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Deciphering human brain development and evolution: insights from brain organoid models
No full textThe evolutionary expansion of the human neocortex is considered to be a key foundation underlying our
exceptional cognitive abilities. This expansion is primarily driven by cortical neurogenesis, which relies
on the activity of cortical neural progenitor cells (cNPCs). Recent studies have identified human-specific
genes that can modulate the proliferation and differentiation dynamics of cNPCs. While few of these
genes have been functionally analyzed using animal models, their roles in primate-specific cortical
expansion remain largely unexplored. In this study, we leverage cerebral organoid models to investigate
the roles of human-specific genes in neocortical expansion. Furthermore, we address a major limitation
of current brain organoid models by introducing vascularization to improve their capacity to model key
aspects of cortical development.
Human-specific genes preferentially expressed in cNPCs constitute a compelling source underlying the
remarkable expansion of the neocortex during human evolution. In this work, we investigated the effects
of the human-specific genes NOTCH2NLB and NBPF14 on cNPCs using a combination of mouse
models and chimpanzee cerebral organoids. We show that NBPF14 induces the delamination of apical
progenitors (APs), by altering cleavage plane orientation during AP division. This leads to an increased
abundance of basal radial glia, the key cNPC type underlying the cortical expansion. In contrast,
NOTCH2NLB promotes AP proliferation and expands the AP pool. When expressed together, NBPF14
and NOTCH2NLB exert coordinated effects, resulting in the expansion of basal progenitors while
maintaining the self-renewal of APs. Together, our findings reveal a mechanistic framework for how
the concerted action of these two human-specific genes contributed to the evolutionary expansion of the
human neocortex.
While brain organoids have proven to be useful tools to study aspects of human cortical development
and evolution, they have certain limitations that must be addressed to enhance their relevance and
functionality. In this work, we introduced vascularized cerebral organoids from human and rhesus
macaque and analyzed the effects of endothelial cells on organoid development. We show that
endothelial cells reduce apoptosis and promote the mitotic activity of neural progenitors, leading to an
increased abundance of neurons in cerebral organoids. Notably, vascularized organoids reveal species-
specific developmental timing, with human and rhesus macaque organoids responding to vascularization
at distinct stages of development. These findings indicate the critical role of endothelial cells in
regulating neural development and highlight vascularized cerebral organoids as promising models for
comparative evolutionary studies.
Together, our findings underscore the potential of cerebral organoids as powerful models for studying
human brain development and evolution. By elucidating the functional roles of human-specific genes
and showing the critical impact of vascularization on cerebral organoid development, our study
highlights how these models can provide mechanistic insights into primate cortical evolution.2026-05-2
Charakterisierung einer unbekannten Interaktionsregion im Aminoterminus des Transkriptionsfaktors STAT1
No full textThis study investigates the roles of two amino acid residues, H58 and R70, in the N-terminal domain of the signal transducer and activator of transcription 1 (STAT1) in the context of JAK-STAT pathway activation following cytokine stimulation. While the H58A mutation had no significant effect compared to wild-type STAT1, the R70A mutation led to increased tyrosine phosphorylation, enhanced DNA binding, and prolonged nuclear accumulation. These changes were associated with increased reporter gene expression using a synthetic promoter, though no global transcriptional differences were observed by RT-PCR. The findings suggest that R70 contributes to stabilizing the antiparallel dimer conformation of STAT1. Its mutation may favor the transcriptionally active, parallel dimer form by disrupting electrostatic interactions, thus altering STAT1 function.2026-07-0
Interactome and Subcellular Analysis of the Tethering Proteins VAPA and VAPB in Cardiomyocytes
No full textHeart muscle contraction is regulated by excitation-contraction-coupling (ECC), where
calcium (Ca2+) released from the sarcoendoplasmic reticulum (SER) triggers myofilament
contraction. The SER is crucial for intracellular Ca2+ cycling in cardiomyocytes, ensuring proper
ECC through specialized proteins responsible for Ca2+ release and reuptake. In a previous
project, we used a proximity labeling assay coupled with mass-spectrometry-based
complexome profiling on murine-isolated ventricular cardiomyocytes (VCMs) to elucidate the
interactome of phospholamban (PLN), a key SER protein associated with calcium reuptake.
This analysis identified two isoforms of the VAMP-associated protein (VAP) family, VAPA and
VAPB, co-migrating with PLN and another key regulator of Ca2+ reuptake, the
sarcoplasmic/endoplasmic reticulum Ca2+-ATPase (SERCA2a).
While VAPA and VAPB have known roles in multiple contact site (MCS) formation, Ca2+
homeostasis, lipid transport, and protein proteostasis, their specific functions in ventricular
cardiomyocytes remain uninvestigated. Our preliminary data suggest that VAPA and VAPB
may regulate Ca2+ homeostasis by interacting with the PLN/SERCA2a complex.
In this study, we investigate the role of VAPA and VAPB in VCMs using state-of-the-art
techniques, such as co-immunoprecipitation (Co-IP), immunofluorescence coupled with
confocal and Stimulated Emission Depletion Microscopy (STED), Ca2+-imaging, and mass
spectrometry. We focused on investigating the functions and interactions between VAPA and
VAPB and Ca2+ handling proteins in wild-type, PLN knock-out, and VAPB knock-out VCMs.
Additionally, we employed a heterologous expression system to elucidate isoform-specific
functions since VAPA and VAPB can form homo- and hetero-dimers.
Our findings revealed that both VAPA and VAPB are expressed in VCMs and localized to the
sarcomeric Z-line alongside SERCA2a. In addition, VAPB and VAPA localized specifically to the
M-band and the nuclear envelope, respectively, indicating isoform-specific distributions.
Affinity MS revealed potential interacting partners, including previously known tethering
proteins, as well as novel interactors. Notably, the novel interactor SERCA2a was detected in
the VAPA and VAPB interactome analysis, and the novel interactor small ankyrin 1.5 (sANK1.5)
was detected in the VAPB interactome analysis. Co-IP confirmed the interaction between
VAPA/VAPB and SERCA2a and PLN, as well as between VAPB and sANK1.5. In VAPB knock-out
VCMs, VAPA interacted with SERCA2A and PLN independently of VAPB; however, VAPA was
redistributed to the M-band and sANK1.5 to the Z-line. Ca2+ imaging showed enhanced SER
Ca2+ load and SERCA2a activity in VAPB knock-out VCMs. Heterologous expression of VAPB,
PLN, and SERCA2a in VAPA/VAPB or VAPB knock-out Rabbit Kidney-13 cells demonstrated
direct and distinct interactions between VAPB and PLN and between VAPA and SERCA2a.
Our findings suggest that VAPA and VAPB act as docking proteins for SERCA2a and PLN,
respectively, potentially facilitating PLN inhibition of SERCA2a. Moreover, our data provides
the novel insight, that VAPA and VAPB appear to be involved in Ca2+ homeostasis and ECC.
Additionally, the mass spectrometry-based interactome analysis confirmed functions in MCS
formation and lipid homeostasis in VCMs. Moreover, our results suggest more regulatory
proteins and events are involved in the PLN-SERCA2a interaction than previously thought,
indicating the presence of fine-tuning proteins that might also serve as potential drug targets
for heart disease.2026-08-1
N-Heterocyclic Electroauxiliaries for the Generation of Alkyl Radicals via C−C Bond Cleavage
No full textAlkyl radical precursors are essential for a wide variety of photocatalytic and 3d-metal-catalyzed C–C bond forming reactions. In the last decade, neutral organic heterocycles as electroauxiliaries have become reliable tools for alkyl radical formation, such as 4-alkyl Hantzsch esters.
In this thesis, 2,2’-biquinoline-derived 2-alkyl-substituted dihydroquinolines were identified and applied for the first time as potent reagents for alkyl radical formation with the aspect of recyclability.
The 2-alkyl-substituted dihydroquinolines were successfully applied as radical progenitors of primary, secondary and tertiary alkyl radicals, demonstrated in C–C, C–S, C–N and C–O bond formation reactions.
Furthermore, alkyl-substituted dihydropyrimidines (DHPyms), synthesized via the Biginelli reaction, were identified as tunable alternatives to 4-alkyl Hantzsch esters in radical chemistry. The work explores their redox properties, UV/vis absorption, and synthetic potential, demonstrating DHPyms as versatile alkyl radical precursors in C–C, C–N, C–S bond forming reactions. DHPyms with lower oxidation potentials showed enhanced reactivity in Ni/photoredox dual catalytic cross-coupling reactions, outperforming traditional Hantzsch esters.2026-07-0
Studies on the Expression, Subcellular Localisation, and Secretion of Ribonuclease T2 in Mice
No full textLoss-of-function Mutationen im RNASET2 Gen führen innerhalb des ersten Lebensjahres zu einer genetischen zystischen Leukenzephalopathie, die phänotypisch eine kongenitale Infektion mit dem Zytomegalievirus imitiert. Kinder mit dieser seltenen autosomal-rezessiven Erkrankung, die als Typ-I-Interferonopathie klassifiziert wurde, zeigen Entwicklungsverzögerungen und können zusätzlich schwerwiegende neurologische Symptome wie Ataxie, Spastizität, Epilepsie und einen sensorineuralen Hörverlust entwickeln. Die biologische Funktion der Ribonuklease T2 (RNase T2) ist bisher nicht ausreichend untersucht. Außerdem besteht in der Literatur Uneinigkeit über die subzelluläre Lokalisation und Sekretion der RNase T2. Vor diesem Hintergrund sollte diese Arbeit maßgeblich zur Aufklärung der subzellulären Lokalisation der RNase T2 beitragen und eine mögliche Sekretion im Mausmodell beweisen. Die Expressionsanalyen von RNase T2 in dieser Arbeit wurden an embryonalen immortalisierten Maus-Fibroblasten (iMEFs) und in murinen Geweben durchgeführt. Die Expression von Rnaset2 in iMEFs wurde dabei mittels quantitativer Polymerase-Kettenreaktion untersucht. Dabei zeigte sich eine geringe endogene Expression in iMEFs, welche durch Western Blot-Analysen bestätigt wurde. Die Expression von RNase T2 in murinen Gewebeschnitten wurde indirekt anhand immunhistochemischer Färbungen von β-Galaktosidase untersucht. Ermöglicht wurde diese indirekte Expressionsanalyse durch Substitution von Rnaset2 mit einem Reportergen. Hierbei konnte eine Expression von RNase T2 in Hepatozyten, Kardiomyozyten, Tubulus-Epithelzellen, Megakaryozyten und in Zellen des blutbildenden Systems nachgewiesen werden. Ferner wurde in dieser Arbeit die subzelluläre Lokalisation der RNase T2 in iMEFs mittels eines markierten RNase T2-Konstrukts durch eine Immunfluoressenz- und hochauflösende Spinning Disk Konfokal-Mikroskopie untersucht. Dabei konnten für die RNase T2 intrazelluläre Lokalisationen im Endoplasmatischen Retikulum und Golgi-Apparat sowie in frühen Endosomen und Exosomen qualitativ gezeigt und quantitativ validiert werden. Lokalisationen der RNase T2 in Lysosomen und Mitochondrien konnten hingegen in iMEFs nicht nachgewiesen werden. Vor diesem Hintergrund ist eine Exosomen-vermittelte Sekretion der RNase T2 anzunehmen. Daher wurde in dieser Arbeit die Sekretion und Endozytose von RNase T2 anhand eines markierten RNase T2-Konstrukts in Western Blot-Analysen in iMEFs untersucht. Dabei konnte eine Sekretion von RNase T2 erstmals durch Nachweis der RNase T2 in Zell-Überständen nachgewiesen werden. Eine Endozytose von RNase T2 ließ sich experimentell durch Western Blot-Analysen unter den gewählten Bedingungen nicht in iMEFs beweisen. Die Erkenntnisse dieser Arbeit erweitern das grundlegende Verständnis über mögliche Funktionen der RNase T2. Sie tragen wesentlich zur Einordnung der funktionellen Zusammenhänge einer Immunregulation durch die RNase T2 bei und bilden damit die Grundlage für weiterführende experimentelle Untersuchungen sowie für die Entwicklung möglicher therapeutischer Strategien.Loss-of-function mutations in the human RNASET2 gene are associated with an early-onset cystic leukoencephalopathy, which typically manifests as a disorder resembling congenital cytomegalovirus infection. This rare autosomal recessive condition has been classified as a type I interferonopathy. It is characterised by developmental delays, along with the potential emergence of severe neurological symptoms such as ataxia, spasticity, epilepsy, and sensorineural hearing loss. The biological function of ribonuclease T2 (RNase T2) remains inadequately understood. Additionally, the existing literature presents conflicting perspectives on the subcellular localisation and potential secretion of RNase T2. This study aimed to elucidate the subcellular localisation of RNase T2 and to demonstrate its secretion in mice. Expression analyses of RNase T2 were conducted in embryonic immortalised mouse fibroblasts (iMEFs) and murine tissues. The expression of Rnaset2 in iMEFs was assessed using quantitative real-time polymerase chain reaction (qRT-PCR), which revealed low endogenous expression that was further confirmed by Western blot analysis. To evaluate RNase T2 expression in murine tissue sections, an indirect approach was taken using immunohistochemical staining of β-galactosidase, achieved by substituting Rnaset2 with a reporter gene in the mouse model. This method successfully demonstrated RNase T2 expression in hepatocytes, cardiomyocytes, tubular epithelial cells, megakaryocytes, and hematopoietic cells. The subcellular localisation of RNase T2 in iMEFs was analysed using a tagged RNase T2 construct through immunofluorescence and high-resolution spinning disk confocal microscopy. RNase T2 was found to be predominantly localised within the endoplasmic reticulum, Golgi apparatus, early endosomes and exosomes. Based on these findings, it is presumed that RNase T2 is secreted via an exosome-mediated pathway. Consequently, the processes of secretion and endocytosis of RNase T2 were further investigated using Western blot analysis of a tagged RNase T2 construct in iMEFs. The presence of RNase T2 in cell culture supernatants confirmed its secretion. However, this study did not experimentally validate the endocytosis of RNase T2. These findings significantly enhance the understanding of the potential RNase T2 functions and clarify its role in immune regulation. This work provides a foundation for further experimental investigations and the development of potential therapeutic strategies.2026-09-2
Mechanisms of Ribosomal Translation studied by Molecular Dynamics Simulations
No full textDuring translation, the ribosome moves along the mRNA and decodes the genetic
information to synthesize proteins. This process proceeds in a step-wise iterative
manner during which the ribosome undergoes conformational rearrangements, together with mRNA, tRNAs and interacting protein factors. In bacteria, mechanisms
have evolved that regulate gene expression by slowing
down or arresting protein synthesis.
I used molecular dynamics (MD) simulations to elucidate the atomistic bases of
these mechanisms. In the first part of this thesis (Chapter 3), I investigated how
single-point mutations in elongation factor G (EF-G), a GTPase that accelerates
the translocation of the ribosome and tRNAs along the mRNA, might cause a slowdown in protein synthesis.
In the second part (Chapters 4 and 5) I studied mechanisms of programmed translational stalling, i.e., the arrest of the ribosome during translation of specific peptides.
In Chapter 4, I elucidated how stalling during translation of peptides containing the
Arg-Ala-Pro-Pro (RAPP) motif takes place. I observed that the RAPP arrest motif
rewires the hydrogen bond network required for the peptide bond formation and
thereby inhibits elongation of the nascent peptide chain. In Chapter 5, I studied
how the stalling in the arrest peptide SecM, which displays a similar arrest motif
(RAGP) is released by a mechanical force acting on the nascent chain.
By elucidating functionally relevant details of the conformational dynamics of unbound and ribosome-bound EF-G, of the peptide containing the RAPP motif, and of
the SecM arrest peptide, the results of my MD simulations helped to connect structural information and biochemical data to obtain a detailed picture of atomistic
mechanisms underlying ribosome regulation.2026-06-2
Dissecting the Atg21 organization at the growing phagophore and the evolutionary conservation of Nvj1 among yeasts
No full textThe first project of this thesis deals with the spatial and temporal regulation of Atg21 at growing phagophores. Macroautophagy is a highly conserved process involved in the degradation and recycling of cellular material reaching from cytoplasmic material to entire defective or superfluous organelles. The main proteins facilitating this process are 42 Atg proteins, that are recruited to the PAS in a highly regulated, hierarchical order. After the initial induction of macroautophagy by the Atg1 kinase complex and the subsequent formation of an isolation membrane, generated from Atg9-rich vesicles, the PI3-kinase complex I is recruited to this membrane. Contained in the PI3-kinase complex is Atg14, which is responsible for the recruitment of the complex to the PAS and also upholds an interaction with the vacuolar protein Vac8, which confines the complex to the vacuolar tethered edge of the isolation membrane. Here the complex is involved in the phosphorylation of phosphatidylinositol (PI) to phosphatidylinositol 3-phosphate (PI3P). The Atg18-Atg2-Atg9 complex further tethers the other side of the isolation membrane to the ER. For the following elongation of this isolation membrane, it is necessary to conjugate the protein Atg8 with phosphatidylethanolamine in the isolation membrane. A major contributor to this process is the β-propeller protein Atg21, which acts as a protein hub and recruits the complexes involved in Atg8 lipidation. As part of the PROPPIN protein family, Atg21 can bind the newly produced PI3P in the isolation membrane. This lipid binding is necessary for its localization, but not sufficient to explain its narrow recruitment to only the vacuolar edge of the isolation membrane. This thesis aimed to examine possible candidates that could provide a concentrated localization of Atg21 to this region. Atg14 was quickly identified as a prime contender since it localizes the PI3-kinase complex I to the vacuolar edge and like Atg38, is only found in the autophagic PI3-kinase, while the other proteins of this complex also localize to endosomes. After initial positive results that demonstrated co-isolation of Atg14 and Atg21 in Co-IPs, it was later shown, that this interaction is at least partially dependent on Vps15. More sensitive methods like the recombinant expression and co-isolation of these proteins as well as a split ubiquitin approach, were not successful in showing a direct interaction between Atg14 and Atg21. Furthermore, efforts were made to narrow down possible binding regions in Atg14, which require further investigation.
The second project included in this thesis deals with the nucleus vacuole junction (NVJ), which is a membrane contact site (MCS) established by the binding of Nvj1 in the outer nuclear membrane with Vac8 in the vacuolar membrane. In its function as an MCS, it promotes lipid biosynthesis and the non-vesicular lipid transport between the membranes, by recruiting multiple proteins involved in these processes. Thereby it contributes to the overall lipid homeostasis in the cell and the formation of membrane subdomains, important for a multitude of processes. The other function of the NVJ lies in the autophagic process of piecemeal microautophagy of the nucleus (PMN), which is induced by nitrogen starvation and leads to the teardrop-shaped invagination of the NVJ into the vacuole, containing nuclear material and the junction itself, together with all previously localized proteins. This structure finally buds off and is degraded. However, the PMN process failed to show any significant effect on cell survivability under standard starvation conditions, which stands in stark contrast to the macroautophagic mechanism. Additionally, the Nvj1 protein consists of a small number of binding domains, connected by a mostly disordered linker region, which is very permissive for mutations. Both the low impact on survivability and the disordered structure could have allowed for an extremely divergent evolution of this protein and led to the hypothesis that Nvj1 is a lineage-specific gene for a small group of close relatives to the Saccharomyces genus. In this thesis, micro-synteny analysis was used to expand on identified Nvj1 orthologs and to examine the possible functional conservation of its roles in NVJ establishment. Multiple positional orthologs, that diverged from S. cerevisiae over 200 million years ago and retain no detectable sequence similarity, were found to engage in the formation of the NVJ, when endogenously expressed or even in S. cerevisiae. Furthermore, it was demonstrated that Nvj1 proteins from distant relatives were still able to facilitate PMN and also partially recruit proteins of the lipid biosynthesis machinery, thereby hinting strongly at a possible functional conservation of these processes in these divergent species. The access to far more, newly identified sequences for Nvj1 homologs, also gave the opportunity to identify a previously elusive, well-conserved motif in the Nvj1 sequence, that evolutionary was bound to the Osh1 binding site of Nvj1. The now-termed Osh1-associated motif, was subsequently mutated and efforts were made to describe the mutant phenotype and identify an interaction partner of this motif.2026-11-1
Manganese and Ruthenium Catalysis for Sustainable C–H Functionalizations and Polymer Synthesis
No full textThe ever-growing scarcity of resources, energy crises, and environmental pollution demand the development of sustainable chemical processes for C–C bond formations and efficient post-consumer plastic waste recycling. While previous work has often relied on late transition metals, chemical oxidants, or toxic and sensitive organometallic reagents, the potential of manganese- or ruthenium-catalyzed C–H functionalizations under photochemical or electrochemical conditions for polymer synthesis and polymer up-cycling remains underexplored. This thesis investigates eco-friendly manganese- and ruthenium-catalyzed methods for C–H functionalizations, polymer synthesis, and polymer up-cycling under mild photochemical and electrochemical conditions, utilizing potentially renewable energy sources and avoiding hazardous reagents. A key achievement is the development of a manganese-catalyzed C–H alkylation using a transient directing group (TDG) approach, enabling the intramolecular C–H alkylation of indoles. Furthermore, a photo-induced ruthenium-catalyzed C–H arylation polymerization (CHAP) with high functional group tolerance and novel electrochemical methods for polymer up-cycling were developed. Additionally, manganese-electrocatalyzed C–H azidation was applied to a broad range of commodity polymers and post-consumer plastic waste, preserving polymer integrity while achieving significant functionalization. The highly efficient 1,3-dipolar cycloaddition proved to convert the azido-decorated polymers effectively and enables the selective introduction of designated material properties by chemical design. Overall, this research showcases innovative C–H functionalization strategies using earth-abundant manganese and cost-effective ruthenium catalysts, emphasizing their potential for sustainable chemistry and effective plastic waste recycling.2026-09-2
Effects of the mask requirement on doctor-patient communication in patients with tumors in the oral and maxillofacial region
No full textUm die schnelle Ausbreitung von SARS-CoV-2 einzudämmen, war das verpflichtende Tragen eines Mund-Nasen-Schutzes während der COVID-19-Pandemie ein wesentlicher Bestandteil der Corona-Schutzmaßnahmen. Diese Maskenpflicht wurde immer wieder kontrovers diskutiert. Da ein Mund-Nasen-Schutz die untere Gesichtshälfte vollständig verdeckt, können emotionale und mimische Informationen verloren gehen. Die Auswirkungen eines Mund-Nasen-Schutzes auf die Arzt-Patienten-Kommunikation und insbesondere auf die klinische Empathie der Behandler sind bisher weitgehend unerforscht. Ziel der vorliegenden Dissertation war es herauszufinden, ob das Tragen eines Mund-Nasen-Schutzes durch die Behandler Auswirkungen auf die Arzt-Patienten-Kommunikation bei Patienten mit Tumoren im Mund-, Kiefer- und Gesichtsbereich hatte und inwiefern die empathische Wirkung der Behandler auf die Patienten beeinflusst wurde. Hierzu wurde eine Fall- Kontrollstudie mit insgesamt 161 Patienten im Rahmen der Tumorsprechstunde in der Abteilung für Mund-, Kiefer- und Gesichtschirurgie mithilfe eines Fragebogens durchgeführt. In der Fallgruppe trugen die Behandler während der gesamten Konsultation einen Mund-Nasen-Schutz, während dieser in der Kontrollgruppe nur bei der direkten klinischen Untersuchung der Patienten aus Gründen des Infektionsschutzes zum Einsatz kam. Kern des Fragebogens war der CARE-Measure, ein Instrument, welches sich weltweit zur Überprüfung der klinischen Empathie von Behandlern bewährt hat. Die aus dem CARE-Measure resultierenden mittleren CARE-Werte können in Bezug auf verschiedene Gruppen untereinander verglichen werden. Insgesamt gab es keinen signifikanten Unterschied zwischen den mittleren CARE-Werten der Fall- und Kontrollgruppe. Auch schwerwiegendere Tumorstadien oder eine Rezidivsituation führten zu keiner signifikanten Beeinflussung des mittleren CARE-Werts. Lediglich die „Bekanntheit eines Behandlers aus vorherigen Konsultationen“ führte zu einer signifikanten Beeinflussung. Patienten, welche ihren Behandler aus vorherigen Konsultationen schon sehr gut kannten, vergaben insgesamt bessere CARE-Werte in der Kontrollgruppe. Da auch zukünftig das Auftreten neuer Pandemien nicht ausgeschlossen ist, kann diese Dissertation einen kleinen Anteil an der Aufarbeitung der vergangenen COVID-19-Pandemie leisten.To contain the rapid spread of SARS-CoV-2, the mandatory wearing of face masks was a key component of COVID-19 safety measures during the pandemic. This mask mandate was repeatedly subject to controversial debate. As a face mask completely conceals the lower half of the face, emotional and facial expression information can be lost. The effects of a face mask on doctor-patient communication and in particular on the clinical empathy of the physician are still largely unexplored. The objective of this dissertation was to determine whether the use of a face mask by the physicians had an impact on doctor-patient communication in patients with tumors in the oral and maxillofacial region. Additionally, the study sought to ascertain to what extent the empathic effect of the physicians on the patients was influenced. For this purpose, a case-control study was conducted using a questionnaire during tumor consultations in the Department of Oral and Maxillofacial Surgery. The study involved a total of 161 patients. In the case group, physicians wore a face mask throughout the entire consultation. In the control group, the face mask was worn only during the direct clinical examination for infection control reasons. The core element of the questionnaire was the CARE Measure, a globally recognized tool for assessing physicians’ empathy. The mean CARE scores resulting from this measure can be used to compare different groups. Overall, there was no significant difference in mean CARE scores between the case and control groups. Neither more advanced tumor stages nor recurrence situations had a significant impact on the mean CARE score. The only factor that showed a significant influence was the “familiarity with the physician from previous consultations.” Patients who already knew their physician well from previous visits gave higher CARE scores in the control group. As the occurrence of new pandemics cannot be ruled out in the future, this dissertation can contribute a small part to the reappraisal of the past COVID-19 pandemic.2026-05-1
Computational Methods for Canonical and Noncanonical Peptide Identification in Immunopeptidomics
No full textThe presentation of peptides via the MHC-I pathway as signals to CD8+ T cells is an essential element of the adaptive immune system. Hence, effective identification of the peptides presented (i.e., the MHC-I immunopeptidome) advances basic science while having immediate translational application in medicine. From a basic science perspective, reliable identification of the MHC-I immunopeptidome sheds light on a fundamental pathway within the cell. The translational applications have been particularly highlighted by the recent Covid-19 pandemic, and the corresponding advances in mRNA-based vaccine delivery provide evidence for continued importance.
Immunopeptidome identification is typically achieved via mass spectrometry (MS). However, identification is significantly more challenging than in standard proteomic experiments, necessitating optimized computational solutions. This is the case even in the identification of canonical peptides (peptides that can be traced to the annotated proteome via standard cleavage of a given protein into peptide fragments). These challenges are further exacerbated when we seek to identify noncanonical peptides – sequences which are not found within the annotated proteome and may be produced by non-standard transcriptional, translational, or post-translational processing. These processes include translation of sections of the genome thought to be non-coding as well the phenomenon of proteasome catalyzed peptide splicing (PCPS).
The work presented in this thesis focusses on peptide identification with special focus on optimizing noncanonical peptide identification. We began by laying the foundations, by developing two software tools which were at the heart of all further analysis. Firstly, the iBench software allowed rigorous benchmarking of peptide identification tools, hence validating all further advances. The other foundational software is the inSPIRE tool. inSPIRE combines multiple advances in machine learning to provide highly sensitive identification of canonical peptides in the MHC-I immunopeptidome.
From this point, we moved quickly to application, firstly with noncanonical peptide identification in an in vitro setting. In our first application focused study, a modified version of inSPIRE was leveraged to identify peptides produced via PCPS (spliced peptides). This study was primarily focused on furthering our understanding of proteasomal function and the amino acid level preferences driving both cleavage and splicing events.
In a second application, the PEPSeek tool was developed to extract pathogen derived peptides from MHC-I immunopeptidomics experiments of pathogen infected cells. Again, PEPSeek leveraged inSPIRE for MS identification while also enabling quantitative analysis of immunopeptidomic changes brought about by pathogen infection. This study demonstrated translational value as peptides identifiable only via our software were found to trigger CD8+ T cell response for peptides from both SARS-CoV-2 and listeria monocytogenes. In this study, we also developed the interact-ms web server, further developed in later projects, which allowed the tools developed to be accessed by the wider scientific community.
Finally, in the cornerstone work of this thesis, we developed a new identification software (PISCES) for the identification of noncanonical peptides in the MHC-I immunopeptidome. This tool allowed reliable and sensitive identification of noncanonical peptides. Large scale application of this software enabled the first integrated analysis of the spliced and cryptic immunopeptidome. Further analysis revealed factors driving both spliced and cryptic peptide presentation. Strong correlation to our in vitro work speaks to the validity of our results in both studies. Thus, through the development of novel computational methods, we provide a reliable and more complete picture of the canonical and noncanonical immunopeptidome. Further analysis of these results provided biological and biochemical insights into the processes generating these peptides.
In conclusion, the work presented in this thesis (i) improves the sensitivity of standard canonical peptide identification, particularly in the MHC-I immunopeptidome, (ii) shows the translational relevance of the improvements presented, (iii) ensures that the advances are available to the wider scientific community, (iv) enable noncanonical peptide identification in the immunopeptidome, and (v) sheds light on the mechanisms behind noncanonical peptide generation.2026-04-1