scholarly journals Structure of the native supercoiled flagellar hook as a universal joint

2019 ◽  
Author(s):  
Takayuki Kato ◽  
Fumiaki Makino ◽  
Tomoko Miyata ◽  
Peter Horváth ◽  
Keiichi Namba
Keyword(s):  
Image Analysis ◽  
Basal Body ◽  
Inner Core ◽  
Three Dimensional ◽  
Approximate Model ◽  
Atomic Model ◽  
Universal Joint ◽  
Supercoiled Form ◽  
Smoke Ring ◽  
Intersubunit Interactions

Bacteria swim in viscous liquid environments by using the flagellum1–3. The flagellum is composed of about 30 different proteins and can be roughly divided into three parts: the basal body, the hook and the filament. The basal body acts as a rotary motor powered by ion motive force across the cytoplasmic membrane as well as a protein export apparatus to construct the axial structure of the flagellum. The filament is as a helical propeller, and it is a supercoiled form of a helical tubular assembly consisting of a few tens of thousands of flagellin molecules4. The hook is a relatively short axial segment working as a universal joint connecting the basal body and the filament for smooth transmission of motor torque to the filament5,6. The structure of hook has been studied by combining X-ray crystal structure of a core fragment of hook protein FlgE and electron cryomicroscopy (cryoEM) helical image analysis of the polyhook in the straight form and has given a deep insight into the universal joint mechanism7. However, the supercoiled structure of the hook was an approximate model based on the atomic model of the straight hook without its inner core domain7 and EM observations of supercoiled polyhook by freeze-dry and Pt/Pd shadow cast8. Here we report the native supercoiled hook structure at 3.1 Å resolution by cryoEM single particle image analysis of the polyhook. The atomic model built on the three-dimensional (3D) density map show the actual changes in subunit conformation and intersubunit interactions upon compression and extension of the 11 protofilaments that occur during their smoke ring-like rotation and allow the hook to function as a dynamic molecular universal joint with high bending flexibility and twisting rigidity.

scholarly journals Structure of the native supercoiled flagellar hook as a universal joint

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Takayuki Kato ◽  
Fumiaki Makino ◽  
Tomoko Miyata ◽  
Péter Horváth ◽  
Keiichi Namba
Keyword(s):  
Image Analysis ◽  
Basal Body ◽  
Single Particle ◽  
Particle Image ◽  
Three Dimensional ◽  
Universal Joint ◽  
Density Map ◽  
Smoke Ring ◽  
Intersubunit Interactions ◽  
Rotary Motor

AbstractThe Bacterial flagellar hook is a short supercoiled tubular structure made from a helical assembly of the hook protein FlgE. The hook acts as a universal joint that connects the flagellar basal body and filament, and smoothly transmits torque generated by the rotary motor to the helical filament propeller. In peritrichously flagellated bacteria, the hook allows the filaments to form a bundle behind the cell for swimming, and for the bundle to fall apart for tumbling. Here we report a native supercoiled hook structure at 3.6 Å resolution by cryoEM single particle image analysis of the polyhook. The atomic model built into the three-dimensional (3D) density map reveals the changes in subunit conformation and intersubunit interactions that occur upon compression and extension of the 11 protofilaments during their smoke ring-like rotation. These observations reveal how the hook functions as a dynamic molecular universal joint with high bending flexibility and twisting rigidity.

The three-dimensional structure of frozen-hydrated left- and right-handed forms of bacterial flagellar filaments from an identical serotype

1986 ◽  
Vol 44 ◽  
pp. 298-299
Author(s):  
S. Trachtenberg ◽  
D. J. DeRosier
Keyword(s):  
Ionic Strength ◽  
Basal Body ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Protein Species ◽  
Liquid Environment ◽  
Bacterial Flagellum ◽  
Left And Right ◽  
Rotary Motor ◽  
Helical Parameters

The bacterial cell is propelled through the liquid environment by means of one or more rotating flagella. The bacterial flagellum is composed of a basal body (rotary motor), hook (universal coupler), and filament (propellor). The filament is a rigid helical assembly of only one protein species — flagellin. The filament can adopt different morphologies and change, reversibly, its helical parameters (pitch and hand) as a function of mechanical stress and chemical changes (pH, ionic strength) in the environment.

High-speed brightfield 3-D imaging and 3-D image analysis of thick and overlapped cell clusters in cytological preparations

1994 ◽  
Vol 52 ◽  
pp. 218-219
Author(s):  
Robert W. Mackin
Keyword(s):  
Image Analysis ◽  
High Speed ◽  
Three Dimensional ◽  
Image Data ◽  
Ccd Camera ◽  
Objective Lens ◽  
Array Processor ◽  
Vaginal Smears ◽  
Low Contrast ◽  
Computer Controlled

This paper presents two advances towards the automated three-dimensional (3-D) analysis of thick and heavily-overlapped regions in cytological preparations such as cervical/vaginal smears. First, a high speed 3-D brightfield microscope has been developed, allowing the acquisition of image data at speeds approaching 30 optical slices per second. Second, algorithms have been developed to detect and segment nuclei in spite of the extremely high image variability and low contrast typical of such regions. The analysis of such regions is inherently a 3-D problem that cannot be solved reliably with conventional 2-D imaging and image analysis methods.High-Speed 3-D imaging of the specimen is accomplished by moving the specimen axially relative to the objective lens of a standard microscope (Zeiss) at a speed of 30 steps per second, where the stepsize is adjustable from 0.2 - 5μm. The specimen is mounted on a computer-controlled, piezoelectric microstage (Burleigh PZS-100, 68/μm displacement). At each step, an optical slice is acquired using a CCD camera (SONY XC-11/71 IP, Dalsa CA-D1-0256, and CA-D2-0512 have been used) connected to a 4-node array processor system based on the Intel i860 chip.

Going Beyond 3-D Imaging: Automated 3-D Montaged image Analysis of Cytological Specimens

1996 ◽  
Vol 54 ◽  
pp. 282-283
Author(s):  
Badrinath Roysam ◽  
Hakan Ancin ◽  
Douglas E. Becker ◽  
Robert W. Mackin ◽  
Matthew M. Chestnut ◽  
...  
Keyword(s):  
Image Analysis ◽  
Structural Changes ◽  
Sampling Methods ◽  
Spatial Clustering ◽  
Three Dimensional ◽  
Field Of View ◽  
Cell Counting ◽  
Depth Of Field ◽  
Tissue Cell ◽  
Tissue Organization

This paper summarizes recent advances made by this group in the automated three-dimensional (3-D) image analysis of cytological specimens that are much thicker than the depth of field, and much wider than the field of view of the microscope. The imaging of thick samples is motivated by the need to sample large volumes of tissue rapidly, make more accurate measurements than possible with 2-D sampling, and also to perform analysis in a manner that preserves the relative locations and 3-D structures of the cells. The motivation to study specimens much wider than the field of view arises when measurements and insights at the tissue, rather than the cell level are needed.The term “analysis” indicates a activities ranging from cell counting, neuron tracing, cell morphometry, measurement of tracers, through characterization of large populations of cells with regard to higher-level tissue organization by detecting patterns such as 3-D spatial clustering, the presence of subpopulations, and their relationships to each other. Of even more interest are changes in these parameters as a function of development, and as a reaction to external stimuli. There is a widespread need to measure structural changes in tissue caused by toxins, physiologic states, biochemicals, aging, development, and electrochemical or physical stimuli. These agents could affect the number of cells per unit volume of tissue, cell volume and shape, and cause structural changes in individual cells, inter-connections, or subtle changes in higher-level tissue architecture. It is important to process large intact volumes of tissue to achieve adequate sampling and sensitivity to subtle changes. It is desirable to perform such studies rapidly, with utmost automation, and at minimal cost. Automated 3-D image analysis methods offer unique advantages and opportunities, without making simplifying assumptions of tissue uniformity, unlike random sampling methods such as stereology.12 Although stereological methods are known to be statistically unbiased, they may not be statistically efficient. Another disadvantage of sampling methods is the lack of full visual confirmation - an attractive feature of image analysis based methods.

Mathematical Model Investigation of Far-Field Transport of Ocean-Dumped Sewage Sludge Related to Remote Sensing

1982 ◽  
Vol 14 (3) ◽  
pp. 33-39
Author(s):  
C Y Kuo
Keyword(s):  
New York ◽  
Sewage Sludge ◽  
Laboratory Data ◽  
Three Dimensional ◽  
Approximate Model ◽  
Transport Processes ◽  
Far Field ◽  
New York Bight ◽  
Mean Current

An existing, three-dimensional, Eulerian-Lagrangian finite-difference model was modified and used to examine the far-field transport processes of dumped sewage sludge in the New York Bight. Both in situ and laboratory data were utilized in an attempt to approximate model inputs such as mean current speed, vertical and horizontal diffusion coefficients, particle size distributions, and specific gravities. Concentrations of the sludge near the sea surface predicted from the computer model were compared qualitatively with those remotely sensed.

scholarly journals Quantitative image analysis of microbial communities with BiofilmQ

2021 ◽  
Author(s):  
Raimo Hartmann ◽  
Hannah Jeckel ◽  
Eric Jelli ◽  
Praveen K. Singh ◽  
Sanika Vaidya ◽  
...  
Keyword(s):  
Image Analysis ◽  
Microbial Communities ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Software Tool ◽  
Image Cytometry ◽  
Quantitative Image Analysis ◽  
Space And Time ◽  
Quantitative Image ◽  
Three Dimensional Space

AbstractBiofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ—a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in three-dimensional space and time.

Experimental and simulation study of impurity transport response to RMPs in RF-heated H-mode plasmas at EAST

2021 ◽  
Vol 87 (2) ◽  
Author(s):  
Germán Vogel ◽  
Hongming Zhang ◽  
Yongcai Shen ◽  
Shuyu Dai ◽  
Youwen Sun ◽  
...  
Keyword(s):  
Inner Core ◽  
Extreme Ultraviolet ◽  
Transport Coefficients ◽  
Three Dimensional ◽  
Line Emission ◽  
Core Region ◽  
Emission Mitigation ◽  
One Dimensional ◽  
Impurity Transport ◽  
Transport Code

Spatial profiles of impurity emission measurements in the extreme ultraviolet (EUV) spectroscopic range in radiofrequency (RF)-heated discharges are combined with one-dimensional and three-dimensional transport simulations to study the effects of resonant magnetic perturbations (RMPs) on core impurity accumulation at EAST. The amount of impurity line emission mitigation by RMPs appears to be correlated with the ion Z for lithium, carbon, iron and tungsten monitored, i.e. stronger suppression of accumulation for heavier ions. The targeted effect on the most detrimental high-Z impurities suggests a possible advantage using RMPs for impurity control. Profiles of transport coefficients are calculated with the STRAHL one-dimensional impurity transport code, keeping $\nu /D$ fixed and using the measured spatial profiles of $\textrm{F}{\textrm{e}^{20 + }}$ , $\textrm{F}{\textrm{e}^{21 + }}$ and $\textrm{F}{\textrm{e}^{22 + }}$ to disentangle the transport coefficients. The iron diffusion coefficient ${D_{\textrm{Fe}}}$ increases from $1.0- 2.0\;{\textrm{m}^2}\;{\textrm{s}^{ - 1}}$ to $1.5- 3.0\;{\textrm{m}^2}\;{\textrm{s}^{ - 1}}$ from the core region to the edge region $(\rho \gt 0.5)$ after the onset of RMPs. Meanwhile, an inward pinch of iron convective velocity ${\nu _{\textrm{Fe}}}$ decreases in magnitude in the inner core region and increases significantly in the outer confined region, simultaneously contributing to preserving centrally peaked $\textrm{Fe}$ profiles and exhausting the impurities. The ${D_{\textrm{Fe}}}$ and ${\nu _{\textrm{Fe}}}$ variations lead to reduced impurity contents in the plasma. The three-dimensional edge impurity transport code EMC3-EIRENE was also applied for a case of RMP-mitigated high-Z accumulation at EAST and compared to that of low-Z carbon. The exhaust of ${\textrm{C}^{6 + }}$ toward the scrape-off layer accompanying an overall suppression of heavier ${\textrm{W}^{30 + }}$ is observed when using RMPs.

Color Reproduction Accuracy Promotion of 3D-Printed Surfaces Based on Microscopic Image Analysis

2019 ◽  
Vol 34 (01) ◽  
pp. 2054004 ◽  
Author(s):  
Xiaochun Wang ◽  
Chen Chen ◽  
Jiangping Yuan ◽  
Guangxue Chen
Keyword(s):  
Surface Roughness ◽  
Image Analysis ◽  
Three Dimensional ◽  
Prediction Method ◽  
Chromatic Aberration ◽  
Optimization Methods ◽  
Experimental Models ◽  
Microscopic Image ◽  
Color Reproduction ◽  
Microscopic Image Analysis

Full-color three-dimensional (3D) printing technology is a powerful process to manufacture intelligent customized colorful objects with improved surface qualities; however, poor surface color optimization methods are the main impeding factors for its commercialization. As such, the paper explored the correlation between microstructure and color reproduction, then an assessment and prediction method of color optimization based on microscopic image analysis was proposed. The experimental models were divided into 24-color plates and 4-color cubes printed by ProJet 860 3D printer, then impregnated according to preset parameters, at last measured by a spectrophotometer and observed using both a digital microscope and a scanning electron microscope. The results revealed that the samples manifested higher saturation and smaller chromatic aberration ([Formula: see text]) after postprocessing. Moreover, the brightness of the same color surface increased with the increasing soaked surface roughness. Further, reduction in surface roughness, impregnation into surface pores, and enhancement of coating transparency effectively improved the accuracy of color reproduction, which could be verified by the measured values. Finally, the chromatic aberration caused by positioning errors on different faces of the samples was optimized, and the value of [Formula: see text] for a black cube was reduced from 8.12 to 0.82, which is undetectable to human eyes.

scholarly journals Determination of the alpha-actinin-binding site on actin filaments by cryoelectron microscopy and image analysis.

1994 ◽  
Vol 126 (2) ◽  
pp. 433-443 ◽  
Author(s):  
A McGough ◽  
M Way ◽  
D DeRosier
Keyword(s):  
Image Analysis ◽  
Smooth Muscle ◽  
Binding Sites ◽  
Actin Filaments ◽  
Three Dimensional ◽  
Actin Binding ◽  
Dimensional Structure ◽  
Outer Face ◽  
Actin Binding Domain

The three-dimensional structure of actin filaments decorated with the actin-binding domain of chick smooth muscle alpha-actinin (alpha A1-2) has been determined to 21-A resolution. The shape and location of alpha A1-2 was determined by subtracting maps of F-actin from the reconstruction of decorated filaments. alpha A1-2 resembles a bell that measures approximately 38 A at its base and extends 42 A from its base to its tip. In decorated filaments, the base of alpha A1-2 is centered about the outer face of subdomain 2 of actin and contacts subdomain 1 of two neighboring monomers along the long-pitch (two-start) helical strands. Using the atomic model of F-actin (Lorenz, M., D. Popp, and K. C. Holmes. 1993. J. Mol. Biol. 234:826-836.), we have been able to test directly the likelihood that specific actin residues, which have been previously identified by others, interact with alpha A1-2. Our results indicate that residues 86-117 and 350-375 comprise distinct binding sites for alpha-actinin on adjacent actin monomers.

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