Cell-penetrating peptides (CPPs) mediate the delivery of macromolecules across the plasma membrane of live cells. These peptides are therefore important due to the potential of making the delivery of protein probes or therapeutics a routine procedure. However, CPP-mediated delivery is currently an inefficient process. CPP-protein conjugates are internalized into cells by endocytosis and the macromolecules remain trapped inside endosomes instead of reaching the target cellular localization. To solve this problem, we report a delivery methodology which relies on the use of a chimera of the TAT and of the Influenza HA2. TAT is a prototypical CPP that can promote macropinocytosis in live cells and HA2 is a pH-sensitive peptide that destabilizes lipid membranes upon acidification. I demonstrate that HA2-TAT can deliver a variety of macromolecular cargos into live mammalian cells by a simple co-incubation protocol. A model is described where TAT causes the endocytic uptake of cargos present in the media and that HA2 disrupts the endosomal membrane upon endosomal acidification. In addition, using red blood cells as a model system, HA2-TAT binds to membranes in a pH-dependent manner and causes the formation of pores through which macromolecules can diffuse. Additionally, the pro-apoptotic domain (PAD) peptide is also successfully delivered by HA2-TAT and shows significant apoptosis in cells through macropinocytosis.

Este trabalho tem como finalidade estudar as melhores condições do cultivo da microalga Chlamydomonas reindhartii geneticamente modificada para a produção da proteína fluorescente mCherry a partir do estudo dos macronutrientes contidos no meio de cultivo. A proteína mCherry possui a vantagem de ser facilmente detectada no meio de cultivo por espectofotometria convencional, convertendo-se, desta forma, em uma molécula interessante para o estudo como modelo de expressão. Inicialmente, foram estudadas três diferentes fontes de nitrogênio para avaliar a expressão da proteína recombinante. Os resultados indicaram que a melhor fonte de nitrogênio para a produção da mCherry foi o NH4NO3. Em seguida, para avaliar os efeitos gerados pelos macronutrientes (acetato, cloreto de cálcio, sultato de magnésio, nitrato de amônio e fostato total) contidos no meio de cultivo TAP, foi realizado um planejamento composto central 25, em cultivos em microplacas, sendo os resultados avaliados por regressão multivariada. Além disso, a análise realizada por regressão multivariada indicou que, dos níveis avaliados das variáveis, as condições que melhor atendem à otimização da produção de mCherry e crescimento celular são: acetato, 33,35 mM; cloreto de cálcio, 0,45 mM; sulfato de magnésio, 0,83 mM; nitrato de amônio, 10,31 mM; fosfato total, 1,96 mM. Essas condições foram escolhidas para cultivo em fotobiorreator tubular, onde foi obtido título de fluorescência de mCherry a 608 nm de 59209 UF, correspondendo a um aumento de 118,5% maior que o título de fluorescência obtido com uso de meio TAP padrão. Com a finalidade de seguir com os processos de produção foi disenhado um biorreator tipo coluna e foi reaizado um estudio de produção em sistema semicontinuo. Os resultados obtidos demostraram que o sistema semicontinuo aumento 2,6 veces a produtividade da biomassa. / This work aims to study the best conditions of the cultivation of the microalgae Chlamydomonas reindhartii genetically modified for the production of the fluorescent protein mCherry from the study of the macronutrients contained in the culture medium. The mCherry protein has the advantage of being easily detected in the culture medium by conventional spectrophotometry, thus becoming an interesting molecule for the study as an expression model. Initially, three different nitrogen sources were studied to evaluate the expression of the recombinant protein. The results indicated that the best source of nitrogen for the production of mCherry was NH4NO3. Then, to evaluate the effects generated by macronutrients (acetate, calcium chloride, magnesium sulphate, ammonium nitrate and total phosphate) contained in the TAP culture medium, a central composite 25 was carried out in cultures on microplates, Results evaluated by multivariate regression. In addition, multivariate regression analysis indicated that, from the evaluated levels of the variables, the conditions that best serve the optimization of mCherry production and cell growth are: acetate, 33.35 mM; Calcium chloride, 0.45 mM; Magnesium sulfate, 0.83 mM; 10.31 mM ammonium nitrate; Total phosphate, 1.96 mM. These conditions were chosen for cultivation in tubular photobioreactor where fluorescence titre of mCherry at 608 nm of 59209 UF was obtained, corresponding to an increase of 118.5% greater than the titer of fluorescence obtained using standard TAP medium. In order to follow the production processes, a column type bioreactor was designed and a production study was carried out in a semicontinuous system. The results showed that the semicontinuous system increased 2.6 times the productivity of the biomass.

Este trabalho tem como finalidade estudar as melhores condições do cultivo da microalga Chlamydomonas reindhartii geneticamente modificada para a produção da proteína fluorescente mCherry a partir do estudo dos macronutrientes contidos no meio de cultivo. A proteína mCherry possui a vantagem de ser facilmente detectada no meio de cultivo por espectofotometria convencional, convertendo-se, desta forma, em uma molécula interessante para o estudo como modelo de expressão. Inicialmente, foram estudadas três diferentes fontes de nitrogênio para avaliar a expressão da proteína recombinante. Os resultados indicaram que a melhor fonte de nitrogênio para a produção da mCherry foi o NH4NO3. Em seguida, para avaliar os efeitos gerados pelos macronutrientes (acetato, cloreto de cálcio, sultato de magnésio, nitrato de amônio e fostato total) contidos no meio de cultivo TAP, foi realizado um planejamento composto central 25, em cultivos em microplacas, sendo os resultados avaliados por regressão multivariada. Além disso, a análise realizada por regressão multivariada indicou que, dos níveis avaliados das variáveis, as condições que melhor atendem à otimização da produção de mCherry e crescimento celular são: acetato, 33,35 mM; cloreto de cálcio, 0,45 mM; sulfato de magnésio, 0,83 mM; nitrato de amônio, 10,31 mM; fosfato total, 1,96 mM. Essas condições foram escolhidas para cultivo em fotobiorreator tubular, onde foi obtido título de fluorescência de mCherry a 608 nm de 59209 UF, correspondendo a um aumento de 118,5% maior que o título de fluorescência obtido com uso de meio TAP padrão. Com a finalidade de seguir com os processos de produção foi disenhado um biorreator tipo coluna e foi reaizado um estudio de produção em sistema semicontinuo. Os resultados obtidos demostraram que o sistema semicontinuo aumento 2,6 veces a produtividade da biomassa. / This work aims to study the best conditions of the cultivation of the microalgae Chlamydomonas reindhartii genetically modified for the production of the fluorescent protein mCherry from the study of the macronutrients contained in the culture medium. The mCherry protein has the advantage of being easily detected in the culture medium by conventional spectrophotometry, thus becoming an interesting molecule for the study as an expression model. Initially, three different nitrogen sources were studied to evaluate the expression of the recombinant protein. The results indicated that the best source of nitrogen for the production of mCherry was NH4NO3. Then, to evaluate the effects generated by macronutrients (acetate, calcium chloride, magnesium sulphate, ammonium nitrate and total phosphate) contained in the TAP culture medium, a central composite 25 was carried out in cultures on microplates, Results evaluated by multivariate regression. In addition, multivariate regression analysis indicated that, from the evaluated levels of the variables, the conditions that best serve the optimization of mCherry production and cell growth are: acetate, 33.35 mM; Calcium chloride, 0.45 mM; Magnesium sulfate, 0.83 mM; 10.31 mM ammonium nitrate; Total phosphate, 1.96 mM. These conditions were chosen for cultivation in tubular photobioreactor where fluorescence titre of mCherry at 608 nm of 59209 UF was obtained, corresponding to an increase of 118.5% greater than the titer of fluorescence obtained using standard TAP medium. In order to follow the production processes, a column type bioreactor was designed and a production study was carried out in a semicontinuous system. The results showed that the semicontinuous system increased 2.6 times the productivity of the biomass.

Calcium (Ca2+), a crucial effector for many biological systems, has been associated with diseases such as cardiovascular disease, Alzheimer’s, Parkinson’s, cancer, and osteoporosis. It is important to develop calcium sensors to measure intracellular Ca2+ dynamics at various biological and pathological states. Our lab has engineered such probes by designing a Ca2+ binding site into fluorescent proteins such as Enhanced Green Fluorescent Protein (EGFP) and mCherry. In this thesis, we aim to improve optical properties and metal binding properties of green EGFP-based sensor CatchER and mCherry based red sensors by site-directed mutagenesis and protein engineering, various spectroscopic methods and cell imaging. The green EGFP-based sensor CatchER, with a Ca2+ binding pocket charge of -5, displays the greatest affinity for Ca2+ and has the greatest fluorescence intensity change with Ca2+ when compared to its variants with a less negative binding pocket charge. In addition, we have also designed several SR/ER targeting CatchER variants using Ryanodine receptor and Calnexin transmembrane domains. These constructs were shown to display a strong presence in the SR/ER lumen and further designed for a new luminal orientation. Further, we have shown that the optical properties of two red calcium sensors can be significantly improved by modifying the local environment of the chromophore.

Cell-to-cell communication is one of the fundamental requisites of making multicellular organisms. G protein-coupled receptors (GPCRs) are one of the most abundant receptor-types within vertebrates. They canonically mediate their signal via hetrotrimeric G proteins, and G protein signaling is regulated by regulators of G protein-signaling (RGS). One of these RGS proteins, RGS4, is preferentially expressed in the central nervous system of humans and has been strongly connected to dopaminergic signaling, along with a number of severe neuronal diseases. rgs4 is not well studied in the model organism Danio rerio, the zebrafish, with only two publications. In this project, a newly constructed transgenic line, tg(rgs4:mCherry), with the fluorophore mCherry regulated by the promoter element of rgs4 was characterized in order to investigate fidelity to endogenous rgs4 expression and the utility of the transgenic line. The mCherry expression is apparent by 48 hours post fertilization, and expression is found mainly in neuronal tissue. Cell bodies are visible only in some labeled areas, while other areas show a more diffuse signal indicative of projections. There is only one transgenically labeled area that also unambiguously expresses rgs4; the pronephric tubule. This line is therefore not particularly well suited for rgs4-specifc studies, but this does not discredit the fidelity of the construct. A transgenic line made with a site-directed technique would most likely confer the fidelity of the promoter to the expression of the fluorophore. A way of increasing the labeling resolution includes exchanging the mCherry fluorophore for one with stronger signal and a lower tendency to aggregate, e.g. eGFP. Increasing the resolution of the characterization, e.g. to the level of sub-nuclei or neuronal types, would serve to enhance the utility of the line. As it is, the tg(rgs4:mCherry) zebrafish line has limited uses, and yet it is not without them.

NMDA (N-methyl D-aspartate) Receptor is a ligand and voltage gated ion channel and involved in many processes such as synaptic plasticity, memory formation, behavioral responses and cell survival. In the sense of functional activity, cellular localization of NMDAR is important since this receptor shows its activity on the membrane. Although NMDA receptor is intensely studied there are no satisfying study showing its localization with microscobic methods. Besides, the effect of florescent protein labelling of NMDA receptor on its distribution is not shown. It is expected to provide basis for further interaction and distribution studies with this comparison. Contrary to literature, in this study it is shown that NMDA receptor does not localize only in ER and membrane instead has a cytosolic pattern and this pattern is compatible with the distribution of wild type NMDA receptor. In addition, florescent protein labelling of NMDA receptor does not interrupt cellular distribution of NMDAR. Moreover, this study shows that N-terminal domain of NR1 subunit is sufficient to prevent degradation of NR2B in the cell. In consideration of this study it can be concluded that EGFP and mCherry labelled NMDA receptors can be used in interaction studies such as FRET and other studies, making use of fluorescent labelling of NMDA receptors, in terms of cellular distribution.

Metabotropic glutamate receptor 1α (mGluR1α) exerts important effects on numerous neurological processes. Although mGluR1α is known to respond to extracellular Ca2+ ([Ca2+]o) and the crystal structures of the extracellular domains (ECDs) of several mGluRs have been determined, the calcium-binding site(s) and structural determinants of Ca2+-modulated signaling in the Glu receptor family remain elusive. Here, we identify a novel Ca2+-binding site (Site 1) in the ECD-mGluR1α using a recently developed computational algorithm. This predicted site (D318, E325, D322 and the bound L-Glu) is situated in the hinge region in the ECD-mGluR1α adjacent to the reported Glu-binding site. Mutagenesis studies indicated that binding of L-Glu and Ca2+ to their distinct but partially overlapping binding sites synergistically modulated mGluR1α activation of intracellular Ca2+ ([Ca2+]i) signaling. Mutating the Glu-binding site completely abolished Glu signaling while leaving its Ca2+-sensing capability largely intact. Mutating the predicted Ca2+-binding residues abolished or significantly reduced the sensitivity of mGluR1α not only to [Ca2+]o and [Gd3+]o but also, in some cases, to Glu. In addition, the Ca2+ effects on drugs targeting mGluR1α were investigated. Ca2+ enhances L-Quis response of the receptor by increasing L-Quis binding to ECD-mGluR1α and promotes the potency of Ro 67-4853, a positive allosteric modulator of mGluR1α. Increasing Ca2+ concentration, the inhibitory effects of a competitive antagonist ((s)-MCPG) and a non-competitive negative allosteric modulator (CPCCOEt), were eliminated. Furthermore, we also identified another potential Ca2+ binding pocket (Site 2) consists of S165, D208, Y236 and D318, which completely overlapped with L-Glu. Thapsigargin (TG) induced ER Ca2+ depletion reduced surface expression of mGluR1α, and D208I and Y236I also decreased the receptor trafficking to plasma membrane suggesting the role of Ca2+ binding in protein folding and trafficking in the ER. Further, to measure ER Ca2+, a series of genetically encoded biosensors were designed by placing a Ca2+ binding pocket at the chromophore sensitive region of red florescent protein mCherry. The designed sensors are able to bind Ca2+ and monitor Ca2+ concentration change both in vitro and in cells. The findings in this dissertation open up new avenues for developing allosteric modulators of mGluR function that target related human diseases.

Nowadays, the organoids structures has become more popular as suitable model systems for clinical research, particularly for development of new medication and drug screening. The standard study approaches include invazive biochemical or molecular-biology analysis as well as non-invasive optical approaches. Among optical methods, various microscopy techniques can give a very detailed information about the structure of organoids. However, the microscopy is time consuming as well as it puts a great demand on instrumentation. Therefore, the microscopy is not suitable for high content analysis of multiple samples. This work is focused on the development of the device and experimental technique for high-throughput screenings of organoids structures for biomedical applications based on microtitrate plates. Literatre search for non-invasive optical methods, suitable for analysis of organoid structures. The necessary adjustements of existing system for algae phenotypization are discussed. An experiment was made to test functionality of designed system. Practical use for clinical use is tested by the experiment of spheroids reaction to selected cytostatics. The results and findings are discussed in the conclusion.

Mycobacterium tuberculosis (Mtb) is the causative agent of Tuberculosis (TB), a life-threatening disease primarily affecting the lungs that infects about one third of the world's population and causes 1.3 million deaths annually. It is estimated that TB has been infecting humans for around 70,000 years and has killed more people than any other infectious disease. The highly effective, persistent, and multifaceted virulence strategies that have allowed Mtb to continue to spread and thrive for so long are still poorly understood at the molecular level. This lack of knowledge contributes to ongoing challenges to curing TB. Although drugs capable of killing Mtb exist, even strains that are susceptible to these drugs remain so difficult to treat that stringent six- to nine-month courses of four-drug cocktails are required. Practical difficulties in administering full treatments and patient noncompliance have contributed to a rise in drug-resistant TB cases globally. To combat this increasing world health problem, new antibiotic treatments that kill Mtb and drug-resistant Mtb more effectively via new mechanisms of action are necessary. Discovering these antibiotics expediently requires that innovative Mtb-specific drug-screening assays are developed. An ideal and innovative TB drug screening method would target validated protein-protein interactions (PPI) essential to Mtb's pathogenesis and would be performed on whole Mtb cells under relevant in vivo-like conditions. This project focused on engineering several tools relevant to creating an ideal TB drug screen. A protein fragment complementation assay capable of studying PPI of the TB gyrase complex was created, and this assay was assessed for future HTS applications. To streamline the readout, this assay was re-engineered to include green fluorescent protein.

Current single molecule localisation microscopy methods allow for multicolour imaging of macromolecules in cells, and for a degree quantification on molecule numbers in one colour. However, that has not yet been an attempt to develop tools capable of quantitative imaging with multiple colours in cells. This work addressed this challenge by designing linker peptides with chemospecific groups to allow attachment of activator and emitter dyes for STORM imaging, and a targeting module. The design ensured a stoichiometric ratio of targeting module to activator and emitter dyes. Peptides with HaloTag ligands attached were labelled with various activator and emitter pairs and used to label HaloTag fusions of S. pombe and mouse embryonic stem cells. These peptides were found to bind non-specifically to various areas of both cell types, and did not localise to HaloTag protein, whereas controls did. Another peptide was also labelled with activator-emitter pairs and attached to expressed anti-GFP and ant-mCherry nanobodies via native chemical ligation. The labelled anti-GFP nanobody was to demonstrate ensemble and single molecule imaging in S. pombe, as well as characterisation on single molecule surfaces in comparison to a conventional randomly labelled antibody. The stoichiometrically labelled nanobody had a more consistent number of photons detected per localisation, number of localisation per molecule and number of blinks per molecule, which implied that it could be more useful than randomly labelled nanobodies for counting experiments. It was also shown to be capable of specific laser activation for STORM imaging with both an Alexa405Cy5 and Cy3Cy5 pairs. These anti-GFP and anti-mCherry nanobodies and peptide linker are new tools for both counting and multicolour imaging in super-resolution, which could be widely applied to constructs that are already tagged with GFP or mCherry.