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  1. Article ; Online: Frequency modulation of the Min-protein oscillator by nucleoid-associated factors in Escherichia coli.

    Shen, Jie-Pan / Chang, Yi-Ren / Chou, Chia-Fu

    Biochemical and biophysical research communications

    2020  Volume 525, Issue 4, Page(s) 857–862

    Abstract: In E. coli, the Min-protein oscillator, together with the nucleoid occlusion (NO), destabilizes the Z-ring assembly away from the midcell to ensure faithful septation. These two inhibitory pathways are thought to be working independently for division ... ...

    Abstract In E. coli, the Min-protein oscillator, together with the nucleoid occlusion (NO), destabilizes the Z-ring assembly away from the midcell to ensure faithful septation. These two inhibitory pathways are thought to be working independently for division site placement. Even though the Min-protein oscillator has been displayed by synthetic minimal systems, it is unclear the interplays of Min proteins and compartment geometry are sufficient to bolster oscillation stability in vivo. By probing if NO plays a role in the Min oscillation, we study the oscillation frequency in the anucleate and nucleoid-perturbed cells. Surprisingly, we found that the oscillation periods of the Min-protein oscillators were seriously deviated in the anucleate and nucleoid-perturbed cells, but the oscillation frequency either went up in the anucleate or down in the nucleoid-perturbed cells. Intriguingly, enhanced stability and reduced frequency were observed in the cells expressing the NO factor SlmA higher than the native level. Our results reveal an unanticipated role of the nucleoid in modulating the frequency and stability of Min-protein system. SlmA is indicated to facilitate such modulations, potentially via directly interacting with the Min-protein system. A fresh perspective is suggested that frequency modulation of Min-protein oscillator is mediated via the act of nucleoid-associated factors.
    MeSH term(s) Adenosine Triphosphatases/genetics ; Adenosine Triphosphatases/metabolism ; Carrier Proteins/metabolism ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Cell Division ; Chromosomal Proteins, Non-Histone/genetics ; Escherichia coli/cytology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Microorganisms, Genetically-Modified ; Mutation
    Chemical Substances Carrier Proteins ; Cell Cycle Proteins ; Chromosomal Proteins, Non-Histone ; Escherichia coli Proteins ; MinE protein, E coli ; MukB protein, E coli ; SlmA protein, E coli ; Adenosine Triphosphatases (EC 3.6.1.-) ; MinD protein, E coli (EC 3.6.1.-)
    Language English
    Publishing date 2020-03-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
    ZDB-ID 205723-2
    ISSN 1090-2104 ; 0006-291X ; 0006-291X
    ISSN (online) 1090-2104 ; 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2020.02.161
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 116: Show issues Location:
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  2. Article: Morphological plasticity of bacteria-Open questions.

    Shen, Jie-Pan / Chou, Chia-Fu

    Biomicrofluidics

    2016  Volume 10, Issue 3, Page(s) 31501

    Abstract: Morphological plasticity of bacteria is a cryptic phenomenon, by which bacteria acquire adaptive benefits for coping with changing environments. Some environmental cues were identified to induce morphological plasticity, but the underlying molecular ... ...

    Abstract Morphological plasticity of bacteria is a cryptic phenomenon, by which bacteria acquire adaptive benefits for coping with changing environments. Some environmental cues were identified to induce morphological plasticity, but the underlying molecular mechanisms remain largely unknown. Physical and chemical factors causing morphological changes in bacteria have been investigated and mostly associated with potential pathways linked to the cell wall synthetic machinery. These include starvation, oxidative stresses, predation effectors, antimicrobial agents, temperature stresses, osmotic shock, and mechanical constraints. In an extreme scenario of morphological plasticity, bacteria can be induced to be shapeshifters when the cell walls are defective or deficient. They follow distinct developmental pathways and transform into assorted morphological variants, and most of them would eventually revert to typical cell morphology. It is suggested that phenotypic heterogeneity might play a functional role in the development of morphological diversity and/or plasticity within an isogenic population. Accordingly, phenotypic heterogeneity and inherited morphological plasticity are found to be survival strategies adopted by bacteria in response to environmental stresses. Here, microfluidic and nanofabrication technology is considered to provide versatile solutions to induce morphological plasticity, sort and isolate morphological variants, and perform single-cell analysis including transcriptional and epigenetic profiling. Questions such as how morphogenesis network is modulated or rewired (if epigenetic controls of cell morphogenesis apply) to induce bacterial morphological plasticity could be resolved with the aid of micro-nanofluidic platforms and optimization algorithms, such as feedback system control.
    Language English
    Publishing date 2016-06-10
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1932-1058
    ISSN 1932-1058
    DOI 10.1063/1.4953660
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Frequency modulation of the Min-protein oscillator by nucleoid-associated factors in Escherichia coli

    Shen, Jie-Pan / Chang, Yi-Ren / Chou, Chia-Fu

    Biochemical and biophysical research communications. 2020 May 14, v. 525, no. 4

    2020  

    Abstract: In E. coli, the Min-protein oscillator, together with the nucleoid occlusion (NO), destabilizes the Z-ring assembly away from the midcell to ensure faithful septation. These two inhibitory pathways are thought to be working independently for division ... ...

    Abstract In E. coli, the Min-protein oscillator, together with the nucleoid occlusion (NO), destabilizes the Z-ring assembly away from the midcell to ensure faithful septation. These two inhibitory pathways are thought to be working independently for division site placement. Even though the Min-protein oscillator has been displayed by synthetic minimal systems, it is unclear the interplays of Min proteins and compartment geometry are sufficient to bolster oscillation stability in vivo. By probing if NO plays a role in the Min oscillation, we study the oscillation frequency in the anucleate and nucleoid-perturbed cells. Surprisingly, we found that the oscillation periods of the Min-protein oscillators were seriously deviated in the anucleate and nucleoid-perturbed cells, but the oscillation frequency either went up in the anucleate or down in the nucleoid-perturbed cells. Intriguingly, enhanced stability and reduced frequency were observed in the cells expressing the NO factor SlmA higher than the native level. Our results reveal an unanticipated role of the nucleoid in modulating the frequency and stability of Min-protein system. SlmA is indicated to facilitate such modulations, potentially via directly interacting with the Min-protein system. A fresh perspective is suggested that frequency modulation of Min-protein oscillator is mediated via the act of nucleoid-associated factors.
    Keywords Escherichia coli ; geometry ; research
    Language English
    Dates of publication 2020-0514
    Size p. 857-862.
    Publishing place Elsevier Inc.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 205723-2
    ISSN 0006-291X ; 0006-291X
    ISSN (online) 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2020.02.161
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 71/706: Show issues
    Z 3.8: Show issues

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  4. Article: Bacteria under the physical constraints of periodic micro-nanofluidic junctions reveal morphological plasticity and dynamic shifting of Min patterns.

    Shen, Jie-Pan / Chou, Chia-Fu

    Biomicrofluidics

    2014  Volume 8, Issue 4, Page(s) 41103

    Abstract: Morphological plasticity is an important survival strategy for bacteria adapting to stressful environments in response to new physical constraints. Here, we demonstrate Escherichia coli morphological plasticity can be induced by switching stress levels ... ...

    Abstract Morphological plasticity is an important survival strategy for bacteria adapting to stressful environments in response to new physical constraints. Here, we demonstrate Escherichia coli morphological plasticity can be induced by switching stress levels through the physical constraints of periodic micro-nanofluidic junctions. Moreover, the generation of diverse morphological aberrancies requires the intact functions of the divisome- and elongasome-directed pathways. It is also intriguing that the altered morphologies are developed in bacteria undergoing morphological reversion as stresses are removed. Cell filamentation underlies the most dominant morphological phenotypes, in which transitions between the novel pattern formations by the spatial regulators of the divisome, i.e., the Min system, are observed, suggesting their potential linkage during morphological reversion.
    Language English
    Publishing date 2014-08-07
    Publishing country United States
    Document type Journal Article
    ISSN 1932-1058
    ISSN 1932-1058
    DOI 10.1063/1.4892860
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Bovine FRAS1: mRNA Expression Profile, Genetic Variations, and Significant Correlations with Ovarian Morphological Traits, Mature Follicle, and Corpus Luteum.

    Zhu, Leijing / Shen, Siyuan / Pan, Chuanying / Lan, Xianyong / Li, Jie

    Animals : an open access journal from MDPI

    2024  Volume 14, Issue 4

    Abstract: The amelioration of bovine fertility caused by a multi-factorial problem has always been a hot topic, among which the detection of available target genes is the most crucial. It was hypothesized that the Fraser extracellular matrix complex subunit 1 ( ...

    Abstract The amelioration of bovine fertility caused by a multi-factorial problem has always been a hot topic, among which the detection of available target genes is the most crucial. It was hypothesized that the Fraser extracellular matrix complex subunit 1 (
    Language English
    Publishing date 2024-02-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606558-7
    ISSN 2076-2615
    ISSN 2076-2615
    DOI 10.3390/ani14040597
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Nanoconfinement-Induced DNA Reptating Motion and Analogy to Fluctuating Interfaces

    Yeh, Jia-Wei / Taloni, Alessandro / Sriram, K. K / Shen, Jie-Pan / Kao, Der-You / Chou, Chia-Fu

    Macromolecules. 2020 Jan. 29, v. 53, no. 3

    2020  

    Abstract: Macromolecules in an entangled environment are constrained to wriggle predominantly along a confining tube, giving rise to the so-called reptation or tube-like motion. While the principles of polymer physics were well developed to understand its ... ...

    Abstract Macromolecules in an entangled environment are constrained to wriggle predominantly along a confining tube, giving rise to the so-called reptation or tube-like motion. While the principles of polymer physics were well developed to understand its conformational dynamics, the quantitative characterization of the tube diameter and resulting reptation remains an open question. Here, using highly confined parallel plate geometry nanoslits down to sub-30 nm, we directly observe reptation in a one-dimensional (1D) confined nanoenvironment. We provide a quantitative analysis scheme, by introducing the segmental tangential vector and its associated correlation function, to characterize the strand reptation and connect it to the confinement degree. Our analysis shows that the amplitude of the transverse fluctuations (the virtual 2D “tube”) exhibits the typical scaling of fluctuating interfaces, contact lines, or charge density waves, with a roughness exponent, which depends on the slit height. Our results are shown to lead to less rough DNA profiles in shallower nanoslits. We anticipate our analysis to be a starting point for a more detailed understanding of the relationship between polymer physics and other nonequilibrium physical systems.
    Keywords DNA ; DNA fingerprinting ; geometry ; polymers ; quantitative analysis ; roughness
    Language English
    Dates of publication 2020-0129
    Size p. 1001-1013.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 1491942-4
    ISSN 1520-5835 ; 0024-9297
    ISSN (online) 1520-5835
    ISSN 0024-9297
    DOI 10.1021/acs.macromol.9b02074
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  7. Article ; Online: Assessing Driving Risk at the Second Phase of Overtaking on Two-Lane Highways for Young Novice Drivers Based on Driving Simulation.

    Pan, Jie / Shen, Yongjun

    International journal of environmental research and public health

    2022  Volume 19, Issue 5

    Abstract: Overtaking on two-lane highways is a complex and multi-phase maneuver associated with high collision risk, especially for young novice drivers. Most of the relevant studies, however, focused mainly on the first phase, i.e., the lane-changing phase, such ... ...

    Abstract Overtaking on two-lane highways is a complex and multi-phase maneuver associated with high collision risk, especially for young novice drivers. Most of the relevant studies, however, focused mainly on the first phase, i.e., the lane-changing phase, such as willingness to overtake, while the second phase, i.e., the back-to-lane phase, has not been investigated systematically. It is a risky phase in which a driver faces the risk of collision with not only the approaching vehicle on the opposite lane but also the impeding vehicle at the original lane. In this study, by designing and conducting a driving simulator experiment, we assess the driving risk of 47 young novice drivers during their second phase of overtaking on two-lane highways. The time-to-collision (TTC) values at the two critical positions are calculated from a micro-geometric point of view, based on which a two-dimensional risk index is proposed and the fuzzy C-means clustering algorithm is applied to group all the samples and to assess their overtaking risk. Furthermore, a multi-class logistic model is developed to understand the potential factors related to the risky overtaking maneuvers at this phase. The results show that most of the young novice drivers cannot make accurate judgments during their second phase of overtaking. When turning back to the original lane, they are more likely to be aware of the opposite vehicle that is approaching them, while how to correctly avoid the collision risk with the impeding vehicle at this phase is probably a more critical issue for young novice drivers.
    MeSH term(s) Accidents, Traffic ; Automobile Driving ; Computer Simulation ; Judgment ; Logistic Models
    Language English
    Publishing date 2022-02-25
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2175195-X
    ISSN 1660-4601 ; 1661-7827
    ISSN (online) 1660-4601
    ISSN 1661-7827
    DOI 10.3390/ijerph19052691
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Loudspeaker array beamforming for sound projection in a half-space with an impedance boundary.

    Pan, Keyu / Huang, Jie / Cheng, Jiazheng / Shen, Yong

    The Journal of the Acoustical Society of America

    2023  Volume 153, Issue 3, Page(s) 1626

    Abstract: Sound projection is a method of using highly focused sources to project sound onto reflective surfaces to create the impression of surround sound, which can be realized via beamforming using loudspeaker arrays. Generally, these devices are mounted near a ...

    Abstract Sound projection is a method of using highly focused sources to project sound onto reflective surfaces to create the impression of surround sound, which can be realized via beamforming using loudspeaker arrays. Generally, these devices are mounted near a surface with a finite acoustic impedance, such as a TV accent wall. The beamforming performance degrades in this half-space with an impedance boundary when the filters are designed using transfer functions measured in the free field. This paper proposes a model for predicting the beamforming performance in a half-space with an impedance boundary in terms of the transfer functions in the free field. A mathematical model is presented, and the results are compared with practical measurements for a 16-driver line array in real-use environments. The results show that reflections from the boundary lead to "dark bands" in the beam, causing the beam to deviate from the designed direction. Using filters designed with transfer functions calculated by the proposed model yields improved beamforming performance.
    Language English
    Publishing date 2023-03-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 219231-7
    ISSN 1520-8524 ; 0001-4966
    ISSN (online) 1520-8524
    ISSN 0001-4966
    DOI 10.1121/10.0017534
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 591: Show issues Location:
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  9. Article: Exploration of the Polymorphism Distribution of Bovine

    Shen, Siyuan / Zhu, Leijing / Yang, Yuanzhe / Bi, Yi / Li, Jie / Wang, Yongsheng / Pan, Chuanying / Wang, Shuilian / Lan, Xianyong

    Animals : an open access journal from MDPI

    2024  Volume 14, Issue 5

    Abstract: The high-mobility group AT-hook 2( ...

    Abstract The high-mobility group AT-hook 2(
    Language English
    Publishing date 2024-03-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606558-7
    ISSN 2076-2615
    ISSN 2076-2615
    DOI 10.3390/ani14050796
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Effects of Short- and Long-Term Detraining on Maximal Oxygen Uptake in Athletes: A Systematic Review and Meta-Analysis.

    Zheng, Jie / Pan, Tian / Jiang, Yankang / Shen, Yupeng

    BioMed research international

    2022  Volume 2022, Page(s) 2130993

    Abstract: ... ...

    Abstract V̇O
    MeSH term(s) Adult ; Athletes ; Exercise ; Humans ; Oxygen ; Oxygen Consumption
    Chemical Substances Oxygen (S88TT14065)
    Language English
    Publishing date 2022-08-16
    Publishing country United States
    Document type Journal Article ; Meta-Analysis ; Systematic Review
    ZDB-ID 2698540-8
    ISSN 2314-6141 ; 2314-6133
    ISSN (online) 2314-6141
    ISSN 2314-6133
    DOI 10.1155/2022/2130993
    Database MEDical Literature Analysis and Retrieval System OnLINE

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