http://hdl.handle.net/11089/1305 2026-07-10T20:49:54Z http://hdl.handle.net/11089/58796 Yeast display for directed evolution of amadoriase, an enzyme capable of cleaving protein glycation products - MINIATURA 8 (2024/08/X/NZ1/01781) (dataset) Studzian, Maciej This dataset was generated as part of the Miniatura 8 project, which focused on amadoriases. These FAD-dependent enzymes catalyze the breakdown of glycated amino acids, producing a free amino acid, glucosone, and hydrogen peroxide. Naturally occurring in fungi and bacteria, they are of considerable practical importance due to their applications in medical diagnostics and their potential therapeutic use, particularly in the treatment of diseases such as diabetes. Previous attempts to improve amadoriase I from Aspergillus through targeted amino acid substitutions increased the enzyme's thermostability but did not enhance its catalytic activity. Similarly, directed evolution of the related enzyme amadoriase II resulted in only marginal improvements. The aim of this project was to develop methods for the in vitro evolution of amadoriases to increase their activity using a non-directed, ultra-high-throughput approach based on yeast surface display. This technique enables the generation of random enzyme variants displayed on the surface of yeast cells, which can then be screened for catalytic activity. A biotin- and azide-modified fructoselysine analogue, designed to mimic a glycated substrate, was successfully synthesized and immobilized on the yeast surface to serve as a substrate for activity screening. Upon catalysis by an amadoriase, the substrate was expected to lose its fluorescence, allowing fluorescence-activated cell sorting (FACS) to isolate yeast cells displaying enzyme variants with higher catalytic activity. A previously engineered variant of amadoriase II from Aspergillus fumigatus (AmaII_SII_82) was used as the starting point for the evolution experiments. Unfortunately, because the initial enzyme exhibited only negligible activity toward the biotin-modified substrate, the variants obtained after three rounds of sorting also failed to show the expected improvement in activity. Nevertheless, the techniques developed during this research provide a strong foundation for future studies aimed at improving other classes of deglycating enzymes, such as FN3K and FrlB/FrlD. 2026-06-01T00:00:00Z http://hdl.handle.net/11089/58757 Ochronna rola CORMs w łagodzeniu stresu oksydacyjnego i stanu zapalnego indukowanego doksorubicyną w modelu prawidłowych komórek skóry - MINIATURA 8 2024/08/X/NZ7/01320 (dataset) Juszczak, Michał Doxorubicin is a potent anticancer drug that unfortunately damages healthy cells. Researchers from the University of Łódź investigated whether carbon monoxide could protect against these side effects. They used CORMs (carbon monoxide-releasing molecules)—specifically CORM-2 and CORM-3—which safely deliver the gas to cells. The team tested these on healthy human fibroblasts exposed to doxorubicin, alongside inactive, gas-free molecules as a control. While pretreating cells with CORMs did not prevent the drug's overall toxicity, it effectively combated oxidative stress. Both CORM-2 and CORM-3 significantly reduced destructive oxygen free radicals induced by doxorubicin. Surprisingly, the inactive, gas-free molecules were equally effective at this. The researchers also assessed programmed cell death by measuring caspase activity. Active CORM-3 inhibited this process, showing a protective effect, whereas CORM-2 unexpectedly accelerated cell death. Additionally, CORM-3 reduced the activity of certain oxidative stress response genes without affecting inflammatory genes or final defensive protein levels. This research highlights the complex relationship between carbon monoxide releasers and chemotherapy. Although these molecules are not a cure-all for doxorubicin's toxicity, they possess valuable antioxidant properties. Crucially, the study reveals that the positive intracellular effects often stemmed from the molecule’s structural backbone itself rather than the released carbon monoxide. This discovery is a significant step toward understanding cellular mechanisms and designing better protective therapies for cancer patients. Dane dotyczą wyników z oznaczeń: cytotoksyczności, reaktywnych form tlenu, apoptozy, ekspresji genów i białek zaangażowanych w stan zapalny i stres oksydacyjny. 2024-12-10T00:00:00Z http://hdl.handle.net/11089/58462 Morphological structure of the vertebra and predisposition to fatigue spondylolysis in the human population - geometric morphometrics studies on skeletal material - MINIATURA 8 (2024/08/X/NZ8/00212) dataset Mietlińska-Sauter, Joanna; Battaglia, Sebastiano; Lorkiewicz, Wieslaw; Fruciano, Carmelo Mietlińska-Sauter, Joanna Fatigue spondylolysis is commonly interpreted in bioarchaeology as a direct skeletal marker of increased axial loading, particularly in pre-industrial populations engaged in strenuous manual labour. However, clinical studies in contemporary populations suggest that vertebral morphology may also play an important role in fracture susceptibility. The present project examined whether anatomical predisposition contributed to fatigue spondylolysis in historical human populations from the Brześć Kujawski microregion (Kuyavia, central Poland), dating from the early Middle Ages to the mid-nineteenth century. Fifth lumbar vertebrae (L5) representing individuals with and without spondylolytic fractures were selected from osteological collections housed at the University of Lodz. Following cleaning and, where necessary, recomposition, the vertebrae were scanned using structured-light 3D surface scanning. Their morphology was analysed using landmark-based geometric morphometrics, including fixed landmarks and sliding semilandmarks, and the resulting data were statistically evaluated in MorphoJ, R software environment and Statistica. The analyses revealed statistically significant differences in L5 anatomy between spondylolytic and non-pathological vertebrae. Fractured vertebrae displayed morphological features suggestive of functional predisposition to injury. In addition, previously undescribed differences in fluctuating asymmetry were identified between the two groups, indicating that developmental instability may also have contributed to fracture susceptibility. These findings suggest that fatigue spondylolysis in pre-industrial populations should not be regarded solely as a simple indicator of increased spinal loading. Instead, its occurrence appears to reflect an interaction between mechanical stress as well as individual anatomical and developmental predispositions. The study demonstrates the utility of geometric morphometrics for investigating vertebral variation in archaeological populations and provides a more nuanced framework for interpreting spondylolysis in bioarchaeological research. 1) Folder 1: representative scans in .STL format (one non-pathological vertebra, SBK4_59_L5, and one vertebra affected by fatigue spondylolysis, SBK4_250_L5) 2) Folder 2: reference landmark configuration used in the study (including a .vtk file containing the vertebral model, 26 .mrk.json files with landmarks assigned to individual landmark sets, an Excel file defining all landmarks, and a readme.txt file with instructions for opening the files) 3) Folder 3: digitization results for all 36 analysed vertebrae - 10 affected by spondylolysis and 26 controls (including two folders corresponding to the first and second digitization rounds, respectively; each folder contains files in four formats: .mrk.json, .json, .fcsv, and .csv). The folder also includes an Excel file defining all landmarks, presented without subdivision into individual vertebral elements, but distinguished as fixed landmarks and sliding semilandmarks on curves and surfaces. 4) Folder 4: output models (including two .ply files representing the mean shape of a spondylolytic vertebra and the mean shape of a non-pathological vertebra and a readme.txt file with instructions for opening the files) 2024-06-26T00:00:00Z http://hdl.handle.net/11089/57929 Wstępna ocena potencjału terapeutycznego miechunki pomidorowej (Physalis philadelphica) w kontekście przebudowy tkanek i gojenia ran (dataset) Liudvytska, Oleksandra Chronic wounds represent a growing problem in lifestyle diseases (e.g., atherosclerosis, diabetes). They are characterized, among other things, by disturbances in the mechanisms controlling the course of inflammatory processes, degeneration of the tissue surrounding the wound, scarring, and susceptibility to infections. Hard‑to‑heal wounds constitute a serious and burdensome issue for patients, as they significantly reduce their quality of life and require long-term, specialized therapy. The search for natural bioactive substances is one of the important directions in contemporary wound‑healing research. Natural compounds can serve as the basis for therapies that support all stages of healing, including modulation of the inflammatory response, fibroblast proliferation, and epithelial regeneration. They are often characterized by high biocompatibility and low cytotoxicity, making them very promising candidates for applications in wound‑healing support. The project focused on key aspects relevant to the potential use of extracts from the tomatillo (Physalis philadelphica) in wound‑healing support: anti‑inflammatory properties, effects on tissue remodeling, assessment of cytotoxicity risk, and metabolism by the skin microbiome. Four extracts were tested: from fruits (green – unripe, and yellow), leaves, and roots. The study employed dermal (fibroblast) and epithelial (keratinocyte) cell lines. Additionally, the effects of the extracts on proteins of the fibrinolytic system were evaluated, as this system plays an important regulatory role in tissue remodeling within the wound area. Spis plików: 1. Generowanie plazminy 2. IL- 6 3. IL- 8 4. Mikrobiota skóry 5. MMP3 6. MMP9 7. MTT 8. PLUA 9. PLUAR soluble 10. PLUAR 11. Test rany 2026-03-31T00:00:00Z