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  1. AU="Nandi, Purbasha"
  2. AU="Lord, Louis-David"
  3. AU="Cheng, Wei-Ting"
  4. AU="Cope, Nathan F"
  5. AU="Bonvin, Raphael"
  6. AU="Cinthya Enríquez"
  7. AU="John T Lear"
  8. AU="Rachidi, Saleh"
  9. AU="Baptista Serna, L" AU="Baptista Serna, L"
  10. AU=Fiandaca Massimo S
  11. AU="Belli, Sara"
  12. AU="Capogiri, Monica"
  13. AU="Al-Hattab, Eyad"
  14. AU="Hou, Tsung-Wei"
  15. AU="Meng, Ying Shirley"
  16. AU="Emanuele Rezoagli"
  17. AU="Verhagen, M A M T"
  18. AU="Haden, Kathleen"
  19. AU="Lee, Ju Yup"
  20. AU="Camilla Caimi"
  21. AU="Huynh, Nancy"
  22. AU="Sun, Weilin"
  23. AU="Whalon, Mark E."
  24. AU=Grishunin Kirill
  25. AU="Quaranta, Gianluigi"
  26. AU="Jitaroon, Kawinyarat"
  27. AU="Anderson, Eric C"
  28. AU="Thiyagarajan, Kamalraj"
  29. AU="Simnica, Donjetë"

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  1. Artikel ; Online: Correlative single-cell hard X-ray computed tomography and X-ray fluorescence imaging.

    Lin, Zihan / Zhang, Xiao / Nandi, Purbasha / Lin, Yuewei / Wang, Liguo / Chu, Yong S / Paape, Timothy / Yang, Yang / Xiao, Xianghui / Liu, Qun

    Communications biology

    2024  Band 7, Heft 1, Seite(n) 280

    Abstract: X-ray computed tomography (XCT) and X-ray fluorescence (XRF) imaging are two non-invasive imaging techniques to study cellular structures and chemical element distributions, respectively. However, correlative X-ray computed tomography and fluorescence ... ...

    Abstract X-ray computed tomography (XCT) and X-ray fluorescence (XRF) imaging are two non-invasive imaging techniques to study cellular structures and chemical element distributions, respectively. However, correlative X-ray computed tomography and fluorescence imaging for the same cell have yet to be routinely realized due to challenges in sample preparation and X-ray radiation damage. Here we report an integrated experimental and computational workflow for achieving correlative multi-modality X-ray imaging of a single cell. The method consists of the preparation of radiation-resistant single-cell samples using live-cell imaging-assisted chemical fixation and freeze-drying procedures, targeting and labeling cells for correlative XCT and XRF measurement, and computational reconstruction of the correlative and multi-modality images. With XCT, cellular structures including the overall structure and intracellular organelles are visualized, while XRF imaging reveals the distribution of multiple chemical elements within the same cell. Our correlative method demonstrates the feasibility and broad applicability of using X-rays to understand cellular structures and the roles of chemical elements and related proteins in signaling and other biological processes.
    Mesh-Begriff(e) X-Rays ; Radiography ; Tomography, X-Ray Computed ; Research ; Optical Imaging
    Sprache Englisch
    Erscheinungsdatum 2024-03-07
    Erscheinungsland England
    Dokumenttyp Journal Article
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-024-05950-y
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Structural and Functional Analysis of Disease-Linked p97 ATPase Mutant Complexes.

    Nandi, Purbasha / Li, Shan / Columbres, Rod Carlo A / Wang, Feng / Williams, Dewight R / Poh, Yu-Ping / Chou, Tsui-Fen / Chiu, Po-Lin

    International journal of molecular sciences

    2021  Band 22, Heft 15

    Abstract: IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase malfunction remains unclear. To understand how the mutation ... ...

    Abstract IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase malfunction remains unclear. To understand how the mutation alters the ATPase regulation, we assembled a full-length p97
    Mesh-Begriff(e) Frontotemporal Dementia/genetics ; Frontotemporal Dementia/metabolism ; Humans ; Microscopy, Electron, Transmission ; Models, Molecular ; Muscular Dystrophies, Limb-Girdle/genetics ; Muscular Dystrophies, Limb-Girdle/metabolism ; Mutation ; Myositis, Inclusion Body/genetics ; Myositis, Inclusion Body/metabolism ; Osteitis Deformans/genetics ; Osteitis Deformans/metabolism ; Protein Conformation ; Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins/metabolism ; Valosin Containing Protein/genetics ; Valosin Containing Protein/metabolism
    Chemische Substanzen Nsfl1c protein, rat ; Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins ; VCP protein, human (EC 3.6.4.6) ; Valosin Containing Protein (EC 3.6.4.6)
    Sprache Englisch
    Erscheinungsdatum 2021-07-28
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22158079
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Hypoelectronic isomeric diiridaboranes [(Cp*Ir)2B6H6]: the "Rule-Breakers"(Cp* = η(5)-C5Me5).

    Borthakur, Rosmita / Mondal, Bijan / Nandi, Purbasha / Ghosh, Sundargopal

    Chemical communications (Cambridge, England)

    2016  Band 52, Heft 15, Seite(n) 3199–3202

    Abstract: In an effort to synthesize supraicosahedral iridaboranes, pyrolysis of [Cp*IrCl2]2 with excess [BH3·] was carried out, and this synthesis afforded the isomeric iridaborane [(Cp*Ir)2B6H6] clusters 1 and 2. The geometry of 1 was determined to be ... ...

    Abstract In an effort to synthesize supraicosahedral iridaboranes, pyrolysis of [Cp*IrCl2]2 with excess [BH3·] was carried out, and this synthesis afforded the isomeric iridaborane [(Cp*Ir)2B6H6] clusters 1 and 2. The geometry of 1 was determined to be dodecahedral, i.e., similar to that of [B8H8](2-), whereas 2 was found to exhibit a cluster shape that can be derived from a nine-vertex tricapped trigonal prism by removing one of the capped vertices. The calculation of a large HOMO-LUMO gap further rationalized the isocloso structures for these isomers.
    Sprache Englisch
    Erscheinungsdatum 2016-02-21
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c5cc09606e
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Coarse-Grained Simulations for the Characterization and Optimization of Hybrid Protein-DNA Nanostructures.

    Narayanan, Raghu Pradeep / Procyk, Jonah / Nandi, Purbasha / Prasad, Abhay / Xu, Yang / Poppleton, Erik / Williams, Dewight / Zhang, Fei / Yan, Hao / Chiu, Po-Lin / Stephanopoulos, Nicholas / Šulc, Petr

    ACS nano

    2022  Band 16, Heft 9, Seite(n) 14086–14096

    Abstract: We present here the combination of experimental and computational modeling tools for the design and characterization of protein-DNA hybrid nanostructures. Our work incorporates several features in the design of these nanostructures: (1) modeling of the ... ...

    Abstract We present here the combination of experimental and computational modeling tools for the design and characterization of protein-DNA hybrid nanostructures. Our work incorporates several features in the design of these nanostructures: (1) modeling of the protein-DNA linker identity and length; (2) optimizing the design of protein-DNA cages to account for mechanical stresses; (3) probing the incorporation efficiency of protein-DNA conjugates into DNA nanostructures. The modeling tools were experimentally validated using structural characterization methods like cryo-TEM and AFM. Our method can be used for fitting low-resolution electron density maps when structural insights cannot be deciphered from experiments, as well as enable
    Mesh-Begriff(e) Cryoelectron Microscopy ; DNA/chemistry ; Molecular Dynamics Simulation ; Nanostructures/chemistry
    Chemische Substanzen DNA (9007-49-2)
    Sprache Englisch
    Erscheinungsdatum 2022-08-18
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1936-086X
    ISSN (online) 1936-086X
    DOI 10.1021/acsnano.2c04013
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: A library of aminoglycoside-derived lipopolymer nanoparticles for delivery of small molecules and nucleic acids.

    Godeshala, Sudhakar / Miryala, Bhavani / Dutta, Subhadeep / Christensen, Matthew D / Nandi, Purbasha / Chiu, Po-Lin / Rege, Kaushal

    Journal of materials chemistry. B

    2020  Band 8, Heft 37, Seite(n) 8558–8572

    Abstract: Simultaneous delivery of small molecules and nucleic acids using a single vehicle can lead to novel combination treatments and multifunctional carriers for a variety of diseases. In this study, we report a novel library of aminoglycoside-derived ... ...

    Abstract Simultaneous delivery of small molecules and nucleic acids using a single vehicle can lead to novel combination treatments and multifunctional carriers for a variety of diseases. In this study, we report a novel library of aminoglycoside-derived lipopolymers nanoparticles (LPNs) for the simultaneous delivery of different molecular cargoes including nucleic acids and small-molecules. The LPN library was screened for transgene expression efficacy following delivery of plasmid DNA, and lead LPNs that showed high transgene expression efficacies were characterized using hydrodynamic size, zeta potential, 1H NMR and FT-IR spectroscopy, and transmission electron microscopy. LPNs demonstrated significantly higher efficacies for transgene expression than 25 kDa polyethyleneamine (PEI) and lipofectamine, including in presence of serum. Self-assembly of these cationic lipopolymers into nanoparticles also facilitated the delivery of small molecule drugs (e.g. doxorubicin) to cancer cells. LPNs were also employed for the simultaneous delivery of the small-molecule histone deacetylase (HDAC) inhibitor AR-42 together with plasmid DNA to cancer cells as a combination treatment approach for enhancing transgene expression. Taken together, our results indicate that aminoglycoside-derived LPNs are attractive vehicles for simultaneous delivery of imaging agents or chemotherapeutic drugs together with nucleic acids for different applications in medicine and biotechnology.
    Mesh-Begriff(e) Aminoglycosides/chemistry ; Animals ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; DNA/genetics ; DNA/pharmacology ; Doxorubicin/chemistry ; Doxorubicin/pharmacology ; Drug Carriers/chemistry ; Drug Liberation ; Gene Transfer Techniques ; Glycolipids/chemistry ; Green Fluorescent Proteins/genetics ; Histone Deacetylase Inhibitors/chemistry ; Histone Deacetylase Inhibitors/pharmacology ; Humans ; Mice ; Nanoparticles/chemistry ; Phenylbutyrates/pharmacology ; Plasmids/genetics ; Plasmids/pharmacology ; Polymers/chemistry ; TNF-Related Apoptosis-Inducing Ligand/genetics
    Chemische Substanzen Aminoglycosides ; Antineoplastic Agents ; Drug Carriers ; Glycolipids ; Histone Deacetylase Inhibitors ; OSU-HDAC42 compound ; Phenylbutyrates ; Polymers ; TNF-Related Apoptosis-Inducing Ligand ; Green Fluorescent Proteins (147336-22-9) ; Doxorubicin (80168379AG) ; DNA (9007-49-2)
    Schlagwörter covid19
    Sprache Englisch
    Erscheinungsdatum 2020-08-22
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2702241-9
    ISSN 2050-7518 ; 2050-750X
    ISSN (online) 2050-7518
    ISSN 2050-750X
    DOI 10.1039/d0tb00924e
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Conserved L464 in p97 D1-D2 linker is critical for p97 cofactor regulated ATPase activity.

    Zhang, Xiaoyi / Gui, Lin / Li, Shan / Nandi, Purbasha / Columbres, Rod Carlo / Wong, Daniel E / Moen, Derek R / Lin, Henry J / Chiu, Po-Lin / Chou, Tsui-Fen

    The Biochemical journal

    2021  Band 478, Heft 17, Seite(n) 3185–3204

    Abstract: p97 protein is a highly conserved, abundant, functionally diverse, structurally dynamic homohexameric AAA enzyme-containing N, D1, and D2 domains. A truncated p97 protein containing the N and D1 domains and the D1-D2 linker (ND1L) exhibits 79% of wild- ... ...

    Abstract p97 protein is a highly conserved, abundant, functionally diverse, structurally dynamic homohexameric AAA enzyme-containing N, D1, and D2 domains. A truncated p97 protein containing the N and D1 domains and the D1-D2 linker (ND1L) exhibits 79% of wild-type (WT) ATPase activity whereas the ND1 domain alone without the linker only has 2% of WT activity. To investigate the relationship between the D1-D2 linker and the D1 domain, we produced p97 ND1L mutants and demonstrated that this 22-residue linker region is essential for D1 ATPase activity. The conserved amino acid leucine 464 (L464) is critical for regulating D1 and D2 ATPase activity by p97 cofactors p37, p47, and Npl4-Ufd1 (NU). Changing leucine to alanine, proline, or glutamate increased the maximum rate of ATP turnover (kcat) of p47-regulated ATPase activities for these mutants, but not for WT. p37 and p47 increased the kcat of the proline substituted linker, suggesting that they induced linker conformations facilitating ATP hydrolysis. NU inhibited D1 ATPase activities of WT and mutant ND1L proteins, but activated D2 ATPase activity of full-length p97. To further understand the mutant mechanism, we used single-particle cryo-EM to visualize the full-length p97L464P and revealed the conformational change of the D1-D2 linker, resulting in a movement of the helix-turn-helix motif (543-569). Taken together with the biochemical and structural results we conclude that the linker helps maintain D1 in a competent conformation and relays the communication to/from the N-domain to the D1 and D2 ATPase domains, which are ∼50 Å away.
    Mesh-Begriff(e) Amino Acid Sequence ; Binding Sites/genetics ; Enzyme Activation/genetics ; HeLa Cells ; Helix-Turn-Helix Motifs/genetics ; Humans ; Hydrolysis ; Leucine/metabolism ; Mutant Proteins/chemistry ; Mutant Proteins/metabolism ; Mutation ; Protein Binding/genetics ; Protein Domains/genetics ; Signal Transduction/genetics ; Transfection ; Valosin Containing Protein/chemistry ; Valosin Containing Protein/genetics ; Valosin Containing Protein/metabolism
    Chemische Substanzen Mutant Proteins ; VCP protein, human (EC 3.6.4.6) ; Valosin Containing Protein (EC 3.6.4.6) ; Leucine (GMW67QNF9C)
    Sprache Englisch
    Erscheinungsdatum 2021-09-17
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2969-5
    ISSN 1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
    ISSN (online) 1470-8728
    ISSN 0006-2936 ; 0306-3275 ; 0264-6021
    DOI 10.1042/BCJ20210288
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel: A library of aminoglycoside-derived lipopolymer nanoparticles for delivery of small molecules and nucleic acids

    Godeshala, Sudhakar / Miryala, Bhavani / Dutta, Subhadeep / Christensen, Matthew D / Nandi, Purbasha / Chiu, Po-Lin / Rege, Kaushal

    Abstract: Simultaneous delivery of small molecules and nucleic acids using a single vehicle can lead to novel combination treatments and multifunctional carriers for a variety of diseases. In this study, we report a novel library of aminoglycoside-derived ... ...

    Abstract Simultaneous delivery of small molecules and nucleic acids using a single vehicle can lead to novel combination treatments and multifunctional carriers for a variety of diseases. In this study, we report a novel library of aminoglycoside-derived lipopolymers nanoparticles (LPNs) for the simultaneous delivery of different molecular cargoes including nucleic acids and small-molecules. The LPN library was screened for transgene expression efficacy following delivery of plasmid DNA, and lead LPNs that showed high transgene expression efficacies were characterized using hydrodynamic size, zeta potential, 1H NMR and FT-IR spectroscopy, and transmission electron microscopy. LPNs demonstrated significantly higher efficacies for transgene expression than 25 kDa polyethyleneamine (PEI) and lipofectamine, including in presence of serum. Self-assembly of these cationic lipopolymers into nanoparticles also facilitated the delivery of small molecule drugs (e.g. doxorubicin) to cancer cells. LPNs were also employed for the simultaneous delivery of the small-molecule histone deacetylase (HDAC) inhibitor AR-42 together with plasmid DNA to cancer cells as a combination treatment approach for enhancing transgene expression. Taken together, our results indicate that aminoglycoside-derived LPNs are attractive vehicles for simultaneous delivery of imaging agents or chemotherapeutic drugs together with nucleic acids for different applications in medicine and biotechnology.
    Schlagwörter covid19
    Verlag WHO
    Dokumenttyp Artikel
    Anmerkung WHO #Covidence: #32830211
    Datenquelle COVID19

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