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  1. Article ; Online: Accurate Prediction of Ion Mobility Collision Cross-Section Using Ion's Polarizability and Molecular Mass with Limited Data.

    Wisanpitayakorn, Pattipong / Sartyoungkul, Sitanan / Kurilung, Alongkorn / Sirivatanauksorn, Yongyut / Visessanguan, Wonnop / Sathirapongsasuti, Nuankanya / Khoomrung, Sakda

    Journal of chemical information and modeling

    2024  Volume 64, Issue 5, Page(s) 1533–1542

    Abstract: The rotationally averaged collision cross-section (CCS) determined by ion mobility-mass spectrometry (IM-MS) facilitates the identification of various biomolecules. Although machine learning (ML) models have recently emerged as a highly accurate approach ...

    Abstract The rotationally averaged collision cross-section (CCS) determined by ion mobility-mass spectrometry (IM-MS) facilitates the identification of various biomolecules. Although machine learning (ML) models have recently emerged as a highly accurate approach for predicting CCS values, they rely on large data sets from various instruments, calibrants, and setups, which can introduce additional errors. In this study, we identified and validated that ion's polarizability and mass-to-charge ratio (
    MeSH term(s) Ions/chemistry ; Ion Mobility Spectrometry/methods
    Chemical Substances Ions
    Language English
    Publishing date 2024-02-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.3c01491
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1230: Show issues Location:
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  2. Article ; Online: Measurement of the persistence length of cytoskeletal filaments using curvature distributions.

    Wisanpitayakorn, Pattipong / Mickolajczyk, Keith J / Hancock, William O / Vidali, Luis / Tüzel, Erkan

    Biophysical journal

    2022  Volume 121, Issue 10, Page(s) 1813–1822

    Abstract: Cytoskeletal filaments, such as microtubules and actin filaments, play important roles in the mechanical integrity of cells and the ability of cells to respond to their environment. Measuring the mechanical properties of cytoskeletal structures is ... ...

    Abstract Cytoskeletal filaments, such as microtubules and actin filaments, play important roles in the mechanical integrity of cells and the ability of cells to respond to their environment. Measuring the mechanical properties of cytoskeletal structures is crucial for gaining insight into intracellular mechanical stresses and their role in regulating cellular processes. One of the ways to characterize these mechanical properties is by measuring their persistence length, the average length over which filaments stay straight. There are several approaches in the literature for measuring filament deformations, such as Fourier analysis of images obtained using fluorescence microscopy. Here, we show how curvature distributions can be used as an alternative tool to quantify biofilament deformations, and investigate how the apparent stiffness of filaments depends on the resolution and noise of the imaging system. We present analytical calculations of the scaling curvature distributions as a function of filament discretization, and test our predictions by comparing Monte Carlo simulations with results from existing techniques. We also apply our approach to microtubules and actin filaments obtained from in vitro gliding assay experiments with high densities of nonfunctional motors, and calculate the persistence length of these filaments. The presented curvature analysis is significantly more accurate compared with existing approaches for small data sets, and can be readily applied to both in vitro and in vivo filament data through the use of the open-source codes we provide.
    MeSH term(s) Actin Cytoskeleton/chemistry ; Cytoskeleton ; Microscopy, Fluorescence ; Microtubules ; Stress, Mechanical
    Language English
    Publishing date 2022-04-20
    Publishing country United States
    Document type 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 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2022.04.020
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  3. Article ; Online: Correction: GC × GC-TOFMS metabolomics analysis identifies elevated levels of plasma sugars and sugar alcohols in diabetic mellitus patients with kidney failure.

    Duangkumpha, Kassaporn / Jariyasopit, Narumol / Wanichthanarak, Kwanjeera / Dhakal, Esha / Wisanpitayakorn, Pattipong / Thotsiri, Sansanee / Sirivatanauksorn, Yongyut / Kitiyakara, Chagriya / Sathirapongsasuti, Nuankanya / Khoomrung, Sakda

    The Journal of biological chemistry

    2023  Volume 299, Issue 12, Page(s) 105422

    Language English
    Publishing date 2023-11-07
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2023.105422
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  4. Article ; Online: GC × GC-TOFMS metabolomics analysis identifies elevated levels of plasma sugars and sugar alcohols in diabetic mellitus patients with kidney failure.

    Duangkumpha, Kassaporn / Jariyasopit, Narumol / Wanichthanarak, Kwanjeera / Dhakal, Esha / Wisanpitayakorn, Pattipong / Thotsiri, Sansanee / Sirivatanauksorn, Yongyut / Kitiyakara, Chagriya / Sathirapongsasuti, Nuankanya / Khoomrung, Sakda

    The Journal of biological chemistry

    2022  Volume 298, Issue 10, Page(s) 102445

    Abstract: Two dimensional GC (GC × GC)-time-of-flight mass spectrometry (TOFMS) has been used to improve accurate metabolite identification in the chemical industry, but this method has not been applied as readily in biomedical research. Here, we evaluated and ... ...

    Abstract Two dimensional GC (GC × GC)-time-of-flight mass spectrometry (TOFMS) has been used to improve accurate metabolite identification in the chemical industry, but this method has not been applied as readily in biomedical research. Here, we evaluated and validated the performance of high resolution GC × GC-TOFMS against that of GC-TOFMS for metabolomics analysis of two different plasma matrices, from healthy controls (CON) and diabetes mellitus (DM) patients with kidney failure (DM with KF). We found GC × GC-TOFMS outperformed traditional GC-TOFMS in terms of separation performance and metabolite coverage. Several metabolites from both the CON and DM with KF matrices, such as carbohydrates and carbohydrate-conjugate metabolites, were exclusively detected using GC × GC-TOFMS. Additionally, we applied this method to characterize significant metabolites in the DM with KF group, with focused analysis of four metabolite groups: sugars, sugar alcohols, amino acids, and free fatty acids. Our plasma metabolomics results revealed 35 significant metabolites (12 unique and 23 concentration-dependent metabolites) in the DM with KF group, as compared with those in the CON and DM groups (N = 20 for each group). Interestingly, we determined 17 of the 35 (14/17 verified with reference standards) significant metabolites identified from both the analyses were metabolites from the sugar and sugar alcohol groups, with significantly higher concentrations in the DM with KF group than in the CON and DM groups. Enrichment analysis of these 14 metabolites also revealed that alterations in galactose metabolism and the polyol pathway are related to DM with KF. Overall, our application of GC × GC-TOFMS identified key metabolites in complex plasma matrices.
    MeSH term(s) Humans ; Gas Chromatography-Mass Spectrometry/methods ; Metabolomics/methods ; Renal Insufficiency/blood ; Sugar Alcohols/blood ; Sugars/blood ; Diabetic Neuropathies/blood
    Chemical Substances Sugar Alcohols ; Sugars
    Language English
    Publishing date 2022-08-31
    Publishing country United States
    Document type Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2022.102445
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  5. Article ; Online: Myosin XI drives polarized growth by vesicle focusing and local enrichment of F-actin in Physcomitrium patens.

    Galotto, Giulia / Wisanpitayakorn, Pattipong / Bibeau, Jeffrey P / Liu, Yen-Chun / Furt, Fabienne / Pierce, Ellen C / Simpson, Parker J / Tüzel, Erkan / Vidali, Luis

    Plant physiology

    2021  Volume 187, Issue 4, Page(s) 2509–2529

    Abstract: In tip-growing plant cells, growth results from myosin XI and F-actin-mediated deposition of cell wall polysaccharides contained in secretory vesicles. Previous evidence showed that myosin XI anticipates F-actin accumulation at the cell's tip, suggesting ...

    Abstract In tip-growing plant cells, growth results from myosin XI and F-actin-mediated deposition of cell wall polysaccharides contained in secretory vesicles. Previous evidence showed that myosin XI anticipates F-actin accumulation at the cell's tip, suggesting a mechanism where vesicle clustering via myosin XI increases F-actin polymerization. To evaluate this model, we used a conditional loss-of-function strategy by generating moss (Physcomitrium patens) plants harboring a myosin XI temperature-sensitive allele. We found that loss of myosin XI function alters tip cell morphology, vacuolar homeostasis, and cell viability but not following F-actin depolymerization. Importantly, our conditional loss-of-function analysis shows that myosin XI focuses and directs vesicles at the tip of the cell, which induces formin-dependent F-actin polymerization, increasing F-actin's local concentration. Our findings support the role of myosin XI in vesicle focusing, possibly via clustering and F-actin organization, necessary for tip growth, and deepen our understanding of additional myosin XI functions.
    MeSH term(s) Actins/metabolism ; Bryopsida/physiology ; Myosins/metabolism ; Organelles/physiology ; Plant Proteins/metabolism
    Chemical Substances Actins ; Plant Proteins ; Myosins (EC 3.6.4.1)
    Language English
    Publishing date 2021-12-09
    Publishing country United States
    Document type 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 208914-2
    ISSN 1532-2548 ; 0032-0889
    ISSN (online) 1532-2548
    ISSN 0032-0889
    DOI 10.1093/plphys/kiab435
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  6. Article ; Online: Traveling Wave Ion Mobility-Derived Collision Cross Section Database for Plant Specialized Metabolites: An Application to

    Jariyasopit, Narumol / Limjiasahapong, Suphitcha / Kurilung, Alongkorn / Sartyoungkul, Sitanan / Wisanpitayakorn, Pattipong / Nuntasaen, Narong / Kuhakarn, Chutima / Reutrakul, Vichai / Kittakoop, Prasat / Sirivatanauksorn, Yongyut / Khoomrung, Sakda

    Journal of proteome research

    2022  Volume 21, Issue 10, Page(s) 2481–2492

    Abstract: The combination of ion mobility mass spectrometry (IM-MS) and chromatography is a valuable tool for identifying compounds in natural products. In this study, using an ultra-performance liquid chromatography system coupled to a high-resolution quadrupole/ ... ...

    Abstract The combination of ion mobility mass spectrometry (IM-MS) and chromatography is a valuable tool for identifying compounds in natural products. In this study, using an ultra-performance liquid chromatography system coupled to a high-resolution quadrupole/traveling wave ion mobility spectrometry/time-of-flight MS (UPLC-TWIMS-QTOF), we have established and validated a comprehensive
    MeSH term(s) Biological Products ; Flavonoids ; Ions/chemistry ; Lipids ; Mass Spectrometry/methods ; Rhamnaceae ; Xanthones
    Chemical Substances Biological Products ; Flavonoids ; Ions ; Lipids ; Xanthones
    Language English
    Publishing date 2022-09-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.2c00413
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  7. Article ; Online: Kinesin-2 from C. reinhardtii Is an Atypically Fast and Auto-inhibited Motor that Is Activated by Heterotrimerization for Intraflagellar Transport.

    Sonar, Punam / Youyen, Wiphu / Cleetus, Augustine / Wisanpitayakorn, Pattipong / Mousavi, Sayed I / Stepp, Willi L / Hancock, William O / Tüzel, Erkan / Ökten, Zeynep

    Current biology : CB

    2020  Volume 30, Issue 6, Page(s) 1160–1166.e5

    Abstract: Construction and function of virtually all cilia require the universally conserved process of intraflagellar transport (IFT) [1, 2]. During the atypically fast IFT in the green alga C. reinhardtii, on average, 10 kinesin-2 motors "line up" in a tight ... ...

    Abstract Construction and function of virtually all cilia require the universally conserved process of intraflagellar transport (IFT) [1, 2]. During the atypically fast IFT in the green alga C. reinhardtii, on average, 10 kinesin-2 motors "line up" in a tight assembly on the trains [3], provoking the question of how these motors coordinate their action to ensure smooth and fast transport along the flagellum without standing in each other's way. Here, we show that the heterodimeric FLA8/10 kinesin-2 alone is responsible for the atypically fast IFT in C. reinhardtii. Notably, in single-molecule studies, FLA8/10 moved at speeds matching those of in vivo IFT [4] but additionally displayed a slow velocity distribution, indicative of auto-inhibition. Addition of the KAP subunit to generate the heterotrimeric FLA8/10/KAP relieved this inhibition, thus providing a mechanistic rationale for heterotrimerization with the KAP subunit fully activating FLA8/10 for IFT in vivo. Finally, we linked fast FLA8/10 and slow KLP11/20 kinesin-2 from C. reinhardtii and C. elegans through a DNA tether to understand the molecular underpinnings of motor coordination during IFT in vivo. For motor pairs from both species, the co-transport velocities very nearly matched the single-molecule velocities, and both complexes spent roughly 80% of the time with only one of the two motors attached to the microtubule. Thus, irrespective of phylogeny and kinetic properties, kinesin-2 motors work mostly alone without sacrificing efficiency. Our findings thus offer a simple mechanism for how efficient IFT is achieved across diverse organisms despite being carried out by motors with different properties.
    MeSH term(s) Biological Transport ; Chlamydomonas reinhardtii/genetics ; Chlamydomonas reinhardtii/physiology ; Flagella/physiology ; Kinesin/physiology ; Microtubule-Associated Proteins/genetics ; Microtubule-Associated Proteins/metabolism ; Protein Transport ; Protozoan Proteins/genetics ; Protozoan Proteins/metabolism
    Chemical Substances KHP1 protein, Chlamydomonas ; Microtubule-Associated Proteins ; Protozoan Proteins ; Kinesin (EC 3.6.4.4)
    Language English
    Publishing date 2020-03-05
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2020.01.046
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3208: Show issues Location:
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