Recherche Papiers

[huichen5796]

Grundlagen:

• Programmierung
  • Angular, Typescript für UI
  • FastApi, Python für Backend
  • was ist front- / backend
• Datenbanken, allgemeine Info
  • (Studienarbeit als Beispiel)

• Bio

  • Zellen

  • Kryokonservierung：https://www.sciencedirect.com/science/article/pii/S0015028206033206

    • Slow freezing | Vitrification

    • non-equilibrium vitrification and equilibrium vitrification

    • CPA: https://onlinelibrary.wiley.com/doi/full/10.1002/advs.202002425

    • DMSO, Me2SO

    • Process: https://www.ingentaconnect.com/contentone/asp/jctn/2010/00000007/00000001/art00003

    • cell revovery vs. cell viability: https://pubs.acs.org/doi/10.1021/acs.biomac.0c00591#

    • ...

• (ggf. KI)

[huichen5796]

Stand der Techink

• Datenbanken
  • mordene Datenbanken
  • Vor- und Nachteile jeder Datenbank
• Datenbanken in Bio
• (ggf. morderne KI Model)
• Kryokonservierung Experiment
  • Beispiel
    • gemesste Parameters
    • (ggf. genutzte Datenbank)
    • Analysemethoden

[huichen5796]

• [x] DE Algorithmus in Kryokonservierung zur Optimierung von CPA ohne DMSO -> #2

  • CPA
  • SGC
  • SGI
  • Zelle
  • recovery

• [x] NN und GPR zur Suche nach besten CPA für bull semen -> #1

  • Zelle
  • post-thaw motility
  • fow cytometry parameters

• [x] optimize a cell culture medium for T cells -> Grzesik, P. & Warth, S. C. One-time optimization of advanced T cell culture media using a machine learning pipeline. Front. Bioeng. Biotechnol. 9, 1 (2021).

  • methode: elastic net regularized general linear models and random forest， for result an ANOVA followed by Tukey post hoc test
  • cell viability on day 3 and expansion on day 6 during Cell Culture
  • pH = 7.2 and osmolality = 300 mOsm/Kg H2O
  • 12 test components in media

• [x] Pollock, K., Budenske, J. W., McKenna, D. H., Dosa, P. I. & Hubel, A. Algorithm-driven optimization of cryopreservation protocols for transfusion model cell types including Jurkat cells and mesenchymal stem cells. J. Tissue Eng. Regen. Med. 11, 2806–2815 (2017).

  • DE Algo
  • solution compositions and cooling rates for Jurkat cells (a lymphocyte model cell type) and mesenchymal stem cells (MSCs) - [x] Cryopreservation of human bone marrow-derived mesenchymal stem cells with reduced dimethylsulfoxide and well-defined freezing solutions
  • human bone marrow-derived mesenchymal stem cells (hBMSCs)
  • post-thawing cell viability and early apoptotic behaviors, cell metabolic activities, and growth dynamics. Cell morphology and osteogenic, adipogenic and chondrogenic differentiation capability

• [x] Comparative studies of different cryopreservation methods for mesenchymal stem cells derived from human fetal liver

  • Morphological studies
  • Flow cytometry analysis
  • Cell viability assays: recovery of viable cells, viable rate; apoptotic rate, dead cells rate
  • Adipogenic and osteogenic differentiation of the HFLCs
  • proliferative activity
  • differentiation potential

• [x] Evaluation of the viability and osteogenic differentiation of cryopreserved human adipose-derived stem cells

  • proliferation potential and osteogenic differentiation of ASCs
  • viability
  • proliferation rate
  • characteristic phenotype

[huichen5796]

TO READ:

review of cryopreservation

• [x] https://www.sciencedirect.com/science/article/pii/S221342201630155X
  • Cryoinjuries are caused, at least in part, by the solution effect (leading to osmotic shock) and intracellular ice formation (leading to breakdown of intracellular structures).
  • In order to achieve the best survival rate of cells and tissues, the sample volume, cooling rate, warming rate, and CPA concentrations should be optimized depending on the different cell types and context of tissues.18
  • CPAs can be divided into two categories: (1) cell membrane-permeating cryoprotectants, such as dimethyl sulfoxide (DMSO), glycerol,19 and 1,2-propanediol; and (2) nonmembrane-permeating cryoprotectants, such as 2-methyl-2,4-pentanediol and polymers such as polyvinyl pyrrolidone, hydroxyethyl starch, and various sugars.
  • Unlike synthetic chemicals, biomaterials such as alginates, polyvinyl alcohol, and chitosan can be used to impede ice crystal growth, along with traditional small molecules.4 The direct inhibition of ice crystal formation and application of antioxidants and other compounds have been used to attempt to reduce cell death from processes such as apoptosis during the freezing and thawing cycle.20, 21, 22, 23
• [x] https://karger.com/tmh/article/38/2/107/300978/Cryopreservation-of-Human-Stem-Cells-for-Clinical
  • In a recent editorial in Regenerative Medicine 75, Mason and Manzotti, using a definition for a regenerative medicine as ‘that which replaces or regenerates human cells, tissue or organs to restore normal function’
  • It is well known that cell lines maintained in serial culture are susceptible to genetic variation. The formation of frozen banks of homogeneous cell aliquots can therefore capture a single desired phenotype allowing researchers to share source material containing functionally identical cells that maintain the desired characteristics; making possible direct comparison between studies performed by different research groups or by single researchers over time. Additionally, the risk of contamination increase when cell lines are maintained for long periods of time in culture. Thus, returning periodically to a well characterised, contamination-free, frozen stock of cells reduces the risk of contamination and increases the validity of any results generated from the cell line.
  • SOMETHING ABOUT COMPONENTS IN CPA
  • SOME studies have indicated that control of the cryobiological variables can significantly improve the recovery of embryonic stem cells preserved by slow cooling.
  • Mechanisms of Slow Cooling Injury
  • Rho-Associated Kinase (ROCK) Inhibitors in CPA and the Survival of Stem Cells
  • Other Additives and Alternative Cryoprotectants
• [x] https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-00976-8

cpa

• [x] https://www.liebertpub.com/doi/full/10.1089/rej.2014.1656
  • Organs could be cryopreserved without ice formation if there were no limit to the amount of CPA that could be used, but toxicity of CPAs limits the amount that can be used.3 CPA toxicity has been described as the major impediment to cryopreservation by vitrification.2,4
  • CPAs are believed to prevent ice formation by interfering with hydrogen bonding between water molecules,9 and this effect has been proposed to cause non-specific toxicity.8
  • ABOPUT Toxicity of CPA such as DMSO
• [x] https://www.ingentaconnect.com/contentone/asp/jctn/2010/00000007/00000001/art00003
  • theory about freezing and ice
  • SOME EFFECTS ON ICE FORMATION
• [x] https://www.sciencedirect.com/science/article/abs/pii/S2214785321042693
• [x] https://www.sciencedirect.com/science/article/abs/pii/S0011224023000238
  • Sperm viability, motility, fine morphology, mitochondrial activity and DNA fragmentation
  • A new cryotop vial device system provides an aseptic cryoprotectant-free and centrifuge-free cryopreservation of human spermatozoa (a closed system)
• [x] https://www.sciencedirect.com/science/article/abs/pii/S0011224023000226
  • In mammals and in fish sperm, nonpermeating cryoprotectants, such as some carbohydrates, lipids and proteins can be added to the freezing solution to act as a membrane stabilizer [109]
• [x] https://www.sciencedirect.com/science/article/abs/pii/S001122402300007X
• [x] https://www.sciencedirect.com/science/article/abs/pii/S001122402200390X
  • sperm function and oxidative stress were evaluated after thawing
  • total and progressive motility, acrosome and membrane integrity, superoxide dismutase, glutathione peroxidase, total antioxidant capacity
  • DNA fragmentation, malondialdehyde and intracellular hydrogen peroxide levels
  • mitochondrial activity
  • abnormality percentage and catalase activity of frozen-thawed sperm
  • motility and velocity variables, quality characteristics (viability, abnormality, acrosome and membrane integrity, mitochondrial activity and DNA fragmentation), and oxidative/antioxidative status markers (hydrogen peroxide [H2O2], superoxide dismutase [SOD], glutathione peroxidase [GPx], catalase, malondialdehyde [MDA], and total antioxidant capacity [TAC])

ftir and dsc

• [x] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821739/
• [x] https://www.researchgate.net/publication/352285943_Fourier_transform_infrared_spectroscopy_coupled_with_machine_learning_classification_for_identification_of_oxidative_damage_in_freeze-dried_heart_valves
  • PCA on FTIR, or ML or DL to classification
  • computing second derivative spectra
  • computing inverted second derivative spectra
  • Band ratios of characteristic molecular group vibrations obtained from the spectra

[tilchl]

Für stand der Technik siehe 09fa3e2

[huichen5796]

DSC

• [x] DSC analysis of cryopreservation on the structure of porcine aortic biograft as a function of storage time
• [x] Determination of glassy state by cryo-SEM and DSC in cryopreservation of mint shoot tips by encapsulation–dehydration
  • To be successful, cryopreservation must avoid the formation of ice crystals inside cells during immersion in LN. This is achieved by reducing cell water content prior to rapid cooling. Therefore, treatments resulting in low cell water content without causing cell death are key factors for successful cryopreservation (Matsumoto et al. 1998).
• [x] Cryopreservation of Equine Sperm: Optimal Cooling Rates in the Presence and Absence of Cryoprotective Agents Determined Using Differential Scanning Calorimetry
• [x] Analysis of freezable water content by DSC for apple dormant bud cryopreservation
• [x] Cryopreservation: Current Advances and Evaluations
  • DSC
  • TMDSC
  • QITMDSC
• [x] Ice Formation of Vitrification Solutions for Cryopreservation of Tissues
• [x] Cryopreservation Theory