transporter ,Context (language use) ,Plant Science ,Computational biology ,biology.organism_classification ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Arabidopsis ,Botany ,Post-transcriptional regulation ,Gene ,010606 plant biology & botany - Abstract
Dicotyledonous plants, such as Arabidopsis, acquire soil iron using a reduction-based mechanism, named Strategy I, where the final step involves Fe2+ import by the ZIP-family transporter AtIRT1. The universal presence of IRT1-like genes, suggests that Strategy I represents a basic process in the green lineage. However, for some green organisms, like Chlamydomonas and rice, alternative iron-acquisition mechanisms are known. We aimed to outline potential interactions between Strategy I and alternative iron acquisition mechanisms. We investigated gene-coexpression networks in Chlamydomonas, rice and Arabidopsis, and used the sequences of the variable regions of the selected IRT proteins to identify the conservation of key amino acids. IRT genes in Chlamydomonas and rice were found to be closely coexpressed with components of alternative available iron-acquisition systems. On protein level, we could observe conservation of potential phosphorylation sites in close proximity to predicted or experimentally-demonstrated ubiquitination sites. Data suggest that the regulation of Strategy I is closely connected to alternative existing iron-acquisition strategies. Transciptional control, together with potential post-transcriptional modifications of IRT transporters, may be involved in fine-tuning iron import. This study provides a basis for experimentally analyzing the regulation of iron acquisition in an evolutionary context.
- Published
- 2016
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33. Bioestimulación láser en semillas y plantas
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Gabriela Sánchez Hernández, José Luis López-Bonilla, Alfredo Cruz-Orea, Rosalba Zepeda Bautista, Anne Podleśna, María Cristina Pérez Reyes, Rumen Ivanov, Claudia Hernández-Aguilar, A. Dominguez-Pacheco, and Aquiles Carballo Carballo
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0301 basic medicine ,Physics ,030103 biophysics ,03 medical and health sciences ,Ecology ,Plant Science ,Horticulture ,Humanities - Abstract
Diversos laseres han demostrado ser potencialmente utiles a determinados parametros de irradiacion y podrian beneficiar el establecimiento de siembra en condiciones adversas por radiacion UV-B, sequia, frio, salinidad, contaminacion por cadmio, etc. Esta revision de literatura cientifica exhibe las aplicaciones posibles de los laseres en los ultimos anos, como tratamiento de semillas y plantas, destacando el uso de los laseres de He-Ne, Ar, Neodimio-YAG, CO y los diodos laser. Es evidente que las aplicaciones de laseres a parametros de irradiacion especificos en semillas y plantas han adquirido cada vez mayor importancia debido a la necesidad de incrementar la produccion de alimentos a nivel global mediante metodos que protejan el medio ambiente y contribuyan a combatir los efectos del cambio climatico y a la conservacion de la biodiversidad, mejorando la calidad de vida humana y animal. De esta manera, en este Ano Internacional de "la Luz y las tecnologias basadas en la luz", fue importante tomar conciencia del posible uso potencial de la luz laser en la agricultura, ya que podria coadyuvar a un desarrollo sostenible y ofrecer soluciones a problematicas diversas. Los avances encontrados por diversos cientificos lo evidencian y en los proximos anos podria tener un auge en su aplicacion en la agricultura como un elemento "bioestimulador" de semillas, plantulas y plantas.
- Published
- 2016
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34. The 2D Continuous Wavelet Transform: Applications in Fringe Pattern Processing for Optical Measurement Techniques
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Daniel Alaniz, Efrén González, José de Jesús Villa Hernández, Jorge L. Flores, GustavoRodríguez, Rumen Ivanov, Ismael de la Rosa, and Guillermo Garcia
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Computer science ,Fringe pattern ,business.industry ,Computer vision ,Artificial intelligence ,business ,GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) ,Continuous wavelet transform - Published
- 2018
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35. Thermal diffusivity measurements in solids by photothermal infrared radiometry: Influence of convection–radiation heat losses
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K Martinez, A. Calderón, Ernesto Marín, Christ Glorieux, Rumen Ivanov, G. Peña Rodríguez, and A. Lara-Bernal
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Convection ,Materials science ,business.industry ,Thermal resistance ,General Engineering ,Heat transfer coefficient ,Condensed Matter Physics ,Thermal diffusivity ,Thermal conduction ,Computational physics ,Thermal transmittance ,Optics ,Thermal radiation ,Heat equation ,business - Abstract
This work demonstrates that in photothermal experiments performed in frequency domain the heat losses due to convection and radiation should be taken into account at low frequencies for poor heat conductors. From a model-solution of the heat diffusion equation a dimensionless frequency dependent parameter M = ZH, with sample's thermal impedance Z and H the convection-radiation heat transfer coefficient, turns out to adequately quantify the importance of the effect of those heat losses. A straightforward photothermal infrared radiometry setup was designed to demonstrate the above hypothesis. Disc shaped samples of different test materials were heated by square wave modulated illumination at one of their surfaces at different frequencies using an amplitude modulated laser beam, and the temperature at the rear surfaces was monitored as a function of time using an infrared sensor. The frequency dependence of peak-to-peak values of the temperature signals was found to be consistent with the amplitude spectrum obtained by Fourier transforming the data. The frequency dependence of the peak-to-peak amplitude was compared with a theoretical model with and without taking convection and radiation induced heat losses (CRHL) into consideration. It is found that for poor heat conductors at low modulation frequencies the conventional model without CRHL does not fit well the experimental data, while the extended model leads to good agreement, resulting in reliable values for the thermal diffusivity. For the investigated samples, the contribution to the signal of thermal wave reflection at the back side of the sample turn out to have a minor effect on the signal spectrum.
- Published
- 2015
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36. ZINC FINGER OF ARABIDOPSIS THALIANA12 (ZAT12) Interacts with FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) Linking Iron Deficiency and Oxidative Stress Responses
- Author
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Cham Thi Tuyet Le, Eva Weber, Claudia Stoof, Julia Mohrbacher, Tzvetina Brumbarova, Rumen Ivanov, Petra Bauer, and Claudia Fink-Straube
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0301 basic medicine ,Leupeptins ,Physiology ,Iron ,Mutant ,Arabidopsis ,Regulator ,Plant Science ,Oxidative phosphorylation ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Basic Helix-Loop-Helix Transcription Factors ,Genetics ,Protein Interaction Domains and Motifs ,Transcription factor ,Regulation of gene expression ,Zinc finger ,biology ,Arabidopsis Proteins ,fungi ,Wild type ,food and beverages ,Hydrogen Peroxide ,Articles ,Plants, Genetically Modified ,biology.organism_classification ,Cell biology ,Oxidative Stress ,030104 developmental biology ,Biochemistry ,Mutation ,Transcription Factors - Abstract
Plants grown under iron (Fe)-deficient conditions induce a set of genes that enhance the efficiency of Fe uptake by the roots. In Arabidopsis (Arabidopsis thaliana), the central regulator of this response is the basic helix-loop-helix transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT). FIT activity is regulated by protein-protein interactions, which also serve to integrate external signals that stimulate and possibly inhibit Fe uptake. In the search of signaling components regulating FIT function, we identified ZINC FINGER OF ARABIDOPSIS THALIANA12 (ZAT12), an abiotic stress-induced transcription factor. ZAT12 interacted with FIT, dependent on the presence of the ethylene-responsive element-binding factor-associated amphiphilic repression motif. ZAT12 protein was found expressed in the root early differentiation zone, where its abundance was modulated in a root layer-specific manner. In the absence of ZAT12, FIT expression was upregulated, suggesting a negative effect of ZAT12 on Fe uptake. Consistently, zat12 loss-of-function mutants had higher Fe content than the wild type at sufficient Fe. We found that under Fe deficiency, hydrogen peroxide (H2O2) levels were enhanced in a FIT-dependent manner. FIT protein, in turn, was stabilized by H2O2 but only in the presence of ZAT12, showing that H2O2 serves as a signal for Fe deficiency responses. We propose that oxidative stress-induced ZAT12 functions as a negative regulator of Fe acquisition. A model where H2O2 mediates the negative regulation of plant responses to prolonged stress might be applicable to a variety of stress conditions.
- Published
- 2015
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37. Thermal Effects of Laser Irradiation on Maize Seeds
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Rumen Ivanov Tsonchev, Claudia Hernández Aguilar, Flavio Arturo Domínguez Pacheco, and Alfredo Cruz Orea
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Wavelength ,Materials science ,Infrared ,law ,Thermal ,Analytical chemistry ,Irradiation ,Laser ,Photoacoustic spectroscopy ,Optical absorption coefficient ,Laser beams ,law.invention - Abstract
A b s t r a c t. It is important to know the temperature changes in seeds that have been irradiated with laser light because this could have substantial practical and theoretical importance. Thus, the thermal effects of low intensity laser irradiation on seeds was studied, showing variation of temperature produced by laser light applied during 60 s on two maize seed genotypes, ‘Toluqueno’ and ‘Cacahuazintle’: crystalline and floury, respectively, under two different conditions: natural colour and dyed black, evaluating the temperature changes by a thermal camera. The optical absorption spectra and the non-radiative relaxation time of the seeds were obtained using photoacoustic spectroscopy. The results indicate that it is possible to produce temperature changes, detected by an infrared camera, in crystalline and floury seeds when they are irradiated with a laser beam at a 650 nm wavelength and 27.4 mW power. The highest variation of temperature in the seeds was obtained for the black-dyed condition, these variations being 5.56 and 9.28°C for crystalline and floury seeds, respec tively. Among the seeds, in the dyed condition, the floury seed had the lower non-radiative relaxation time, the higher optical absorption coefficient and a lower optical penetration length at the laser wavelength (650 nm). K e y w o r d s: maize, temperature, thermal camera, laser
- Published
- 2015
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38. Molecular mechanisms governing Arabidopsis iron uptake
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Rumen Ivanov, Tzvetina Brumbarova, and Petra Bauer
- Subjects
Regulation of gene expression ,education.field_of_study ,Transcription, Genetic ,biology ,Arabidopsis Proteins ,Iron ,Population ,Arabidopsis ,Transporter ,Plant Science ,biology.organism_classification ,Cell biology ,Gene Expression Regulation, Plant ,Botany ,Transcriptional regulation ,Iron deficiency (plant disorder) ,education ,Cation Transport Proteins ,Transcription factor ,Intracellular - Abstract
Plants are the principal source of dietary iron (Fe) for most of Earth's population and Fe deficiency can lead to major health problems. Developing strategies to improve plant Fe content is a challenge because Fe is essential and toxic and therefore regulating Fe uptake is crucial for plant survival. Acquiring soil Fe relies on complex regulatory events that occur in root epidermal cells. We review recent advances in elucidating many aspects of the regulation of Fe acquisition. These include the expanding protein network involved in FER-LIKE IRON DEFICIENCY INDUCED TRANSCRIPTION FACTOR (FIT)-dependent gene regulation and novel findings on the intracellular trafficking of the Fe transporter IRON-REGULATED TRANSPORTER 1 (IRT1). We outline future challenges and propose strategies, such as exploiting natural variation, to further expand our knowledge.
- Published
- 2015
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39. Demodulation of single interferograms using a sliding 2-D continuous wavelet transform method
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Jesús Villa, Efrén González, Rumen Ivanov, Ismael de la Rosa, and Daniel Alaniz
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Optics ,Wavelet ,business.industry ,Computer science ,media_common.quotation_subject ,Phase (waves) ,Demodulation ,Ambiguity ,business ,Algorithm ,Atomic and Molecular Physics, and Optics ,Continuous wavelet transform ,media_common - Abstract
In this paper, we present an alternative technique for the demodulation of single interferograms using a sliding 2-D continuous wavelet transform (2-D CWT) method. The sliding strategy proposed in this work is used with two purposes: to reduce the processing time when the 2-D CWT is applied, and to solve the problem of the phase ambiguity when closed fringes are present. Experimental results with real and simulated interferograms show that the proposed multiresolution method is a proper alternative for many applications of interferogram demodulation with closed fringes.
- Published
- 2015
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40. Self-normalized front photopyroelectric technique for thermal effusivity measurements in liquids
- Author
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J.A. Bermejo Arenas, P.D. Alaniz, Ernesto Marín, Rumen Ivanov, and Jesús Villa
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Materials science ,business.industry ,Front (oceanography) ,Analytical chemistry ,Self normalized ,Condensed Matter Physics ,Pyroelectricity ,Optics ,Reference sample ,Calibration ,Physical and Theoretical Chemistry ,business ,Instrumentation ,Thermal effusivity - Abstract
In this paper a measurement methodology is proposed to avoid some limitations of conventional front photopyroelectric technique for thermal effusivity measurements, related to the necessity of calibration using a reference sample. The same pyroelectric sensor heated at high frequencies acts as a reference sample. The proposed method is tested with measurements of thermal effusivity in liquid samples.
- Published
- 2015
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41. SNX1-mediated protein recycling: Piecing together the tissue-specific regulation of arabidopsis iron acquisition
- Author
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Tzvetina Brumbarova and Rumen Ivanov
- Subjects
0106 biological sciences ,0301 basic medicine ,Iron ,Arabidopsis ,Plant Science ,medicine.disease_cause ,01 natural sciences ,Models, Biological ,03 medical and health sciences ,Gene expression ,Protein targeting ,medicine ,Tissue specific ,Endomembrane system ,Sorting Nexins ,biology ,Arabidopsis Proteins ,Transporter ,Iron deficiency ,biology.organism_classification ,medicine.disease ,Endocytosis ,Cell biology ,Article Addendum ,030104 developmental biology ,Organ Specificity ,Iron acquisition ,010606 plant biology & botany - Abstract
Endomembrane protein trafficking has emerged as important means of regulating stress responses in plants. The Arabidopsis SNX1 protein is involved in recycling the iron transporter IRT1, thus promoting its presence at the plasma membrane. SNX1 and its interacting partners undergo stress-related regulation at both transcriptional and posttranslational level, which may include differential regulation at tissue level. Based on this, we explore the tissue-specific regulation of iron import, specifically concentrating on the factors involved in the expression and recycling of IRT1 in root tissues. We propose that different processes affecting IRT1 regulation may lead to similar outcomes, allowing for fine-tuning iron acquisition and distribution.
- Published
- 2017
42. CIPK11-Dependent Phosphorylation Modulates FIT Activity to Promote Arabidopsis Iron Acquisition in Response to Calcium Signaling
- Author
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Philipp Köster, Uwe Karst, Maria M. Drerup, Prabha Manishankar, Ksenia Trofimov, Johannes Meiser, Tzvetina Brumbarova, Petra Bauer, Michael Holtkamp, Jörg Kudla, Hans-Jörg Mai, Rumen Ivanov, Leonie Steinhorst, Inga Mohr, Sibylle Arendt, and Regina Gratz
- Subjects
Arabidopsis ,Protein Serine-Threonine Kinases ,Plant Roots ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Gene Expression Regulation, Plant ,Basic Helix-Loop-Helix Transcription Factors ,Protein phosphorylation ,Calcium Signaling ,Phosphorylation ,Protein kinase A ,Molecular Biology ,Transcription factor ,030304 developmental biology ,Calcium signaling ,Regulation of gene expression ,Cell Nucleus ,0303 health sciences ,biology ,Arabidopsis Proteins ,Cell Biology ,biology.organism_classification ,Plants, Genetically Modified ,Cell biology ,Cytosol ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Summary Nutrient acquisition is entangled with growth and stress in sessile organisms. The bHLH transcription factor FIT is a key regulator of Arabidopsis iron (Fe) acquisition and post-translationally activated upon low Fe. We identified CBL-INTERACTING PROTEIN KINASE CIPK11 as a FIT interactor. Cytosolic Ca2+ concentration and CIPK11 expression are induced by Fe deficiency. cipk11 mutant plants display compromised root Fe mobilization and seed Fe content. Fe uptake is dependent on CBL1/CBL9. CIPK11 phosphorylates FIT at Ser272, and mutation of this target site modulates FIT nuclear accumulation, homo-dimerization, interaction with bHLH039, and transcriptional activity and affects the plant’s Fe-uptake ability. We propose that Ca2+-triggered CBL1/9-mediated activation of CIPK11 and subsequent phosphorylation of FIT shifts inactive into active FIT, allowing regulatory protein interactions in the nucleus. This biochemical link between Fe deficiency and the cellular Ca2+ decoding machinery represents an environment-sensing mechanism to adjust nutrient uptake.
- Published
- 2017
43. Towards the automatization of the Foucault knife-edge quantitative test
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José de Jesús Villa Hernández, Gustavo Rodrı́guez, Gonzalo Márquez Martínez, Rumen Ivanov, and José Ismael De la Rosa Vargas
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Computer science ,business.industry ,Computer vision ,Artificial intelligence ,Edge (geometry) ,business ,Test (assessment) ,Developmental psychology - Published
- 2017
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44. The retromer, sorting nexins and the plant endomembrane protein trafficking
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Nicole Heucken and Rumen Ivanov
- Subjects
0301 basic medicine ,Protein family ,Retromer ,Endosome ,Sorting Nexins ,Cell Membrane ,Cell Biology ,Plants ,Biology ,medicine.disease_cause ,biology.organism_classification ,Cell biology ,Retromer complex ,Protein Transport ,03 medical and health sciences ,Sorting nexin ,030104 developmental biology ,Multiprotein Complexes ,Arabidopsis ,Vacuoles ,Protein targeting ,medicine - Abstract
Protein sorting in the endomembrane system is responsible for the coordination of cellular functions. Plant intracellular trafficking has its own unique features, which include specific regulatory aspects of endosomal sorting and recycling of cargo proteins, mediated by the retromer complex. Recent work has led to significant progress in understanding the role of Arabidopsis retromer subunits in recycling vacuolar sorting receptors and plasma membrane proteins. As a consequence, members of the sorting nexin (SNX) protein family and their interaction partners have emerged as critical protein trafficking regulators, in particular with regard to adaptation to environmental change, such as temperature fluctuations and nutrient deficiency. In this Review, we discuss the known and proposed functions of the comparatively small Arabidopsis SNX protein family. We review the available information on the role of the three Bin-Amphiphysin-Rvs (BAR)-domain-containing Arabidopsis thaliana (At)SNX proteins and discuss their function in the context of their potential participation in the plant retromer complex. We also summarize the role of AtSNX1-interacting proteins in different aspects of SNX-dependent protein trafficking and comment on the potential function of three novel, as yet unexplored, Arabidopsis SNX proteins.
- Published
- 2017
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45. Turnover of Tonoplast Proteins
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David Robinson and Rumen Ivanov
- Subjects
0106 biological sciences ,0301 basic medicine ,biology ,Physiology ,Chemistry ,Endoplasmic reticulum ,Arabidopsis Proteins ,Plant Science ,Vacuole ,Meristem ,biology.organism_classification ,01 natural sciences ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,Arabidopsis ,Genetics ,Vacuole biogenesis ,010606 plant biology & botany - Abstract
Our knowledge of vacuole biogenesis and the transport of proteins to the vacuole has advanced consistently over the last 30 years. In meristematic cells, the tonoplast appears to develop directly out of the endoplasmic reticulum ([Viotti et al., 2013][1]). Once it is established as a functioning
- Published
- 2018
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46. A LED-based smart illumination system for studying plant growth
- Author
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E. Gonzalez-Ramirez, Ma. Araiza-Esquivel, Ernesto Olvera-Gonzalez, Victor M. Castaño, Vianey Torres-Arguelles, Jesús Villa-Hernández, Daniel Alaniz-Lumbreras, Carlos Olvera-Olvera, and Rumen Ivanov-Tsonchev
- Subjects
Plant growth ,Quality (physics) ,business.industry ,law ,Greenhouse ,Environmental science ,Optoelectronics ,Electrical and Electronic Engineering ,business ,Light-emitting diode ,law.invention - Abstract
A smart illumination system for greenhouses and growing rooms capable of controlling the quantity and quality of light emitted by a number of LEDs is described. The system uses lamps containing blue and red LEDs programmed to emit various spectra at sixteen different frequencies and ten different pulse widths. The performance of the system is evaluated by determining the effect of pulsed light emission at different frequencies with a pulse width of 50% on tomato plants ( Lycopersicon esculentum). The results show that low frequencies (0.1, 1, 10 Hz) have higher quantum efficiency in photosystem II compared to higher frequencies (50 and 100 kHz) and continuous light. They also show that the electron transport rate decreases when the frequency of pulses increases.
- Published
- 2013
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47. Intelligent lighting system for plant growth and development
- Author
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Ma. Araiza-Esquivel, E. Gonzalez-Ramirez, Victor M. Castaño, Daniel Alaniz-Lumbreras, Carlos Olvera-Olvera, Ernesto Olvera-Gonzalez, Jesús Villa-Hernández, Vianey Torres-Arguelles, and Rumen Ivanov-Tsonchev
- Subjects
Materials science ,Photosystem II ,business.industry ,Pulse (signal processing) ,Forestry ,Horticulture ,Fluorescence ,Computer Science Applications ,law.invention ,LED lamp ,Optics ,law ,Optoelectronics ,Quantum efficiency ,business ,Agronomy and Crop Science ,Chlorophyll fluorescence ,Pulse-width modulation ,Light-emitting diode - Abstract
A smart illumination system (ILSys) to study the growth process of green plants was developed. This system can control commercial LED lamps that can be turned on to emit continuous or pulsed light. ILSys was applied to determine the effect of pulsed light on the fluorescence emission in tomato plants (Lycopersicon esculentum). The fluorescence emission was measured when the plants were radiated with continuous light and light pulsed at different frequencies (0.1Hz, 1Hz, 10Hz, 50Hz, 100Hz, 500Hz, 1kHz, 5kHz, 10kHz, 50kHz and 100kHz). For the experiment three red and blue-LEDs lamps and a Pulse Modulated Chlorophyll Fluorescence Monitoring System were connected to the ILSys. Results showed the highest quantum efficiencies in the Photosystem II (@fPSII) was obtained when applying pulse frequency of 0.1Hz and 1Hz with 50% light pulse width. ILSys allowed the finding of a significant difference in the response of the quantum efficiency in the Photosystem II between pulsed light at a number of frequencies and continuous light.
- Published
- 2013
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48. Chlorophyll fluorescence emission of tomato plants as a response to pulsed light based LEDs
- Author
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Ismael de la Rosa-Vargas, Jesús Villa-Hernández, Alfredo Lara-Herrera, Héctor Silos-Espino, Daniel Alaniz-Lumbreras, Ernesto Olvera-Gonzalez, Rumen Ivanov-Tsonchev, and Irineo L. López-Cruz
- Subjects
Photosystem II ,Physiology ,Analytical chemistry ,Quantum yield ,Plant Science ,Fluorescence ,law.invention ,chemistry.chemical_compound ,chemistry ,Duty cycle ,law ,Chlorophyll ,Quantum efficiency ,Agronomy and Crop Science ,Chlorophyll fluorescence ,Light-emitting diode - Abstract
The effects of pulsed light based-LEDs at eleven frequencies (0.1, 1, 10, 50, 100, 500 Hz, 1, 5, 10, 50 and 100 kHz) programmed at 50 % duty cycle were analyzed, obtaining important parameters of the fluorescence emission of chlorophyll such as: maximum fluorescence (Fm′), minimum fluorescence, the fluorescence emission in steady state, maximum efficiency of PSII (Fv′/Fm′), the fraction of PSII centers that are open, photochemical quenching, nonphotochemical quenching (NPQ), quantum efficiency of photosystem II (ΦPSII), electron transport rate (ETR) and quantum yield of CO2 assimilation (ϕCO2). For the study and validation of the results obtained in the experiments, the analysis of variance (ANOVA) was applied 0for each parameter with confidence intervals of 95 %. The results show that the frequencies of pulsed light had positive and negative effects on the fluorescence parameters with respect to the control treatment (continuous light). The frequencies that generated the best performance of Fv′/Fm′, NPQ, ΦPSII, ETR, ϕCO2 in tomato plants were 0.1, 1, 100 Hz, and 1 kHz. The increase obtained in these parameters can represent an optimal growth and productivity conditions for optimal energy consumption.
- Published
- 2013
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49. Absolute measurements of thermal effusivity using the electropyroelectric technique
- Author
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Jesús Villa, J. I. de la Rosa-Vargas, E. I. Martínez-Ordoñez, Ernesto Marín, C. Araujo, Rumen Ivanov, Daniel Alaniz, and M.E. Araiza
- Subjects
Materials science ,business.industry ,Inverse ,Condensed Matter Physics ,Signal ,Transfer function ,Pyroelectricity ,Amplitude ,Optics ,Thermal ,Physical and Theoretical Chemistry ,business ,Instrumentation ,Excitation ,Thermal effusivity - Abstract
The so-called electropyroelectric technique uses amplitude modulated electrical current as excitation source of thermal waves in a pyroelectric sensor in contact with a liquid sample. Here it is showed that this technique allows absolute measurements of the thermal effusivity using the quotient of the signal amplitudes obtained from the inverse and the direct configurations. In this way the influence on the experimental results of the frequency dependent instrumental transfer function can be straightforwardly eliminated. Measurements performed in various test liquid samples are presented that demonstrate the good accuracy and usefulness of the method.
- Published
- 2013
- Full Text
- View/download PDF
50. Optimized configuration of the pyroelectric sensor metal electrodes in the photopyroelectric technique
- Author
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Rumen Ivanov, C. Araujo, E. I. Martínez-Ordoñez, and Ernesto Marín
- Subjects
Materials science ,Physics and Astronomy (miscellaneous) ,business.industry ,General Engineering ,General Physics and Astronomy ,Signal ,Pyroelectricity ,Amplitude ,Thermal ,Optoelectronics ,Laser power scaling ,Spectroscopy ,business ,Intensity (heat transfer) ,Voltage - Abstract
This article deals with the photopyroelectric (PPE) technique, a useful tool for optical spectroscopy and for measurement of thermal properties of condensed mater samples, in particular in the liquid state. It has been demonstrated here that, for constant laser power, the pyroelectric (PE) sensor response does not depend on the spatial distribution of the laser beam intensity. As a consequence of this, it follows that in the case of measurements in voltage mode, the signal amplitude is inversely proportional to the active area of the sensor. Then, if the active area is diminished, leaving the total area of the sensor constant, it is possible to increase the pyroelectric signal. On the basis of this result, a method is proposed to enhance the PPE signal measured in voltage mode by means of the optimization in the configuration of the sensor metal electrodes. It was experimentally demonstrated that using this improved technique, it is possible to increase up to ten times the amplitude of the signal without electrical noise rise.
- Published
- 2012
- Full Text
- View/download PDF
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