CryoEM SPA of Apo-SrpI Encapsulin Complex (Raw Frames)
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ABSTRACT:
SUBMITTER: Benjamin LaFrance
PROVIDER: EMPIAR-10510 | biostudies-other |
REPOSITORIES: biostudies-other
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Project description:Encapsulin is a class of nanocompartments that is unique in bacteria and archaea to confine enzymatic activities and sequester toxic reaction products. Here we present a 2.87 Å resolution cryo-EM structure of Thermotoga maritima encapsulin with heterologous protein complex loaded. It is the first successful case of expressing encapsulin and heterologous cargo protein in the insect cell system. Although we failed to reconstruct the cargo protein complex structure due to the signal interference of the capsid shell, we were able to observe some unique features of the cargo-loaded encapsulin shell, for example, an extra density at the fivefold pore that has not been reported before. These results would lead to a more complete understanding of the encapsulin cargo assembly process of T. maritima.
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| EMPIAR-10503 | biostudies-other
Project description:Single particle reconstruction (SPR) in cryoEM is an image processing task with an elaborate hierarchy that starts with many very noisy multi-frame images. Efficient representation of the intermediary image structures is critical for keeping the calculations manageable. One such intermediary structure is called a particle stack and contains cut-out images of particles in square boxes of predefined size. The micrograph that is the source of the boxed images is usually corrected for motion between frames prior to particle stack creation. However, the contrast transfer function (CTF) or its Fourier Transform point spread function (PSF) are not considered at this step. Historically, the particle stack was intended for large particles and for a tighter PSF, which is characteristic of lower resolution data. The field now performs analyses of smaller particles and to higher resolution, and these conditions result in a broader PSF that requires larger padding and slower calculations to integrate information for each particle. Consequently, the approach to handling structures such as the particle stack should be reexamined to optimize data processing. Here we propose to use as a source image for the particle stack a complex-valued image, in which CTF correction is implicitly applied as a real component of the image. We can achieve it by applying an initial CTF correction to the entire micrograph first and perform box cutouts as a subsequent step. The final CTF correction that we refine and apply later has a very narrow PSF, and so cutting out particles from micrographs that were approximately corrected for CTF does not require extended buffering, i.e. the boxes during the analysis only have to be large enough to encompass the particle. The Fourier Transform of an exit-wave reconstruction creates an image that has complex values. This is a complex value image considered in real space, opposed to standard SPR data processing where complex numbers appear only in Fourier space. This extension of the micrograph concept provides multiple advantages because the particle box size can be small and calculations crucial for high resolution reconstruction such as Ewald sphere correction, aberration refinement, and particle-specific defocus refinement can be performed on the small box data.
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Project description:BackgroundKivach Clinic has developed a special medical spa program to prevent aging-related conditions in metabolic, cardio-vascular, and neurological states. Spa programs modify diet, physical activity, and lymphatic drainage, as it deteriorates with aging. We investigated its influence on the blood markers of biological age of patients during their stay to objectify the potential of spa treatment for influencing the risk of age-related events.MethodsThe artificial deep learning model Aging.ai 3.0 was based on blood parameters. The change in the biological age of 43 patients was assessed after their 14-day spa treatment at Kivach Clinic.ResultsBiological age decreased in 29 patients (median decrease: 8 years, mean: 8.83 years), increased in 10 patients (median increase: 3 years, mean: 5.33 years) and remained unchanged in 4 patients. Overall mean values for the entire patient group were as follows: median value was -3 years, and mean was -4.79 ± 1.2 years (p-value = 0.00025, t-test).ConclusionsThe capability of specially selected medical spa treatment to reduce human biological age (assessed by Aging.AI 3.0) has been established.
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