Exploring selected modern Mass Spectrometry techniques in applied sciences

Mass Spectrometry (MS) is a powerful analytical technique that has revolutionized our ability to analyze complex mixtures and has diverse applications in various scientific disciplines. It is widely used in chemistry and biology to determine the molecular composition, structure, and quantification of samples. In this dissertation, we aimed to explore novel applications of mass spectrometry techniques, including electrospray ionization (ESI) and tandem mass spectrometry (MS/MS), as well as mass spectrometry imaging (MSI) techniques such as matrix-assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI). The objective was to strengthen our knowledge and skills in various MS methodologies and gain practical experience in using these techniques, for developing methods to chemically profile, separate, detect, map, and quantify a wide range of targeted and untargeted analytes from complex matrices. Given the versatility of MS-based techniques, we focused on specific applications within this field. First and foremost, forensic and pharmaceutical cannabis-related applications require accurate and sensitive analytical methods. Hence, we developed and validated a DESI-MS method for detecting cannabinoids in cannabis-infused chocolate, utilizing TLC-DESI-MS and QuEChERS extraction for THC quantification. Additionally, we investigated metabolic differences associated with soybean alleles (QTLs E and M) conferring resistance to leaf-chewing insects. Non-targeted mass spectrometry reveals distinct metabolite sets influenced by the QTLs, highlighting daidzein as a significant marker. This suggests a novel mechanism impeding the insects' ability to evolve tolerance. Moreover, we explored the sublimation technique for the application of a matrix coating in MALDI-MSI. Specifically, we investigated the optimal conditions for the sublimation of the 5-chloro-2-mercaptobenzothiazole (CMBT) matrix on mouse kidney samples. We successfully obtained high-quality MALDI-MSI images of phospholipids (PC, PG) and phosphatidylinositol (PI) in mouse kidney sections, providing valuable spatially resolved information. Lastly, we discussed the importance of phosphatidylinositols (PI) and phosphoinositides and their involvement in various diseases, emphasizing the need to optimize the MALDI-matrix type and thickness for enhanced sensitivity in detecting these molecules. The label-free data obtained through this optimized approach holds the potential for investigating the relative m/z factors associated with PI-related pathogenesis. Overall, this dissertation demonstrated the versatility and potential of mass spectrometry techniques. The findings lay the groundwork for future research in the field of MS analysis, particularly in the detection, quantification, and understanding of phosphatidylinositols and phosphoinositides in biological systems and disease pathologies

Probing into the evolution of a polymorphic semiconductor at nanoscale / Alireza Yaghoubi Taemeh

Graphene is considered to be the most likely candidate for the post-silicon era however the problem with its zero band gap is challenging to overcome. A close relative of silicon, silicon carbide is expected to have a stable 2D polymorph which happens to be a wide-gap semiconductor. Unfortunately, the so-called silagraphene has proven to be elusive. To date, neither theoretical, nor experimental studies have been conclusive. In this thesis, we employ computational methods to determine the stable arrangements of silagraphene, and establish their accurate band structure. We also experimentally validate our models by preparing and characterizing a number of graphitic features. Silagraphene exhibits a wide spectrum of optoelectronic properties (360-690 nm) as well as an unusual band structure with highly anisotropic transport properties, which originates from its non-dispersive band near its K-point. This feature makes direct-indirect gap crossover extremely sensitive to ambient conditions, making silagraphene suitable for a range of sensors. We also demonstrate that a particular arrangement of atoms that represent 9R-SiC occurs when the metastable AA’ silagraphene is relaxed. This structure has a very similar microscopic and crystallographic signature to that of 3C-SiC and 15R-SiC, respectively, which might explain why it has evaded detection until now. Its vibrational footprint on the other hand is quite distinct thanks to its fewer active phonon modes. Surprisingly, the indirect band gap of this polytype is slightly wider than that of 2H-SiC, despite its lower hexagonality, and is equivalent to that of GaN. Due to its unique conduction band structure, 9R-SiC may also exhibit improved electron transport properties as compared to other SiC polytypes; and therefore could be suitable for high-frequency and high-voltage applications

Metabolomics Differences of Glycine max QTLs Resistant to Soybean Looper

Quantitative trait loci (QTLs) E and M are major soybean alleles that confer resistance to leaf-chewing insects, and are particularly effective in combination. Flavonoids and/or isoflavonoids are classes of plant secondary metabolites that previous studies agree are the causative agents of resistance of these QTLs. However, all previous studies have compared soybean genotypes that are of dissimilar genetic backgrounds, leaving it questionable what metabolites are a result of the QTL rather than the genetic background. Here, we conducted a non-targeted mass spectrometry approach without liquid chromatography to identify differences in metabolite levels among QTLs E, M, and both (EM) that were introgressed into the background of the susceptible variety Benning. Our results found that E and M mainly confer low-level, global differences in distinct sets of metabolites. The isoflavonoid daidzein was the only metabolite that demonstrated major increases, specifically in insect-treated M and EM. Interestingly, M confers increased daidzein levels in response to insect, whereas E restores M’s depleted daidzein levels in the absence of insect. Since daidzein levels do not parallel levels of resistance, our data suggest a novel mechanism that the QTLs confer resistance to insects by mediating changes in hundreds of metabolites, which would be difficult for the insect to evolve tolerance. Collective global metabolite differences conferred by E and M might explain the increased resistance of EM

Study of the regulatory elements of the Ovalbumin gene promoter using CRISPR technology in chicken cells

Abstract Background Hormone-dependent promoters are very efficient in transgene expression. Plasmid-based reporter assays have identified regulatory sequences of the Ovalbumin promoter that are involved in response to estrogen and have shown that the deletion of the steroid-dependent regulatory element (SDRE) and negative regulatory element (NRE) leads to a steroid-independent expression of a reporter. However, the functional roles of these regulatory elements within the native genomic context of the Ovalbumin promoter have not been evaluated. Results In this study, we show that the negative effects of the NRE element on the Ovalbumin gene can be counteracted by CRISPR interference. We also show that the CRISPR-mediated deletion of SDRE and NRE promoter elements in a non-oviduct cell can lead to the significant expression of the Ovalbumin gene. In addition, the targeted knock-in of a transgene reporter in the Ovalbumin coding region and its expression confirms that the truncated promoter of the Ovalbumin gene can be efficiently used for an estrogen-independent expression of a foreign gene. Conclusions The methodology applied in this paper allowed the study of promoter regulatory sequences in their native nuclear organization

Integrating Omics and CRISPR Technology for Identification and Verification of Genomic Safe Harbor Loci in the Chicken Genome

Abstract Background One of the most prominent questions in the field of transgenesis is ‘Where in the genome to integrate a transgene?’. Escape from epigenetic silencing and promoter shutdown of the transgene needs reliable genomic safe harbor (GSH) loci. Advances in genome engineering technologies combined with multi-omics bioinformatics data have enabled rational evaluation of GSH loci in the host genome. Currently, no validated GSH loci have been evaluated in the chicken genome. Results Here, we analyzed and experimentally examined two GSH loci in the genome of chicken cells. To this end, putative GSH loci including chicken HIPP-like (cHIPP; between DRG1 and EIF4ENIF1 genes) and chicken ROSA-like (cROSA; upstream of the THUMPD3 gene) were predicted using multi-omics bioinformatics data. Then, the durable expression of the transgene was validated by experimental characterization of continuously-cultured isogenous cell clones harboring DsRed2-ΔCMV-EGFP cassette in the predicted loci. The weakened form of the CMV promoter (ΔCMV) allowed the precise evaluation of GSH loci in a locus-dependent manner compared to the full-length CMV promoter. Conclusions cHIPP and cROSA loci introduced in this study can be reliably exploited for consistent bio-manufacturing of recombinant proteins in the genetically-engineered chickens. Also, results showed that the genomic context dictates the expression of transgene controlled by ΔCMV in GSH loci

Enhanced cultivation of chicken primordial germ cells

Abstract The cultivation and expansion of chicken primordial germ cells (cPGCs) are of critical importance for both biotechnological applications and the management of poultry genetic biodiversity. The feeder-free culture system has become the most popular approach for the cultivation and expansion of cPGCs. However, despite some success in the cultivation of cPGCs, the reproducibility of culture conditions across different laboratories remains a challenge. This study aimed to compare two defined and enriched media for the growth of cPGCs originating from the Hubbard JA57 broiler. To this end, cPGCs were isolated from the embryonic blood of Hamburger–Hamilton (HH) stages 14–16 and cultured at various time points. The Growth properties and characteristics of these cells were evaluated in two different culture conditions (the defined or enriched medium) and their migratory properties were assessed after genetic engineering and injection into the vasculature of 2.5-day-old chicken embryos. The main finding of this study was that the use of an enriched medium (the defined medium with Knock-Out Serum Replacement; KOSR) resulted in improved growth properties of cPGCs originating from the Hubbard JA57 broiler compared to a defined medium. The ability to cultivate and expand cPGCs is crucial for the generation of both genetically engineered birds and breeds of interest from local or commercial origins. Therefore, these results highlight the importance of choosing an appropriate culture medium for cPGCs growth and expansion