24 results on '"CLMS"'
Search Results
2. Spatial planning needs towards Copernicus Land Monitoring Services: Case studies from Poland and Norway
- Author
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Monika Cysek-Pawlak, Jakub Misiak, Agata Hościło, Geir-Harald Strand, and Sebastian Eiter
- Subjects
clms ,spatial planning ,poland ,norway ,Social Sciences ,Social sciences (General) ,H1-99 - Abstract
The objective of this study is to identify the needs related to geospatial LC, LU, and LCLUC information for spatial planning in Poland and Norway, and examine the usefulness of CLMS products in the context of these planning systems. The research has conducted based on a comparative analysis of two planning systems, to indicate areas where CLMS can improve or supplement national spatial data. The study shows that CLMS can provide information on up-to-date spatial data showing actual LC/LU/LCLUC, but that the degree of detail and the accuracy may be insufficient. CLMS data is harmonised across Europe and thus meets the need expressed by international organisations, for data that are consistent at a continental level. This is not a requirement in national planning systems in Poland and Norway, where the needs are regulated by national legislation. The thematic and geometric accuracy of national data sources are usually better than the data provided by CLMS, but CLMS might fill gaps when specific topics are missing in national mapping programs.
- Published
- 2024
- Full Text
- View/download PDF
3. SPATIAL PLANNING NEEDS TOWARDS COPERNICUS LAND MONITORING SERVICES: CASE STUDIES FROM POLAND AND NORWAY.
- Author
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CYSEK-PAWLAK, Monika Maria, MISIAK, Jakub, HOŚCIŁO, Agata, STRAND, Geir-Harald, and EITER, Sebastian
- Subjects
- *
CENTRAL economic planning , *NEW product development , *CARTOGRAPHY software , *COMPARATIVE studies - Abstract
The objective of this study is to identify the needs related to geospatial LC, LU, and LCLUC information for spatial planning in Poland and Norway, and examine the usefulness of CLMS products in the context of these planning systems. The research has conducted based on a comparative analysis of two planning systems, to indicate areas where CLMS can improve or supplement national spatial data. The study shows that CLMS can provide information on up-to-date spatial data showing actual LC/LU/LCLUC, but that the degree of detail and the accuracy may be insufficient. CLMS data is harmonised across Europe and thus meets the need expressed by international organisations, for data that are consistent at a continental level. This is not a requirement in national planning systems in Poland and Norway, where the needs are regulated by national legislation. The thematic and geometric accuracy of national data sources are usually better than the data provided by CLMS, but CLMS might fill gaps when specific topics are missing in national mapping programs. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
4. Using salted egg white in steamed bread: Impact on functional and structural characteristics.
- Author
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Abker, Adil M., Xia, Zhijun, Hu, Gan, Fu, Xiaowen, Zhang, Yixin, Jin, Yongguo, Ma, Meihu, and Fu, Xing
- Subjects
- *
BREAD , *EGG whites , *FOURIER transform infrared spectroscopy , *SCANNING electron microscopes , *BREAD quality , *RHEOLOGY - Abstract
[Display omitted] • SEW improved the texture properties of steamed bread. • SEW is utilised as a sustainable ingredient in steamed bread formulations. • Micromorphology showed a compact and smooth structure after adding SEW. • Enrichment of steamed bread with 15% SEW shows significant acceptability. Steamed bread has long been an important part of Chinese cuisine. This study investigated the effects of salted egg white (SEW) (5, 10, 15, and 20% w/w) on the quality of steamed breads. Findings revealed that SEW notably enhanced the bread's volume and texture, with a 20% inclusion significantly boosting water retention and rheological properties, albeit reducing bread's lightness. In addition, the H-bond absorption band intensity in the Fourier transform infrared spectroscopy (FTIR) analysis showed increased peak intensities with higher SEW levels, indicative of protein structure alterations. X-ray diffraction confirmed the presence of an amylose–lipid complex. Scanning electron microscope (SEM) and Confocal laser scanning microscope (CLSM) imaging depicted a smooth, consistent protein network with SEW addition. Consumer sensory evaluation responded favourably to the SEW15 steamed bread, suggesting its potential for food industry application. Overall, the study considers SEW an effective ingredient for improving steamed bread quality. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
5. New insights into the structure and assembly of nuclear lamins from chemical cross-linking and mass spectrometry
- Author
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Makarov, Alexandr, Schirmer, Eric, and Sawin, Ken
- Subjects
Lamin A ,CLMS ,Laminopathies ,chemical cross-linking ,coiled coil - Abstract
Now that the functioning of microtubules and the actin cytoskeleton has been worked out in enormous detail, the next important task is defining the structure of intermediate filaments that are far behind the other two major skeletal networks due to their inherent resistance to most structural techniques. The evolution of novel structural approaches for flexible proteins is making this possible now. In my thesis I will aim to elucidate the structure and assembly principles of lamin A nuclear intermediate filament protein. To study lamin A, I principally employed chemical cross-linking that allows the capturing of full-length protein structures in solution. I combined this with mass spectrometry approaches to identify cross-linked residues at the various stages of lamin A assembly that were additionally tracked with SILAC labelling and rotary metal shadowing TEM. Unlike previous cross-linking studies on intermediate filaments I use a zero-length self-excluding cross-linking agent EDC that is better tailored for investigation of the polar interactions between multiple unstructured or otherwise flexible charged sequences of lamins. Using this composite approach I interrogated lamin A dimeric and tetrameric assemblies. I elucidated hinge-like properties of the L12 and found indications that L1 and the region containing coil 2A and L2 and the beginning of coil 2B possess properties of linker-like flexibility and of predicted linear α-helical bundle and could act as molecular springs or compression buffers for the nuclear intermediate filaments. Further I confirm the role of the N-terminal unstructured region in lamin A assembly and for the first time show similar role for the C-terminal unstructured region flanking the rod domain of lamin A. Collected data strongly supports the model where both positively charged unstructured regions participate in extensive interaction with acidic rod termini and act as molecular bridges between these in the head-to-tail interface, confirming the uniformity of this principle between cytoplasmic and nuclear intermediate filaments. Formation of these bridges requires conformational change likely happening due to proline residues in the mitotic phosphorylation sites. Finally I suggest a mechanism of regulation of the order of assembly unique to the nuclear intermediate filament where C-terminal unstructured region blocks lateral interactions until it is tethered to the head-to-tail interface. Collected data on the dynamic behaviour of the C-terminal unstructured region and its ability to tether lamin A Ig domain may have far reaching implications for filament assembly and regulation of binding of hundreds of lamin A partner proteins presenting an important step in our understanding of relationship between lamin A structure and function and how altering the former could lead to disease.
- Published
- 2017
6. Co-encapsulation of probiotic Lactobacillus acidophilus and Reishi medicinal mushroom (Ganoderma lingzhi) extract in moist calcium alginate beads.
- Author
-
Mirmazloum, Iman, Ladányi, Márta, Omran, Mohammad, Papp, Viktor, Ronkainen, Veli-Pekka, Pónya, Zsolt, Papp, István, Némedi, Erzsébet, and Kiss, Attila
- Subjects
- *
GANODERMA lucidum , *LACTOBACILLUS acidophilus , *CALCIUM alginate , *MALTOSE , *GANODERMA , *PROBIOTICS , *CELL survival - Abstract
Probiotic L. acidophilus La-14 cells were co-encapsulated with Ganoderma lingzhi extract to prolong the viability of the cells under simulated gastrointestinal (SGI) condition and to protect the active ingredients of Reishi mushroom during the storage period. Combinations of distinctive reagents (sodium alginate, chitosan, maltose, Hydroxyethyl-cellulose (HEC), hydroxypropyl methylcellulose (HPMC), and calcium lactate) were tested. Optimal double layer Ca-alginate hydrogel beads were fabricated with significantly improved characteristics. The incorporation of maltose significantly decreases the release rate of mushrooms' phenolics, antioxidants, and β-glucan during the storage time. Significant improvement in probiotic cells viability under SGI condition has been found and confirmed by confocal laser microscopy in maltose containing double layer coated calcium alginate beads variants. The encapsulation of newly formulated prebiotic Reishi extract and probiotic L. acidophilus is creating a new potential food application for such medicinal mushrooms and natural products with unpleasant taste upon oral consumption. • L. acidophilus is co-encapsulated with Reishi mushroom extract in Ca-alginate beads. • The cells' viability under SGI condition is enhanced after encapsulation. • Antioxidants & β-glucan release rate significantly diminished after encapsulation. • Application of sodium alginate, chitosan and maltose showed the best preserving effect. • Supplementation of HPMC and HEC did not enhance the beads' protective property. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
7. Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)
- Author
-
Umesh Kalathiya, Monikaben Padariya, Jakub Faktor, Etienne Coyaud, Javier A. Alfaro, Robin Fahraeus, Ted R. Hupp, and David R. Goodlett
- Subjects
cross-linking mass spectrometry ,proteomics ,chemical cross-linkers ,CLMS ,protein–protein ,protein–DNA ,Microbiology ,QR1-502 - Abstract
The fundamentals of how protein–protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein–protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.
- Published
- 2021
- Full Text
- View/download PDF
8. Structural Studies of the Cutin from Two Apple Varieties: Golden Delicious and Red Delicious (Malus domestica)
- Author
-
Daniel Arrieta-Baez, María de Jesús Perea Flores, Juan Vicente Méndez-Méndez, Héctor Francisco Mendoza León, and Mayra Beatriz Gómez-Patiño
- Subjects
cutin ,cuticle ,Malus domestica ,CPMAS 13C NMR ,AFM ,CLMS ,Organic chemistry ,QD241-441 - Abstract
The cuticle, a protective cuticular barrier present in almost all primary aerial plant organs, has a composition that varies between plant species. As a part of the apple peel, cuticle and epicuticular waxes have an important role in the skin appearance and quality characteristic in fresh fruits destined for human consumption. The specific composition and structural characteristics of cutin from two apple varieties, “golden delicious” and “red delicious”, were obtained by enzymatic protocols and studied by means of cross polarization magic angle spinning nuclear magnetic resonance (CP-MAS 13C NMR), attenuated total reflection infrared spectroscopy (ATR-FTIR), and mass spectrometry, and were morphologically characterized by specialized microscopy techniques (atomic force microscopy (AFM), confocal laser scanning microscopy (CLMS), and scanning electron microscopy (SEM)). According to CP-MAS 13C NMR and ATR-FTIR analysis, cutins from both varieties are mainly composed of aliphatics and a small difference is shown between them. This was corroborated from the hydrolyzed cutins analysis by mass spectrometry, where 9,10,18-trihydroxy-octadecanoic acid; 10,20-Dihydroxy-icosanoic acid; 10,16-dihydroxy hexadecenoic acid (10,16-DHPA); 9,10-epoxy-12-octadecenoic acid; and 9,10-epoxy-18-hydroxy-12-octadecenoic acid were the main monomers isolated. The low presence of polysaccharides and phenolics in the cutins obtained could be related to the low elastic behavior of this biocomposite and the presence of cracks in the apple cutin’s surface. These cracks have an average depth of 1.57 µm ± 0.57 in the golden apple, and 1.77 µm ± 0.64 in those found in the red apple. The results obtained in this work may facilitate a better understanding that mechanical properties of the apple fruit skin are mainly related to the specific aliphatic composition of cutin and help to much better investigate the formation of microcracks, an important symptom of russet formation.
- Published
- 2020
- Full Text
- View/download PDF
9. Pembelajaran Awan Berbasis Perangkat Lunak Sebagai Suatu Layanan Analisis Deskriptif.
- Author
-
Yahfizham, Rukun, Kasman, Ihsan, M., Yusti, Irwan, and Padli, M. Irwan
- Abstract
Copyright of Techno.com is the property of Universitas Dian Nuswantoro, Fakultas Ilmu Komputer and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2018
- Full Text
- View/download PDF
10. European Ground Motion Service (EGMS): General Description, Product Quality, and Examples
- Author
-
Costantini, Mario, Minati, Federico, Trillo, Francesco, Ferretti, Alessandro, Passera, Emanuele, Rucci, Alessio, Dehls, John, Larsen, Yngvar, Marinkovic, Petar, Eineder, Michael, Brcic, Ramon, Siegmund, Robert, Kotzerke, Paul, Kenyeres, Ambrus, Proietti, Sergio, Solari, Lorenzo, and Andersen, Henrik S.
- Subjects
InSAR ,EGMS ,DSI ,CLMS ,PSI ,SAR - Published
- 2022
11. First look at the European Ground Motion Service products
- Author
-
Solari, Lorenzo, Crosetto, Michele, Balasis-Levinsen, Joanna, Bateson, Luke, Casagli, Nicola, Comerci, Valerio, Guerrieri, Luca, Frei, Michaela, Mróz, Marek, Moldestad, Dag Anders, Oyen, Anneleen, Costantini, Mario, Minati, Federico, Trillo, Francesco, Proietti, Sergio, Ferretti, Alessandro, Passera, Emanuele, Dehls, John, Larsen, Yngvar, Marinkovic, Petar, Eineder, Michael, Brcic, Ramon, Siegmund, Robert, Kotzerke, Paul, Kenyeres, Ambrus, and Andersen, Henrik S.
- Subjects
InSAR ,EGMS ,DSI ,CLMS ,PSI ,SAR - Published
- 2022
12. Co-encapsulation of probiotic Lactobacillus acidophilus and Reishi medicinal mushroom (Ganoderma lingzhi) extract in moist calcium alginate beads
- Author
-
Mirmazloum, I. (Iman), Ladányi, M. (Márta), Omran, M. (Mohammad), Papp, V. (Viktor), Ronkainen, V.-P. (Veli-Pekka), Pónya, Z. (Zsolt), Papp, I. (István), Némedi, E. (Erzsébet), Kiss, A. (Attila), Mirmazloum, I. (Iman), Ladányi, M. (Márta), Omran, M. (Mohammad), Papp, V. (Viktor), Ronkainen, V.-P. (Veli-Pekka), Pónya, Z. (Zsolt), Papp, I. (István), Némedi, E. (Erzsébet), and Kiss, A. (Attila)
- Abstract
Probiotic L. acidophilus La-14 cells were co-encapsulated with Ganoderma lingzhi extract to prolong the viability of the cells under simulated gastrointestinal (SGI) condition and to protect the active ingredients of Reishi mushroom during the storage period. Combinations of distinctive reagents (sodium alginate, chitosan, maltose, Hydroxyethyl-cellulose (HEC), hydroxypropyl methylcellulose (HPMC), and calcium lactate) were tested. Optimal double layer Ca-alginate hydrogel beads were fabricated with significantly improved characteristics. The incorporation of maltose significantly decreases the release rate of mushrooms’ phenolics, antioxidants, and β-glucan during the storage time. Significant improvement in probiotic cells viability under SGI condition has been found and confirmed by confocal laser microscopy in maltose containing double layer coated calcium alginate beads variants. The encapsulation of newly formulated prebiotic Reishi extract and probiotic L. acidophilus is creating a new potential food application for such medicinal mushrooms and natural products with unpleasant taste upon oral consumption.
- Published
- 2021
13. Co-encapsulation of probiotic Lactobacillus acidophilus and Reishi medicinal mushroom (Ganoderma lingzhi) extract in moist calcium alginate beads
- Author
-
Viktor Papp, Erzsébet Némedi, Iman Mirmazloum, Mohammad Omran, István Papp, Zsolt Pónya, Attila Kiss, Veli-Pekka Ronkainen, and Márta Ladányi
- Subjects
Calcium alginate ,beta-Glucans ,Chemical Phenomena ,Alginates ,medicine.medical_treatment ,Drug Compounding ,Prebiotic ,Chemical Fractionation ,Methylcellulose ,Biochemistry ,Antioxidants ,law.invention ,Chitosan ,chemistry.chemical_compound ,Probiotic ,Lactobacillus acidophilus ,Structural Biology ,law ,β-Glucan ,medicine ,Calcium lactate ,Food science ,Molecular Biology ,Active ingredient ,Mushroom ,Biological Products ,Double layer coat ,Chemistry ,Probiotics ,technology, industry, and agriculture ,Probiotic protection ,CLMS ,Ganoderma ,General Medicine ,Maltose ,Glucose ,Agaricales - Abstract
Probiotic L. acidophilus La-14 cells were co-encapsulated with Ganoderma lingzhi extract to prolong the viability of the cells under simulated gastrointestinal (SGI) condition and to protect the active ingredients of Reishi mushroom during the storage period. Combinations of distinctive reagents (sodium alginate, chitosan, maltose, Hydroxyethyl-cellulose (HEC), hydroxypropyl methylcellulose (HPMC), and calcium lactate) were tested. Optimal double layer Ca-alginate hydrogel beads were fabricated with significantly improved characteristics. The incorporation of maltose significantly decreases the release rate of mushrooms’ phenolics, antioxidants, and β-glucan during the storage time. Significant improvement in probiotic cells viability under SGI condition has been found and confirmed by confocal laser microscopy in maltose containing double layer coated calcium alginate beads variants. The encapsulation of newly formulated prebiotic Reishi extract and probiotic L. acidophilus is creating a new potential food application for such medicinal mushrooms and natural products with unpleasant taste upon oral consumption.
- Published
- 2021
14. Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)
- Author
-
Robin Fahraeus, Javier A. Alfaro, Umesh Kalathiya, Etienne Coyaud, Ted R. Hupp, David R. Goodlett, Monikaben Padariya, Jakub Faktor, Medical University of Gdańsk, Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM) - U 1192 (PRISM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), CHU Lille, University of Edinburgh, University of Victoria [Canada] (UVIC), INSERM, Université de Lille, Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM) - U1192, and University of Victoria [Canada] [UVIC]
- Subjects
protein–protein ,Protein Conformation ,[SDV]Life Sciences [q-bio] ,Dna interaction ,lcsh:QR1-502 ,Computational biology ,Review ,Mass spectrometry ,Proteomics ,01 natural sciences ,Biochemistry ,protein–DNA ,lcsh:Microbiology ,Mass Spectrometry ,03 medical and health sciences ,chemistry.chemical_compound ,proteomics ,proteinprotein ,protein-DNA ,protein–RNA interactions ,structural biology ,Animals ,Humans ,Molecular Biology ,Topology (chemistry) ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,protein-RNA interactions ,chemical cross-linkers ,Biomolecule ,010401 analytical chemistry ,cross-linking mass spectrometry ,RNA ,Proteins ,CLMS ,DNA ,0104 chemical sciences ,chemistry ,Structural biology ,Protein Binding - Abstract
International audience; The fundamentals of how protein-protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein-protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.
- Published
- 2021
- Full Text
- View/download PDF
15. Relationship between wood anatomy, tree-ring widths and wood density of Pinus sylvestris L. and climate at high latitudes in northern Sweden.
- Author
-
Pritzkow, C., Heinrich, I., Grudd, H., and Helle, G.
- Abstract
In this study, wood anatomy, tree-ring width and wood density of Pinus sylvestris at the northern timberline in Fennoscandia were used to identify relationships among the parameters and to screen them for their climatic signals. Furthermore we investigated the influence of the juvenile wood section for all parameters developed. The measurements of wood anatomy were conducted with confocal laser scanning microscopy (CLSM) while the density profiles were produced using an Itrax MultiScanner. We developed chronologies of ring width, wood density and anatomy for a period between 1940 and 2010. Correlations between wood density and wood anatomy were strong in the latewood part. For some wood anatomy and density chronologies youth trends were found in the juvenile part. Wood density decreased from the pith up to the 9th ring and stabilized afterwards, while cell lumen diameter and lumen area increased simultaneously up to the 15th ring. All chronologies contained strong summer temperature signals. The wood anatomical variables provided additional information about seasonal precipitation which could not be found in wood density and tree-ring widths. Our study confirmed previous results stating that the parameter maximum density contains the strongest climate signal, that is, summer temperatures at the northern timberline. Nevertheless, the intra-annual data on tracheid dimensions showed good potential to supply seasonal climatic information and improve our understanding of climatic effects on tree growth and wood formation. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
16. Complex dual channel estimation: Cost effective widely linear adaptive filtering.
- Author
-
Jahanchahi, Cyrus, Kanna, Sithan, and Mandic, Danilo
- Subjects
- *
ESTIMATION theory , *MEAN square algorithms , *ADAPTIVE filters , *COMPUTATIONAL complexity , *STOCHASTIC analysis - Abstract
Abstract: Widely linear estimation for complex-valued data allows for a unified treatment of both second order circular (proper) and non-circular (improper) signals. We propose the complex dual channel (CDC) estimation technique as an alternative to widely linear estimation to both gain further insights into complex valued minimum mean square error (MMSE) estimation and to design computationally efficient adaptive filtering algorithms. This is achieved by finding two sets of optimal weights that minimize the mean square error (MSE) in estimating the real and imaginary parts of the signal independently. The concept is used in a stochastic gradient setting to design the dual channel complex least mean square (DC-CLMS). The analysis shows that any one of the sub-filters within the DC-CLMS can be used to estimate strictly linear models while the DC-CLMS is equivalent to widely linear estimation. This results in a reduction of computational complexity of complex-valued adaptive filters by a half, while providing enhanced physical insight and control over complex-valued estimation algorithms. [Copyright &y& Elsevier]
- Published
- 2014
- Full Text
- View/download PDF
17. Microtubule Nucleation Properties of Single Human γTuRCs Explained by Their Cryo-EM Structure
- Author
-
Tanja Consolati, Julia Locke, Juri Rappsilber, Johanna Roostalu, Zhuo A. Chen, Jayant Asthana, Thomas Surrey, Wei Ming Lim, Fabrizio Martino, Alessandro Costa, Julian Gannon, and Milos A. Cvetkovic
- Subjects
Cryo-electron microscopy ,Protein Conformation ,microtubule nucleation ,Nucleation ,Microtúbuls ,cryo-electron microscopy ,Biology ,Molecular Dynamics Simulation ,Microtubules ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Microtubule ,Tubulin ,Humans ,Molecular Biology ,Actin ,030304 developmental biology ,Microtubule nucleation ,γTuRC structure ,0303 health sciences ,MZT2 ,Total internal reflection fluorescence microscope ,TPX2 ,Resolution (electron density) ,Cryoelectron Microscopy ,CLMS ,Cell Biology ,Actins ,Single Molecule Imaging ,chTOG ,3. Good health ,Biophysics ,γ-tubulin ring complex ,Elongation ,actin ,Microtubule-Associated Proteins ,Microtubule-Organizing Center ,030217 neurology & neurosurgery ,TIRF microscopy ,Developmental Biology ,Nucleació ,HeLa Cells - Abstract
Summary The γ-tubulin ring complex (γTuRC) is the major microtubule nucleator in cells. The mechanism of its regulation is not understood. We purified human γTuRC and measured its nucleation properties in a total internal reflection fluorescence (TIRF) microscopy-based real-time nucleation assay. We find that γTuRC stably caps the minus ends of microtubules that it nucleates stochastically. Nucleation is inefficient compared with microtubule elongation. The 4 Å resolution cryoelectron microscopy (cryo-EM) structure of γTuRC, combined with crosslinking mass spectrometry analysis, reveals an asymmetric conformation with only part of the complex in a “closed” conformation matching the microtubule geometry. Actin in the core of the complex, and MZT2 at the outer perimeter of the closed part of γTuRC appear to stabilize the closed conformation. The opposite side of γTuRC is in an “open,” nucleation-incompetent conformation, leading to a structural asymmetry explaining the low nucleation efficiency of purified human γTuRC. Our data suggest possible regulatory mechanisms for microtubule nucleation by γTuRC closure., Graphical Abstract, Highlights • The γ-tubulin ring complex (γTuRC) nucleates microtubules and caps their minus ends • Microtubule nucleation from purified γTuRC is highly cooperative, yet inefficient • A partly open, asymmetric structure of γTuRC explains inefficient nucleation • Actin and MZT2 stabilize the closed part of the γTuRC structure, Consolati et al. find that microtubule nucleation by individual γTuRC complexes is inefficient despite its proposed role as a nucleating template. A 4 Å structure of the complex reveals a mismatch with the microtubule structure, explaining the inefficiency of nucleation and providing a possible mechanism for the regulation of nucleation.
- Published
- 2020
- Full Text
- View/download PDF
18. Variable Step-Size Convex Combination of LMS Adaptive Filtering: Algorithm and Analysis.
- Author
-
MIAO Jun, RUI Guo-sheng, and ZHANG Yang
- Abstract
The article discusses the proposal of variable step-size adaptive filter, which has been determined to have a better tracking performance than the original variable step-size convex combination of least mean squares (VSCLMS) algorithm.
- Published
- 2013
- Full Text
- View/download PDF
19. Structural Studies of the Cutin from Two Apple Varieties: Golden Delicious and Red Delicious (Malus domestica)
- Author
-
María de Jesús Perea Flores, J.V. Méndez-Méndez, Hector Mendoza León, Daniel Arrieta-Baez, and Mayra Beatriz Gómez-Patiño
- Subjects
0106 biological sciences ,Malus ,Cuticle ,Pharmaceutical Science ,Cutin ,01 natural sciences ,Analytical Chemistry ,lcsh:QD241-441 ,03 medical and health sciences ,lcsh:Organic chemistry ,Drug Discovery ,Microscopy ,Magic angle spinning ,Food science ,Physical and Theoretical Chemistry ,030304 developmental biology ,0303 health sciences ,Wax ,biology ,Chemistry ,cutin ,Organic Chemistry ,CPMAS 13C NMR ,food and beverages ,CLMS ,biology.organism_classification ,Chemistry (miscellaneous) ,Attenuated total reflection ,visual_art ,SEM ,visual_art.visual_art_medium ,Molecular Medicine ,cuticle ,Composition (visual arts) ,AFM ,Malus domestica ,010606 plant biology & botany - Abstract
The cuticle, a protective cuticular barrier present in almost all primary aerial plant organs, has a composition that varies between plant species. As a part of the apple peel, cuticle and epicuticular waxes have an important role in the skin appearance and quality characteristic in fresh fruits destined for human consumption. The specific composition and structural characteristics of cutin from two apple varieties, &ldquo, golden delicious&rdquo, and &ldquo, red delicious&rdquo, were obtained by enzymatic protocols and studied by means of cross polarization magic angle spinning nuclear magnetic resonance (CP-MAS 13C NMR), attenuated total reflection infrared spectroscopy (ATR-FTIR), and mass spectrometry, and were morphologically characterized by specialized microscopy techniques (atomic force microscopy (AFM), confocal laser scanning microscopy (CLMS), and scanning electron microscopy (SEM)). According to CP-MAS 13C NMR and ATR-FTIR analysis, cutins from both varieties are mainly composed of aliphatics and a small difference is shown between them. This was corroborated from the hydrolyzed cutins analysis by mass spectrometry, where 9,10,18-trihydroxy-octadecanoic acid, 10,20-Dihydroxy-icosanoic acid, 10,16-dihydroxy hexadecenoic acid (10,16-DHPA), 9,10-epoxy-12-octadecenoic acid, and 9,10-epoxy-18-hydroxy-12-octadecenoic acid were the main monomers isolated. The low presence of polysaccharides and phenolics in the cutins obtained could be related to the low elastic behavior of this biocomposite and the presence of cracks in the apple cutin&rsquo, s surface. These cracks have an average depth of 1.57 µ, m ±, 0.57 in the golden apple, and 1.77 µ, 0.64 in those found in the red apple. The results obtained in this work may facilitate a better understanding that mechanical properties of the apple fruit skin are mainly related to the specific aliphatic composition of cutin and help to much better investigate the formation of microcracks, an important symptom of russet formation.
- Published
- 2020
- Full Text
- View/download PDF
20. Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS).
- Author
-
Kalathiya, Umesh, Padariya, Monikaben, Faktor, Jakub, Coyaud, Etienne, Alfaro, Javier A., Fahraeus, Robin, Hupp, Ted R., Goodlett, David R., and Uversky, Vladimir N.
- Subjects
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MASS spectrometry , *INTERFACE structures , *INTERFACE dynamics , *BIOLOGICAL systems , *PROXIMITY spaces - Abstract
The fundamentals of how protein–protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein–protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
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21. Structural Studies of the Cutin from Two Apple Varieties: Golden Delicious and Red Delicious (Malus domestica).
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Arrieta-Baez, Daniel, Perea Flores, María de Jesús, Méndez-Méndez, Juan Vicente, Mendoza León, Héctor Francisco, and Gómez-Patiño, Mayra Beatriz
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APPLES , *BAEL (Tree) , *MAGIC angle spinning , *MASS analysis (Spectrometry) , *NUCLEAR magnetic resonance , *ATOMIC force microscopy - Abstract
The cuticle, a protective cuticular barrier present in almost all primary aerial plant organs, has a composition that varies between plant species. As a part of the apple peel, cuticle and epicuticular waxes have an important role in the skin appearance and quality characteristic in fresh fruits destined for human consumption. The specific composition and structural characteristics of cutin from two apple varieties, "golden delicious" and "red delicious", were obtained by enzymatic protocols and studied by means of cross polarization magic angle spinning nuclear magnetic resonance (CP-MAS 13C NMR), attenuated total reflection infrared spectroscopy (ATR-FTIR), and mass spectrometry, and were morphologically characterized by specialized microscopy techniques (atomic force microscopy (AFM), confocal laser scanning microscopy (CLMS), and scanning electron microscopy (SEM)). According to CP-MAS 13C NMR and ATR-FTIR analysis, cutins from both varieties are mainly composed of aliphatics and a small difference is shown between them. This was corroborated from the hydrolyzed cutins analysis by mass spectrometry, where 9,10,18-trihydroxy-octadecanoic acid; 10,20-Dihydroxy-icosanoic acid; 10,16-dihydroxy hexadecenoic acid (10,16-DHPA); 9,10-epoxy-12-octadecenoic acid; and 9,10-epoxy-18-hydroxy-12-octadecenoic acid were the main monomers isolated. The low presence of polysaccharides and phenolics in the cutins obtained could be related to the low elastic behavior of this biocomposite and the presence of cracks in the apple cutin's surface. These cracks have an average depth of 1.57 µm ± 0.57 in the golden apple, and 1.77 µm ± 0.64 in those found in the red apple. The results obtained in this work may facilitate a better understanding that mechanical properties of the apple fruit skin are mainly related to the specific aliphatic composition of cutin and help to much better investigate the formation of microcracks, an important symptom of russet formation. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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22. Microtubule Nucleation Properties of Single Human γTuRCs Explained by Their Cryo-EM Structure.
- Author
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Consolati, Tanja, Locke, Julia, Roostalu, Johanna, Chen, Zhuo Angel, Gannon, Julian, Asthana, Jayant, Lim, Wei Ming, Martino, Fabrizio, Cvetkovic, Milos A., Rappsilber, Juri, Costa, Alessandro, and Surrey, Thomas
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MICROTUBULES , *TUBULINS , *NUCLEATION , *MASS analysis (Spectrometry) - Abstract
The γ-tubulin ring complex (γTuRC) is the major microtubule nucleator in cells. The mechanism of its regulation is not understood. We purified human γTuRC and measured its nucleation properties in a total internal reflection fluorescence (TIRF) microscopy-based real-time nucleation assay. We find that γTuRC stably caps the minus ends of microtubules that it nucleates stochastically. Nucleation is inefficient compared with microtubule elongation. The 4 Å resolution cryoelectron microscopy (cryo-EM) structure of γTuRC, combined with crosslinking mass spectrometry analysis, reveals an asymmetric conformation with only part of the complex in a "closed" conformation matching the microtubule geometry. Actin in the core of the complex, and MZT2 at the outer perimeter of the closed part of γTuRC appear to stabilize the closed conformation. The opposite side of γTuRC is in an "open," nucleation-incompetent conformation, leading to a structural asymmetry explaining the low nucleation efficiency of purified human γTuRC. Our data suggest possible regulatory mechanisms for microtubule nucleation by γTuRC closure. • The γ-tubulin ring complex (γTuRC) nucleates microtubules and caps their minus ends • Microtubule nucleation from purified γTuRC is highly cooperative, yet inefficient • A partly open, asymmetric structure of γTuRC explains inefficient nucleation • Actin and MZT2 stabilize the closed part of the γTuRC structure Consolati et al. find that microtubule nucleation by individual γTuRC complexes is inefficient despite its proposed role as a nucleating template. A 4 Å structure of the complex reveals a mismatch with the microtubule structure, explaining the inefficiency of nucleation and providing a possible mechanism for the regulation of nucleation. [ABSTRACT FROM AUTHOR]
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- 2020
- Full Text
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23. eLearning needs eTaxonomy
- Author
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Pogarčić, Ivan, Raspor, Sanja, Babić, Snježana, Bakić-Tomić, Ljubica, and Šimović, Vladimir (ur.).
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eLearning ,eTeaching ,Taxonomy ,Assessment ,Evaluation ,CLMS - Abstract
The overall value of education is determined by dynamics, quantity, and quality of the interaction between main elements. It is very important how values or quality of each element are assessed and further to this assessment the value of the whole process. Each methodology for determining these values requires the use of certain taxonomy. Bloom’ s taxonomy is applicable in the assessment of the level the goals level achieved by instruction. The application of ICT technology changes the interaction between the elements of tuition, the manner of realization and indirectly it might affect instruction quality. This paper poses the question of how strong is the need for revising Bloom’ s taxonomy, especially in semantic mean, with the goal being to have the best quality assessment of instruction, especially eLearning and how it can be implemented
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- 2008
24. eLearning : Is time for eTaxonomy?
- Author
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Pogarčić, Ivan, Žiljak-Vujić, Jana, Revetria, Roberto, Cecchi, Antonella, Schenone, Maurizio, Mladenov, Valeri, and Zemliak, Alexander
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taxonomy ,assessment ,evaluation ,LMS ,CMS ,CLMS - Abstract
Learning and teaching as supplement processes are parts of education. Instruction is the concrete realization of this process with concrete participants and goals that they set before them and wish to achieve. The overall value of instruction is determined by dynamics, quantity, and quality of the interaction between elements: students, teachers and contents that carry out a concrete tutoring process. In respect to this it is very important how values or quality of each element are assessed and further to this assessment the value of the whole process. Each methodology for determining these values requires the use of certain taxonomy. Bloom’ s taxonomy is applicable in the assessment of the level the goals level achieved by instruction. The application of ICT technology changes in a more significant way the interaction between the elements of tuition, the manner of realization and indirectly it might affect instruction quality. This paper poses the question of how strong is the need for revising Bloom’ s taxonomy with the goal being to have the best quality assessment of instruction, especially eLearning and how it can be implemented.
- Published
- 2007
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