Refine
Has Fulltext
- yes (122) (remove)
Year of publication
- 2020 (122) (remove)
Document Type
- Doctoral Thesis (122) (remove)
Is part of the Bibliography
- yes (122)
Keywords
- Maschinelles Lernen (3)
- Anden (2)
- Andes (2)
- Arktis (2)
- Boden (2)
- Chemometrie (2)
- Datenassimilation (2)
- Diffusion (2)
- Galaktische Archäologie (2)
- Geomagnetic activity (2)
Institute
- Institut für Physik und Astronomie (26)
- Institut für Geowissenschaften (20)
- Institut für Biochemie und Biologie (18)
- Institut für Chemie (13)
- Hasso-Plattner-Institut für Digital Engineering GmbH (8)
- Institut für Umweltwissenschaften und Geographie (7)
- Department Psychologie (3)
- Institut für Mathematik (3)
- Department Linguistik (2)
- Department Sport- und Gesundheitswissenschaften (2)
Depending on the biochemical and biotechnical approach, the aim of this work was to understand the mechanism of protein-glucan interactions in regulation and control of starch degradation. Although starch degradation starts with the phosphorylation process, the mechanisms by which this process is controlling and adjusting starch degradation are not yet fully understood. Phosphorylation is a major process performed by the two dikinases enzymes α-glucan, water dikinase (GWD) and phosphoglucan water dikinase (PWD). GWD and PWD enzymes phosphorylate the starch granule surface; thereby stimulate starch degradation by hydrolytic enzymes. Despite these important roles for GWD and PWD, so far the biochemical processes by which these enzymes are able to regulate and adjust the rate of phosphate incorporation into starch during the degradation process haven‘t been understood. Recently, some proteins were found associated with the starch granule. Two of these proteins are named Early Starvation Protein 1 (ESV1) and its homologue Like-Early Starvation Protein 1 (LESV). It was supposed that both are involved in the control of starch degradation, but their function has not been clearly known until now. To understand how ESV1 and LESV-glucan interactions are regulated and affect the starch breakdown, it was analyzed the influence of ESV1 and LESV proteins on the phosphorylating enzyme GWD and PWD and hydrolysing enzymes ISA, BAM, and AMY. However, the analysis determined the location of LESV and ESV1 in the chloroplast stroma of Arabidopsis. Mass spectrometry data predicted ESV1and LESV proteins as a product of the At1g42430 and At3g55760 genes with a predicted mass of ~50 kDa and ~66 kDa, respectively. The ChloroP program predicted that ESV1 lacks the chloroplast transit peptide, but it predicted the first 56 amino acids N-terminal region as a chloroplast transit peptide for LESV. Usually, the transit peptide is processed during transport of the proteins into plastids. Given that this processing is critical, two forms of each ESV1 and LESV were generated and purified, a full-length form and a truncated form that lacks the transit peptide, namely, (ESV1and tESV1) and (LESV and tLESV), respectively. Both protein forms were included in the analysis assays, but only slight differences in glucan binding and protein action between ESV1 and tESV1 were observed, while no differences in the glucan binding and effect on the GWD and PWD action were observed between LESV and tLESV. The results revealed that the presence of the N-terminal is not massively altering the action of ESV1 or LESV. Therefore, it was only used the ESV1 and tLESV forms data to explain the function of both proteins.
However, the analysis of the results revealed that LESV and ESV1 proteins bind strongly at the starch granule surface. Furthermore, not all of both proteins were released after their incubation with starches after washing the granules with 2% [w/v] SDS indicates to their binding to the deeper layers of the granule surface. Supporting of this finding comes after the binding of both proteins to starches after removing the free glucans chains from the surface by the action of ISA and BAM. Although both proteins are capable of binding to the starch structure, only LESV showed binding to amylose, while in ESV1, binding was not observed. The alteration of glucan structures at the starch granule surface is essential for the incorporation of phosphate into starch granule while the phosphorylation of starch by GWD and PWD increased after removing the free glucan chains by ISA. Furthermore, PWD showed the possibility of starch phosphorylation without prephosphorylation by GWD.
Biochemical studies on protein-glucan interactions between LESV or ESV1 with different types of starch showed a potentially important mechanism of regulating and adjusting the phosphorylation process while the binding of LESV and ESV1 leads to altering the glucan structures of starches, hence, render the effect of the action of dikinases enzymes (GWD and PWD) more able to control the rate of starch degradation. Despite the presence of ESV1 which revealed an antagonistic effect on the PWD action as the PWD action was decreased without prephosphorylation by GWD and increased after prephosphorylation by GWD (Chapter 4), PWD showed a significant reduction in its action with or without prephosphorylation by GWD in the presence of ESV1 whether separately or together with LESV (Chapter 5). However, the presence of LESV and ESV1 together revealed the same effect compared to the effect of each one alone on the phosphorylation process, therefore it is difficult to distinguish the specific function between them. However, non-interactions were detected between LESV and ESV1 or between each of them with GWD and PWD or between GWD and PWD indicating the independent work for these proteins. It was also observed that the alteration of the starch structure by LESV and ESV1 plays a role in adjusting starch degradation rates not only by affecting the dikinases but also by affecting some of the hydrolysing enzymes since it was found that the presence of LESV and ESV1leads to the reduction of the action of BAM, but does not abolish it.
Bacteria are one of the most widespread kinds of microorganisms that play essential roles in many biological and ecological processes. Bacteria live either as independent individuals or in organized communities. At the level of single cells, interactions between bacteria, their neighbors, and the surrounding physical and chemical environment are the foundations of microbial processes. Modern microscopy imaging techniques provide attractive and promising means to study the impact of these interactions on the dynamics of bacteria. The aim of this dissertation is to deepen our understanding four fundamental bacterial processes – single-cell motility, chemotaxis, bacterial interactions with environmental constraints, and their communication with neighbors – through a live cell imaging technique. By exploring these processes, we expanded our knowledge on so far unexplained mechanisms of bacterial interactions.
Firstly, we studied the motility of the soil bacterium Pseudomonas putida (P. putida), which swims through flagella propulsion, and has a complex, multi-mode swimming tactic. It was recently reported that P. putida exhibits several distinct swimming modes – the flagella can push and pull the cell body or wrap around it. Using a new combined phase-contrast and fluorescence imaging set-up, the swimming mode (push, pull, or wrapped) of each run phase was automatically recorded, which provided the full swimming statistics of the multi-mode swimmer. Furthermore, the investigation of cell interactions with a solid boundary illustrated an asymmetry for the different swimming modes; in contrast to the push and pull modes, the curvature of runs in wrapped mode was not affected by the solid boundary. This finding suggested that having a multi-mode swimming strategy may provide further versatility to react to environmental constraints.
Then we determined how P. putida navigates toward chemoattractants, i.e. its chemotaxis strategies. We found that individual run modes show distinct chemotactic responses in nutrition gradients. In particular, P. putida cells exhibited an asymmetry in their chemotactic responsiveness; the wrapped mode (slow swimming mode) was affected by the chemoattractant, whereas the push mode (fast swimming mode) was not. These results can be seen as a starting point to understand more complex chemotaxis strategies of multi-mode swimmers going beyond the well-known paradigm of Escherichia coli, that exhibits only one swimming mode.
Finally we considered the cell dynamics in a dense population. Besides physical interactions with their neighbors, cells communicate their activities and orchestrate their population behaviors via quorum-sensing. Molecules that are secreted to the surrounding by the bacterial cells, act as signals and regulate the cell population behaviour. We studied P. putida’s motility in a dense population by exposing the cells to environments with different concentrations of chemical signals. We found that higher amounts of chemical signals in the surrounding influenced the single-cell behaviourr, suggesting that cell-cell communications may also affect the flagellar dynamics.
In summary, this dissertation studies the dynamics of a bacterium with a multi-mode swimming tactic and how it is affected by the surrounding environment using microscopy imaging. The detailed description of the bacterial motility in fundamental bacterial processes can provide new insights into the ecology of microorganisms.
In this thesis, I examine different A-bar movement dependencies in Igbo, a Benue-Congo language spoken in southern Nigeria. Movement dependencies are found in constructions where an element is moved to the left edge of the clause to express information-structural categories such as in questions, relativization and focus. I show that these constructions in Igbo are very uniform from a syntactic point of view. The constructions are built on two basic fronting operations: relativization and focus movement, and are biclausal. I further investigate several morphophonological effects that are found in these A-bar constructions. I propose that these effects are reflexes of movement that are triggered when an element is moved overtly in relativization or focus. This proposal helps to explain the tone patterns that have previously been assumed to be a property of relative clauses. The thesis adds to the growing body of tonal reflexes of A-bar movement reported for a few African languages. The thesis also provides an insight into the complementizer domain (C-domain) of Igbo.
Die vorliegende Arbeit untersucht Urlaubsfotografien bei Facebook und beschreibt, welche sozio-technischen Medienpraktiken sich innerhalb der Social-Media Plattform über die Fotografien vollziehen. Fotografische Praktiken sind durch aktive Handlungen und soziale Gebrauchsweisen bestimmt. Urlaubsfotografien tragen zum Beispiel zur Strukturierung von Reiserouten und Vorstellungen bei, indem genrespezifische Motive und Rahmungen mit Hilfe von Medien reproduziert und wiederholt werden. Praktiken des Zeigens, Teilens und Kommunizierens werden durch Social Plug-Ins (Like/Share Buttons) und Tagging-Funktionen auch in die Benutzeroberflächen von Facebook integriert. Dadurch werden Nutzer*innen Aktivitäten und technische Prozesse miteinander verbunden. Am Beispiel der automatischen Generierung von Urlaubsfotografien auf Geotagseiten wird gezeigt, dass Social-Tagging zur Entstehung und Aushandlung geographischer Räume und Ortsvorstellungen beiträgt. Mithilfe technischer Strukturierungen von Fotografien auf Taggingseiten werden genrespezifische Motive, fotografische Trends und Ästhetiken besonders sichtbar. Allerdings wird ihre Visualisierung auch durch algorithmische Priorisierung einzelner Inhalte mitbestimmt. Dadurch werden Urlaubsfotografien für ein fotografisches Profiling genutzt, da sie das algorithmische Erfassen und Auswerten von Nutzer*innen-Informationen ermöglichen. Die Arbeit zeigt, dass der Einsatz von Bilderkennungsverfahren und fotografischen Datenanalysen zu einer optimierten Informationsgewinnung und zu einer Standardisierung von Fotografien beiträgt.
Potato is the 4th most important food crop in the world. Especially in tropical and sub-tropical potato production, drought is a yield limiting factor. Potato is sensitive to water stress. Potato yield loss under water stress could be reduced by using tolerant varieties and adjusted agronomic practices. Direct selection for yield under water-stressed conditions requires long selection cycles. Thus, identification of markers for marker-assisted selection may speed up breeding. The objective of this thesis is to identify morphological markers for drought tolerance by continuously monitoring plant growth and canopy temperature with an automatic phenotyping system.
The phenotyping was performed in drought-stress experiments that were conducted in population A with 64 genotypes and population B with 21 genotypes in the screenhouse in 2015 and 2016 (population A) and in 2017 and 2018 (population B). Drought tolerance was quantified as deviation of the relative tuber starch yield from the experimental median (DRYM) and parent median (DRYMp). Relative tuber starch yield is starch yield under drought stress relative to the average starch yield of the respective cultivar under control conditions in the same experiment. The specific DRYM value was calculated based on the yield data of the same experiment or the global DRYM that was calculated from yield data derived from data combined over yeas of respective population or across multiple experiments including VALDIS and TROST experiments (2011-2016).
Analysis of variance found a significant effect of genotype on DRYM indicating that the tolerance variation required for marker identification was given in both populations.
Canopy growth was monitored continuously six times a day over five to ten weeks by a laser scanner system and yielded information on leaf area, plant height and leaf angle for population A and additionally on leaf inclination and light penetration depth for population B. Canopy temperature was measured 48 times a day over six to seven weeks by infrared thermometry in population B. From the continuous IRT surface temperature data set, the canopy temperature for each plant was selected by matching the time stamp of the IRT data with laser scanner data.
Mean, maximum, range and growth rate values were calculated from continuous laser scanner measurements of respective canopy parameters. Among the canopy parameters, the maximum and mean values in long-term stress conditions showed better correlation with DRYM values calculated in the same experiment than growth rate and diurnal range values. Therefore, drought tolerance index prediction was done from maximum and mean values of canopy parameters.
The tolerance index in specific experiment condition was linearly predicted by simple regression model from different single canopy parameters under long-term stress condition in population A (2016) and population B (2017 and 2018). Among the canopy parameters maximum light penetration depth (2017), mean leaf angle (2017, 2018, and 2016), mean leaf inclination or mean canopy temperature depression (2017 and 2018), maximum plant height (2017) were selected as tolerance predictors. However, no single parameters were sufficient to predict DRYM. Therefore, several independent parameters were integrated in a multiple regression model.
In multiple regression model, specific experiment DRYM values in population A was predicted from mean leaf angle (2016). In population B, specific tolerance could be predicted from maximum light penetration depth and mean leaf inclination (2017) and mean leaf inclination (2018) or mean canopy temperature depression and mean leaf angle (2018).
In data combined over season of population A, the multiple linear regression model selected maximum plant height and mean leaf angle as tolerance predictor. In Population B, mean leaf inclination was selected as tolerance predictor. However, in population A, the variation explained by the final model was too low.
Furthermore, the average tolerances respective to parent median (2011-2018) across FGH plants or all plants (FGH and field) were predicted from maximum plant height (population A) and maximum plant height and mean leaf inclination (population B). Altogether, canopy parameters could be used as markers for drought tolerance. Therefore, water stress breeding in potato could be speed up through using leaf inclination, light penetration depth, plant height and canopy temperature depression as markers for drought tolerance, especially in long-term stress conditions.
During a dark night, it is possible to observe thousands of stars by eye. All these stars are located within the Milky Way, our home. Not all stars are the same, they can have different sizes, masses, temperatures and ages. Heavy stars do not live long (in astronomical terms), only a few million years, but stars less massive than the Sun can get more than ten billion years old. Such small stars that formed in the beginning of the Universe still shine today. These ancient stars are very helpful to learn more about the early Universe, the First Stars and the history of the Milky Way. But how do you recognise an ancient star? Using their chemical fingerprints! In the beginning of the Universe, there were only two chemical elements: hydrogen and helium (and a tiny bit of lithium). All the heavier elements like carbon, calcium and iron were only made later within stars and their explosions. The amount of chemical elements in the Universe increases with the number of stars that are born, evolve and explode. Stars that form later are born with more heavy elements, or a greater metallicity. In the field of astronomy that is called “Galactic Archaeology”, stars of various metallicities are used to study the history of the Milky Way. In this doctoral thesis, the focus is on metal-poor stars because these are expected to be the oldest and can therefore tell us a lot about the early history of our Galaxy.
Until today, we still have not discovered a metal-free star. The most metal-poor stars, however, give us important insights in the lives and deaths of the First Stars. Many of the oldest, most metal-poor stars have an unexpectedly large amount of carbon, compared to for example iron. These carbon-enhanced metal-poor (CEMP) stars tell us something about the very first stars in the Universe: they somehow produced a lot of carbon. If we look at the precise chemical fingerprints of the CEMP stars, we can learn a lot more. But our interpretation depends on the assumption that the chemical fingerprint of a star does not change during its life. In this thesis, new data is presented that shows that this assumption may be too simple: many extremely metal-poor CEMP stars are members of binary systems. Interactions between two stars in a binary system can pollute the surface of the stars. Likely not all of the CEMP stars in binary systems were actually polluted, but we should be very careful in our interpretations of the fingerprints of these stars.
The CEMP stars and other metal-poor stars are also important for our understanding of the early history of the Milky Way. Most researchers who study metal-poor stars look for these stars in the halo of the Milky Way: a huge diffuse Galactic component containing about 1% of the stars in our Galaxy. However, models predict that the oldest metal-poor stars are located in the center of the Milky Way, in the bulge. The metal-poor inner Galaxy is unfortunately difficult to study due to large amounts of dust between us and the center and an overwhelming majority of metal-rich stars. This thesis presents results from the successful Pristine Inner Galaxy Survey (PIGS), a new survey looking for (and finding) the oldest stars in the bulge of the Milky Way. PIGS is using images with a specific color that is sensitive to the metallicity of stars, and can therefore efficiently select the metal-poor stars among millions of other, more metal-rich stars. The interesting candidates are followed up with spectroscopy, which is then analysed using two independent methods. With this strategy, PIGS has discovered the largest sample of metal-poor stars in the inner Galaxy to date. A new result from the PIGS data is that the metal-poor stars rotate more slowly around the Galactic center compared to the more metal-rich stars, and they show larger randomness in their motions as well. Another important contribution from PIGS is the discovery of tens of CEMP stars in the inner Galaxy, where previously only two such stars were known.
The new results from this thesis help us to understand the First Stars and the early history of the Milky Way. Ongoing and future large surveys will provide us with a lot of additional data in the coming years. It is an exciting time for the field of Galactic Archaeology.
In this dissertation we introduce a concept of light driven active and passive manipulation of colloids trapped at solid/liquid interface. The motion is induced due to generation of light driven diffusioosmotic flow (LDDO) upon irradiation with light of appropriate wavelength. The origin of the flow is due to osmotic pressure gradient resulting from a concentration gradient at the solid/liquid interface of the photosensitive surfactant present in colloidal dispersion. The photosensitive surfactant consists of a cationic head group and a hydrophobic tail in which azobenzene group is integrated in. The azobenzene is known to undergo reversible photo-isomerization from a stable trans to a meta stable cis state under irradiation with UV light. Exposure to light of larger wavelength results in back photo-isomerization from cis to trans state. The two isomers have different molecular properties, for instance, trans isomer has a rod like structure and low polarity (0 dipole moment), whereas cis one is bent and has a dipole moment of ~3 Debye. Being integrated in the hydrophobic tail of the surfactant molecule, the azobenzene state determines the hydrophobicity of the whole molecule: in the trans state the surfactant is more hydrophobic than in the cis-state. In this way many properties of the surfactant such as the CMC, solubility and the interaction potential with a solid surface can be altered by light. When the solution containing such a surfactant is irradiated with focused light, a concentration gradient of different isomers is formed near the boundary of the irradiated area near the solid surface resulting in osmotic pressure gradient. The generated diffusioosmotic (DO) flow carries the particles passively along.
The local-LDDO flow can be generated around and by each particle when mesoporous silica colloids are dispersed in the surfactant solution. This is because porous particles act as a sink/source which absorbs azobenzene molecule in trans state and expels it when it is in the cis state. The DO flows generated at each particle interact resulting in aggregation or separation depending upon the initial state of surfactant molecules. The kinetic of aggregation and separation can be controlled and manipulated by altering the parameters such as the wavelength and intensity of the applied light, as well as surfactant and particle concentration. Using two wavelengths simultaneously allows for dynamic gathering and separation creating fascinating patterns such as 2D disk of well separated particles or establishing collective complex behaviour of particle ensemble as described in this thesis.
The mechanism of l-LDDO is also used to generate self-propelled motion. This is possible when half of the porous particle is covered by metal layer, basically blocking the pores on one side. The LDDO flow generated on uncapped side pushes the particle forward resulting in a super diffusive motion. The system of porous particle and azobenzene containing surfactant molecule can be utilized for various application such as drug delivery, cargo transportation, self-assembling, micro motors/ machines or micro patterning.
The Earth's inner magnetosphere is a very dynamic system, mostly driven by the external solar wind forcing exerted upon the magnetic field of our planet. Disturbances in the solar wind, such as coronal mass ejections and co-rotating interaction regions, cause geomagnetic storms, which lead to prominent changes in charged particle populations of the inner magnetosphere - the plasmasphere, ring current, and radiation belts. Satellites operating in the regions of elevated energetic and relativistic electron fluxes can be damaged by deep dielectric or surface charging during severe space weather events. Predicting the dynamics of the charged particles and mitigating their effects on the infrastructure is of particular importance, due to our increasing reliance on space technologies.
The dynamics of particles in the plasmasphere, ring current, and radiation belts are strongly coupled by means of collisions and collisionless interactions with electromagnetic fields induced by the motion of charged particles. Multidimensional numerical models simplify the treatment of transport, acceleration, and loss processes of these particles, and allow us to predict how the near-Earth space environment responds to solar storms. The models inevitably rely on a number of simplifications and assumptions that affect model accuracy and complicate the interpretation of the results. In this dissertation, we quantify the processes that control electron dynamics in the inner magnetosphere, paying particular attention to the uncertainties of the employed numerical codes and tools.
We use a set of convenient analytical solutions for advection and diffusion equations to test the accuracy and stability of the four-dimensional Versatile Electron Radiation Belt (VERB-4D) code. We show that numerical schemes implemented in the code converge to the analytical solutions and that the VERB-4D code demonstrates stable behavior independent of the assumed time step. The order of the numerical scheme for the convection equation is demonstrated to affect results of ring current and radiation belt simulations, and it is crucially important to use high-order numerical schemes to decrease numerical errors in the model.
Using the thoroughly tested VERB-4D code, we model the dynamics of the ring current electrons during the 17 March 2013 storm. The discrepancies between the model and observations above 4.5 Earth's radii can be explained by uncertainties in the outer boundary conditions. Simulation results indicate that the electrons were transported from the geostationary orbit towards the Earth by the global-scale electric and magnetic fields.
We investigate how simulation results depend on the input models and parameters. The model is shown to be particularly sensitive to the global electric field and electron lifetimes below 4.5 Earth's radii. The effects of radial diffusion and subauroral polarization streams are also quantified.
We developed a data-assimilative code that blends together a convection model of energetic electron transport and loss and Van Allen Probes satellite data by means of the Kalman filter. We show that the Kalman filter can correct model uncertainties in the convection electric field, electron lifetimes, and boundary conditions. It is also demonstrated how the innovation vector - the difference between observations and model prediction - can be used to identify physical processes missing in the model of energetic electron dynamics.
We computed radial profiles of phase space density of ultrarelativistic electrons, using Van Allen Probes measurements. We analyze the shape of the profiles during geomagnetically quiet and disturbed times and show that the formation of new local minimums in the radial profiles coincides with the ground observations of electromagnetic ion-cyclotron (EMIC) waves. This correlation indicates that EMIC waves are responsible for the loss of ultrarelativistic electrons from the heart of the outer radiation belt into the Earth's atmosphere.
Glycosylphosphatidylinositols (GPIs) are highly complex glycolipids that serve as membrane anchors to a large variety of eukaryotic proteins. These are covalently attached to a group of peripheral proteins called GPI-anchored proteins (GPI-APs) through a post-translational modification in the endoplasmic reticulum. The GPI anchor is a unique structure composed of a glycan, with phospholipid tail at one end and a phosphoethanolamine linker at the other where the protein attaches. The glycan part of the GPI comprises a conserved pseudopentasaccharide core that could branch out to carry additional glycosyl or phosphoethanolamine units. GPI-APs are involved in a diverse range of cellular processes, few of which are signal transduction, protein trafficking, pathogenesis by protozoan parasites like the malaria- causing parasite Plasmodium falciparum. GPIs can also exist freely on the membrane surface without an attached protein such as those found in parasites like Toxoplasma gondii, the causative agent of Toxoplasmosis. These molecules are both structurally and functionally diverse, however, their structure-function relationship is still poorly understood. This is mainly because no clear picture exists regarding how the protein and the glycan arrange with respect to the lipid layer. Direct experimental evidence is rather scarce, due to which inconclusive pictures have emerged, especially regarding the orientation of GPIs and GPI-APs on membrane surfaces and the role of GPIs in membrane organization. It appears that computational modelling through molecular dynamics simulations would be a useful method to make progress. In this thesis, we attempt to explore characteristics of GPI anchors and GPI-APs embedded in lipid bilayers by constructing molecular models at two different resolutions – all-atom and coarse-grained.
First, we show how to construct a modular molecular model of GPIs and GPI-anchored proteins that can be readily extended to a broad variety of systems, addressing the micro-heterogeneity of GPIs. We do so by creating a hybrid link to which GPIs of diverse branching and lipid tails of varying saturation with their optimized force fields, GLYCAM06 and Lipid14 respectively, can be attached. Using microsecond simulations, we demonstrate that GPI prefers to “flop-down” on the membrane, thereby, strongly interacting with the lipid heads, over standing upright like a “lollipop”. Secondly, we extend the model of the GPI core to carry out a systematic study of the structural aspects of GPIs carrying different side chains (parasitic and human GPI variants) inserted in lipid bilayers. Our results demonstrate the importance of the side branch residues as these are the most accessible, and thereby, recognizable epitopes. This finding qualitatively agrees with experimental observations that highlight the role of the side branches in immunogenicity of GPIs and the specificity thereof. The overall flop-down orientation of the GPIs with respect to the bilayer surface presents the side chain residues to face the solvent. Upon attaching the green fluorescent protein (GFP) to the GPI, it is seen to lie in close proximity to the bilayer, interacting both with the lipid heads and glycan part of the GPI. However the orientation of GFP is sensitive to the type of GPI it is attached to. Finally, we construct a coarse-grained model of the GPI and GPI-anchored GFP using a modified version of the MARTINI force-field, using which the timescale is enhanced by at least an order of magnitude compared to the atomistic system.
This study provides a theoretical perspective on the conformational behavior of the GPI core and some of its branched variations in presence of lipid bilayers, as well as draws comparisons with experimental observations. Our modular atomistic model of GPI can be further employed to study GPIs of variable branching, and thereby, aid in designing future experiments especially in the area of vaccines and drug therapies. Our coarse-grained model can be used to study dynamic aspects of GPIs and GPI-APs w.r.t plasma membrane organization. Furthermore, the backmapping technique of converting coarse-grained trajectory back to the atomistic model would enable in-depth structural analysis with ample conformational sampling.
Studies on the unsustainable use of groundwater resources are still considered incipient since it is frequently a poorly understood and managed, devalued and inadequately protected natural resource. Groundwater Recharge (GWR) is one of the most challenging elements to estimate since it can rarely be measured directly and cannot easily be derived from existing data. To overcome these limitations, many hydro(geo)logists have combined different approaches to estimate large-scale GWR, namely: remote sensing products, such as IMERG product; Water Budget Equation, also in combination with hydrological models, and; Geographic Information System (GIS), using estimation formulas. For intermediary-scale GWR estimation, there exist: Non-invasive Cosmic-Ray Neutron Sensing (CRNS); wireless networks from local soil probes; and soil hydrological models, such as HYDRUS. Accordingly, this PhD thesis aims, on the one hand, to demonstrate a GIS-based model coupling for estimating the GWR distribution on a large scale in tropical wet basins. On the other hand, it aims to use the time series from CRNS and invasive soil moisture probes to inversely calibrate the soil hydraulic properties, and based on this, estimating the intermediary-scale GWR using a soil hydrological model. For such purpose, two tropical wet basins located in a complex sedimentary aquifer in the coastal Northeast region of Brazil were selected. These are the João Pessoa Case Study Area and the Guaraíra Experimental Basin. Several satellite products in the first area were used as input to the GIS-based water budget equation model for estimating the water balance components and GWR in 2016 and 2017. In addition, the point-scale measurement and CRNS data were used in the second area to determine the soil hydraulic properties, and to estimate the GWR in the 2017-2018 and 2018-2019 hydrological years. The resulting values of GWR on large- and intermediary-scale were then compared and validated by the estimates obtained by groundwater table fluctuations. The GWR rates for IMERG- and rain-gauge-based scenarios showed similar coefficients between 68% and 89%, similar mean errors between 30% and 34%, and slightly-different bias between -13% and 11%. The results of GWR rates for soil probes and CRNS soil moisture scenarios ranged from -5.87 to -61.81 cm yr-1, which corresponds to 5% and 38% of the precipitation. The calculations of the mean GWR rates on large-scale, based on remote sensing data, and on intermediary-scale, based on CRNS data, held similar results for the Podzol soil type, namely 17.87% and 17% of the precipitation. It is then concluded that the proposed methodologies allowed for estimating realistically the GWR over the study areas, which can be a ground-breaking step towards improving the water management and decision-making in the Northeast of Brazil.