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Stalk cell polar ion transport provide for bladder‐based salinity tolerance in Chenopodium quinoa
(2022)
Chenopodium quinoa uses epidermal bladder cells (EBCs) to sequester excess salt. Each EBC complex consists of a leaf epidermal cell, a stalk cell, and the bladder.
Under salt stress, sodium (Na\(^{+}\)), chloride (Cl\(^{−}\)), potassium (K\(^{+}\)) and various metabolites are shuttled from the leaf lamina to the bladders. Stalk cells operate as both a selectivity filter and a flux controller.
In line with the nature of a transfer cell, advanced transmission electron tomography, electrophysiology, and fluorescent tracer flux studies revealed the stalk cell’s polar organization and bladder‐directed solute flow.
RNA sequencing and cluster analysis revealed the gene expression profiles of the stalk cells. Among the stalk cell enriched genes, ion channels and carriers as well as sugar transporters were most pronounced. Based on their electrophysiological fingerprint and thermodynamic considerations, a model for stalk cell transcellular transport was derived.
Ein Weg, der von Rezeptor-Tyrosin-Kinasen benutzt wird um Signale auf "downstream" gelegene Effektormoleküle zu übertragen, erfolgt über Adaptorproteine, die Bindungsstellen für verschiedene Proteine zur Verfügung stellen. Das daughter of sevenless (dos) Gen wurde in einem Screen nach Downstream-Komponenten der Sevenless (Sev) Rezeptor-Tyrosin-Kinase gefunden. Dos besitzt eine N-terminale PH-Domäne und mehrere Tyrosinreste in Konsensussequenzen für SH2-Domänen Bindungsstellen von verschiedenen Proteinen. Die strukturellen Merkmale von Dos und Experimente, die zeigten, daß Tyrosine im Dos Protein nach der Aktivierung von Sev phosphoryliert werden, legen den Schluß nahe, daß Dos zur Familie der Multi-Adaptor-Proteine gehört. Zu dieser Familie werden die Insulin-Rezeptor-Substrat (IRS) Proteine, Gab1 und Gab2 gerechnet. In dieser Arbeit wurde ein monoklonaler Maus anti-Dos Antikörper etabliert. Das Epitop dieses Antikörpers liegt im Bereich der C-terminalen 416 Aminosäuren des Dos Proteins. Mittels Westernblot Analysen wurde für Dos ein Molekulargewicht von 115 kD ermittelt. Antikörperfärbungen von wildtypischen Augenimaginalscheiben dritter Larven zeigten, daß das Dos Protein in Zellen in und posterior der morphogenetischen Furche exprimiert wird und in diesen Zellen apikal lokalisiert ist. Zur Charakterisierung des homozygot letalen dosR31 Allels, wurde der genomische Bereich sequenziert und die erhaltenen Daten mit der cDNA Sequenz verglichen. Die so etablierte Aminosäuresequenz für das DosR31 Protein hat sechs Aminosäuresubstitutionen, die möglicherweise die Tertiärstruktur beeinflussen. Zusätzlich wurde ein Stopcodon in Position 463 der Aminosäuresequenz gefunden. Bei dosR31 handelt es sich um ein "loss of function" Allel, das nicht in der Lage ist, die normale Dos Funktion zu erfüllen. Um die funktionelle Rolle der potentiellen SH2-Domänen Bindungsstellen für die Dos Funktion in der Rezeptor-Tyrosin-Kinasen vermittelten Signaltransduktion zu untersuchen, wurden mutierte dos Transgene in Fliegen exprimiert. Die potentiellen Bindungsstellen für die SH2-Domänen des SH2/SH3 Adaptorproteins Shc, der PhospholipaseC-g (PLCg), der regulatorische Untereinheit der Phosphatidylinositol-3-Kinase (PI3Kinase) und der Corkscrew (Csw) Tyrosin Phosphatase wurden durch den Austausch des für die Bindung wichtigen Tyrosins gegen ein Phenylalanin mutiert. Die ektopische Expression der mutierten Konstrukte ohne Bindungsstellen für die Shc, PLCg und PI3Kinasen SH2-Domänen konnte in Abwesenheit von endogenem Dos die fehlende Dos Funktion während der Entwicklung vollständig ersetzen. Im Gegensatz dazu ist das Tyrosin 801 als nachgewiesene Bindungsstelle für Csw SH2-Domänen essentiell für die Funktion von Dos. Ektopische Expression von Transgene durch Hitzeschock kann zu phänotypischen Effekten führen, die nicht auf das Transgen zurückzuführen sind. Um dieses Problem zu umgehen wurde das endogene dos Enhancer/Promotor Element kloniert, damit die Funktion von mutierten Transgenen auch im endogenen Expressionsmuster untersucht werden konnte. Das klonierte genE-dos Minigen war in der Lage, den Verlust von endogenem Dos in dosR31 und dosP115 Tieren vollständig zu ersetzen und zeigte eine völlig wildtypische Expression in Augenimaginalscheiben. Zur Untersuchung, welche Rolle die mutierten SH2-Domänen Bindungsstellen bei der Dos Funktion in der Augenentwicklung spielen, wurde ein neues in vivo Testsystem basierend auf der Flp/FRT Flipase Rekombinase Technik etabliert. Dieses klonale Testsystem erlaubt die Expression mutierter Transgene unter der Kontrolle der dos Enhancer/Promotor Sequenzen in Klonen von Zellen, denen die endogene Dos Funktion fehlt. Die klonale Analyse der mutierten Konstrukte konnte zeigen, daß das Tyrosin 801, als Bindungsstelle für eine Csw SH2-Domäne, eine essentielle Rolle für die Dos Funktion spielt. Die Tyrosinreste in den potentiellen SH2-Domänen Bindungsstellen für Shc, PLCg und PI3Kinase spielen hingegen keine essentielle Rolle für die Dos Funktion bei der Augenentwicklung. Das etablierte klonale Testsystem kann allgemein zur Untersuchung der in vivo Funktion von potentiellen Protein-Protein Interaktionsregionen im Dos Protein bei der Augenentwicklung eingesetzt werden unabhängig von deren Erfordernis für andere Entwicklungsprozesse.
Nasal colonization is a major risk factor for S. aureus infections. The mechanisms responsible for colonization are still not well understood and involve several factors on the host and the bacterial side. One key factor is the cell wall teichoic acid (WTA) of S. aureus, which governs direct interactions with nasal epithelial surfaces. We report here the first receptor for the cell wall glycopolymer WTA on nasal epithelial cells. In several assay systems this type F-scavenger receptor, termed SREC-I, bound WTA in a charge dependent manner and mediated adhesion to nasal epithelial cells in vitro. The impact of WTA and SREC-I interaction on epithelial adhesion was especially pronounced under shear stress, which resembles the conditions found in the nasal cavity. Most importantly, we demonstrate here a key role of the WTA-receptor interaction in a cotton rat model of nasal colonization. When we inhibited WTA mediated adhesion with a SREC-I antibody, nasal colonization in the animal model was strongly reduced at the early onset of colonization. More importantly, colonization stayed low over an extended period of 6 days. Therefore we propose targeting of this glycopolymer-receptor interaction as a novel strategy to prevent or control S. aureus nasal colonization.
To improve and focus preclinical testing, we combine tumor models based on a decellularized tissue matrix with bioinformatics to stratify tumors according to stage-specific mutations that are linked to central cancer pathways. We generated tissue models with BRAF-mutant colorectal cancer (CRC) cells (HROC24 and HROC87) and compared treatment responses to two-dimensional (2D) cultures and xenografts. As the BRAF inhibitor vemurafenib is—in contrast to melanoma—not effective in CRC, we combined it with the EGFR inhibitor gefitinib. In general, our 3D models showed higher chemoresistance and in contrast to 2D a more active HGFR after gefitinib and combination-therapy. In xenograft models murine HGF could not activate the human HGFR, stressing the importance of the human microenvironment. In order to stratify patient groups for targeted treatment options in CRC, an in silico topology with different stages including mutations and changes in common signaling pathways was developed. We applied the established topology for in silico simulations to predict new therapeutic options for BRAF-mutated CRC patients in advanced stages. Our in silico tool connects genome information with a deeper understanding of tumor engines in clinically relevant signaling networks which goes beyond the consideration of single drivers to improve CRC patient stratification.
Galectin-1 (Gal-1) has been described to promote tumour growth by inducing angiogenesis and to contribute to the tumour immune escape. We had previously identified up-regulation of Gal-1 in preclinical models of aggressive neuroblastoma (NB), the most common extracranial tumour of childhood. While Gal-1 did not confer a survival advantage in the absence of exogenous stressors, Gal-1 contributed to enhanced cell migratory and invasive properties. Here, we review these findings and extend them by analyzing Gal-1 mediated effects on immune cell regulation and radiation resistance. In line with previous results, cell autonomous effects as well as paracrine functions contribute to Gal-1 mediated pro-tumourigenic functions. Interfering with Gal-1 functions in vivo will add to a better understanding of the role of the Gal-1 axis in the complex tumour-host interaction during immune-, chemo- and radiotherapy of neuroblastoma.
Yersinia enterocolitica subsp. palearctica serobiotype O:3/4 comprises about 80-90 % of all human patient isolates in Germany and Europe and is responsible for sporadic cases worldwide. Even though this serobiotype is low pathogenic, Y. enterocolitica subsp. palearctica serobiotype O:3/4 is involved in gastroenteritis, lymphadenitis and various extraintestinal sequelae as reactive arthritis. The main animal reservoir of this serobiotype are pigs, causing a high rate of O:3/4 contaminations of raw pork in butcher shops in Germany (e.g. Bavaria 25 %) and countries in north-east Europe. As Y. enterocolitica O:3/4 is geographically and phylogenetically distinct from the so far sequenced mouse-virulent O:8/1B strain, complete genome sequencing has been performed for the European serobiotype O:3/4 DSMZ reference strain Y11, which has been isolated from a patient stool. To gain greater insight into the Y. enterocolitica subspecies palearctica group, also draft genome sequences of two other human O:3/4 isolates (strains Y8265, patient isolate, and Y5307, patient isolate associated with reactive arthritis), a closely related Y. enterocolitica palearctica serobiotype O:5,27/3 (strain Y527P), and two biotype 1A strains (a nosocomial strain of serogroup O:5 and an environmental serogroup O:36 isolate) have been performed. Those strains were compared to the high-pathogenic Y. enterocolitica subsp. enterocolitica serobiotype O:8/1B strain 8081 to address the peculiarities of the strain Y11 and the Y. enterocolitica subspecies palearctica group. The main focus was to unravel the pathogenic potential of strain Y11 and thus to identify novel putative virulence genes and fitness factors, especially those that may constitute host specificity of serobiotype O:3/4. Y. enterocolitica subspecies palearctica serobiotype O:3/4 strains lack most of the mouse-virulence-associated determinants of Y. enterocolitica subsp. enterocolitica serotype O:8, for example the HPI, Yts1 type 2 and Ysa type three secretion systems. In comparison, serobiotype O:3/4 strains obviously acquired a different set of genes and genomic islands for virulence and fitness such as the Ysp type three secretion system, an RtxA-like putative toxin, insecticidal toxins and a functional PTS system for N-acetyl-galactosamine uptake, named aga-operon. The aga-operon is able to support the growth of the Y. enterocolitica subsp. enterocolitica O:8/1B on N-acetyl-galactosamine after transformation with the aga operon. Besides these genes, also two prophages, PhiYep-2 and PhiYep-3, and a asn tRNA-associated GIYep-01 genomic island might influence the Y. enterocolitica subsp. palearctica serobiotype O:3/4 pathoadaptation. The PhiYep-3 prophage and the GIYep-01 island show recombination activity and PhiYep-3 was not found in all O:3/4 strains of a small strain collection tested. Y. enterocolitica subsp. palearctica serobiotype O:5,27/3 strain Y527P was found to be closely related to all serobiotype O:3/4 strains, whereas the biotype 1A isolates have more mosaic-segmented genomes and share putative virulence genes both with serobiotypes O:8/1B and O:3/4, which implies their common descent. Besides the pYV virulence plasmid, biotype 1A strains lack classical virulence markers as the Ail adhesin, the YstA enterotoxin, and the virulence-associated protein C. Interestingly, there are no notable differences between the known virulence factors present in nosocomial and environmental strains, except the presence of a truncated Rtx toxin-like gene cluster and remnants of a P2-like prophage in the hospital serogroup O:5 isolate.
We have discovered a new mechanism of monoallelic gene expression that links antigenic variation, cell cycle, and development in the model parasite Trypanosoma brucei. African trypanosomes possess hundreds of variant surface glycoprotein (VSG) genes, but only one is expressed from a telomeric expression site (ES) at any given time. We found that the expression of a second VSG alone is sufficient to silence the active VSG gene and directionally attenuate the ES by disruptor of telomeric silencing-1B (DOT1B)-mediated histone methylation. Three conserved expression-site-associated genes (ESAGs) appear to serve as signal for ES attenuation. Their depletion causes G1-phase dormancy and reversible initiation of the slender-to-stumpy differentiation pathway. ES-attenuated slender bloodstream trypanosomes gain full developmental competence for transformation to the tsetse fly stage. This surprising connection between antigenic variation and developmental progression provides an unexpected point of attack against the deadly sleeping sickness.
Quantifying the spatio-temporal distribution of arthropods in tropical rainforests represents a first step towards scrutinizing the global distribution of biodiversity on Earth. To date most studies have focused on narrow taxonomic groups or lack a design that allows partitioning of the components of diversity. Here, we consider an exceptionally large dataset (113,952 individuals representing 5,858 species), obtained from the San Lorenzo forest in Panama, where the phylogenetic breadth of arthropod taxa was surveyed using 14 protocols targeting the soil, litter, understory, lower and upper canopy habitats, replicated across seasons in 2003 and 2004. This dataset is used to explore the relative influence of horizontal, vertical and seasonal drivers of arthropod distribution in this forest. We considered arthropod abundance, observed and estimated species richness, additive decomposition of species richness, multiplicative partitioning of species diversity, variation in species composition, species turnover and guild structure as components of diversity. At the scale of our study (2km of distance, 40m in height and 400 days), the effects related to the vertical and seasonal dimensions were most important. Most adult arthropods were collected from the soil/litter or the upper canopy and species richness was highest in the canopy. We compared the distribution of arthropods and trees within our study system. Effects related to the seasonal dimension were stronger for arthropods than for trees. We conclude that: (1) models of beta diversity developed for tropical trees are unlikely to be applicable to tropical arthropods; (2) it is imperative that estimates of global biodiversity derived from mass collecting of arthropods in tropical rainforests embrace the strong vertical and seasonal partitioning observed here; and (3) given the high species turnover observed between seasons, global climate change may have severe consequences for rainforest arthropods.
Like many other social insect societies, honeybees collectively share the resources they gather by feeding each other. These feeding contacts, known as trophallaxis, are regarded as the fundamental basis for social behavior in honeybees and other social insects for assuring the survival of the individual and the welfare of the group. In honeybees, where most of the trophallactic contacts are formed in the total darkness of the hive, the antennae play a decisive role in initiation and maintenance of the feeding contact, because they are sensitive to gustatory stimuli. The sequences of behaviors performed by the receiver bees at the beginning of a feeding contact includes the contact of one antenna with the mouthparts of a donor bee where the regurgitated food is located. The antennal motor action is characterized by behavioral asymmetry, which is novel among communicative motor actions in invertebrates. This preference of right over left antenna is without exception even after removal of the antennal flagellum. This case of laterality in basic social interaction might have its reason in the gustatory asymmetry in the antennae, because the right antenna turns out to be significantly more sensitive to stimulation with sugar water of various concentrations than the left one. Trophallactic contacts which guarantee a constant access to food for every individual in the hive are vitally important to the honeybee society, because honeybees are heterothermic insects which actively regulate their thoracic temperature. Even though the individual can regulate its body temperature, its heating performance is strictly limited by the amount of sugar ingested. The reason for this is that honeybees use mostly the glucose in their hemolymph as the energy substrate for muscular activity, and the heat producing flight muscles are among the metabolically most active tissues known. The fuel for their activity is honey; processed nectar with a sugar content of ~80% stored in the honeycomb. The results show that the sugar content of the ingested food correlates positively with the thoracic temperature of the honeybees even if they are caged and show no actual heating-related behavior as in brood warming or heating in the centre of the winter cluster. Honeybees actively regulate their brood temperature by heating to keep the temperature between 33 °C to 36 °C if ambient temperatures are lower. Heating rapidly depletes the worker’s internal energy; therefore the heating performance is limited by the honey that is ingested before the heating process. This study focused on the behavior and the thoracic temperature of the participants in trophallactic food exchanges on the brood comb. The brood area is the centre of heating activity in the hive, and therefore the region of highest energy demand. The results show that the recipients in a trophallactic food exchange have a higher thoracic temperature during feeding contacts than donors, and after the feeding contact the former engage in brood heating more often. The donor bees have lower thoracic temperature and shuttle constantly between honey stores and the brood comb, where they transfer the stored honey to heating bees. In addition, the results show a heat-triggered mechanism that enables donor and recipient to accomplish trophallactic contacts without delay in the total darkness of the hive in the brood area as the most energy consuming part of the hive. Providing heat-emitting workers with small doses of high performance fuel contributes to an economic distribution of resources consistent with the physiological conditions of the bees and the ecological requirements of the hive, resulting in a highly economical resource management system which might be one of the factors favouring the evolution of perennial bee colonies in temperate regions. The conclusion of these findings suggests a resource management strategy that has evolved from submissive placation behavior as it is seen in honeybees, bumblebees and other hymenopterans. The heat-triggered feedback mechanism behind the resource management of the honeybee´s thermoregulatory behavior reveals a new aspect of the division of labor and a new aspect of communication, and sheds new light on sociality in honeybees.
Trypanosoma brucei is an obligate parasite and causative agent of severe diseases affecting humans and livestock. The protist lives extracellularly in the bloodstream of the mammalian host, where it is prone to attacks by the host immune system. As a sophisticated means of defence against the immune response, the parasite’s surface is coated in a dense layer of the variant surface glycoprotein (VSG), that reduces identification of invariant epitopes on the cell surface by the immune system to levels that prevent host immunity. The VSG has to form a coat that is both dense and mobile, to shield invariant surface proteins from detection and to allow quick recycling of the protective coat during immune evasion. This coat effectively protects the parasite from the harsh environment that is the mammalian bloodstream and leads to a persistent parasitemia if the infection remains untreated. The available treatment against African Trypanosomiasis involves the use of drugs that are themselves severely toxic and that can lead to the death of the patient. Most of the drugs used as treatment were developed in the early-to-mid 20th century, and while developments continue, they still represent the best medical means to fight the parasite. The discovery of a fluorescent VSG gave rise to speculations about a potential interaction between the VSG coat and components of the surrounding medium, that could also lead to a new approach in the treatment of African Trypanosomiasis that involves the VSG coat. The initially observed fluorescence signal was specific for a combination of a VSG called VSG’Y’ and the triphenylmethane (TPM) dye phenol red. Exchanging this TPM to a bromo-derivative led to the observation of another fluorescence effect termed trypanicidal effect which killed the parasite independent of the expressed VSG and suggests a structurally conserved feature between VSGs that could function as a specific drug target against T. b. brucei. The work of this thesis aims to identify the mechanisms that govern the unique VSG’Y’ fluorescence and the trypanocidal effect. Fluorescence experiments and protein mutagenesis of VSG’Y’ as well as crystallographic trials with a range of different VSGs were utilized in the endeavour to identify the binding mechanisms between TPM compounds and VSGs, to find potentially conserved structural features between VSGs and to identify the working mechanisms of VSG fluorescence and the trypanocidal effect. These trials have the potential to lead to the formulation of highly specific drugs that
target the parasites VSG coat.
During the crystallographic trials of this thesis, the complete structure of a VSG was solved experimentally for the first time. This complete structure is a key component in furthering the understanding of the mechanisms governing VSG coat formation. X-ray scattering techniques, involving x-ray crystallography and small angle x-ray scattering were applied to elucidate the first complete VSG structures, which reveal high flexibility of the protein and supplies insight into the importance of this flexibility in the formation of a densely packed but highly mobile surface coat.
Background. Up to 75% of crop species benefit at least to some degree from animal pollination for fruit or seed set and yield. However, basic information on the level of pollinator dependence and pollinator contribution to yield is lacking for many crops. Even less is known about how insect pollination affects crop quality. Given that habitat loss and agricultural intensification are known to decrease pollinator richness and abundance, there is a need to assess the consequences for different components of crop production. Methods. We used pollination exclusion on flowers or inflorescences on a whole plant basis to assess the contribution of insect pollination to crop yield and quality in four flowering crops (spring oilseed rape, field bean, strawberry, and buckwheat) located in four regions of Europe. For each crop, we recorded abundance and species richness of flower visiting insects in ten fields located along a gradient from simple to heterogeneous landscapes. Results. Insect pollination enhanced average crop yield between 18 and 71% depending on the crop. Yield quality was also enhanced in most crops. For instance, oilseed rape had higher oil and lower chlorophyll contents when adequately pollinated, the proportion of empty seeds decreased in buckwheat, and strawberries' commercial grade improved; however, we did not find higher nitrogen content in open pollinated field beans. Complex landscapes had a higher overall species richness of wild pollinators across crops, but visitation rates were only higher in complex landscapes for some crops. On the contrary, the overall yield was consistently enhanced by higher visitation rates, but not by higher pollinator richness. Discussion. For the four crops in this study, there is clear benefit delivered by pollinators on yield quantity and/or quality, but it is not maximized under current agricultural intensification. Honeybees, the most abundant pollinator, might partially compensate the loss of wild pollinators in some areas, but our results suggest the need of landscape-scale actions to enhance wild pollinator populations.
Background:
Ketogenic diets (KDs) or short-term fasting are popular trends amongst supportive approaches for cancer patients. Beta-hydroxybutyrate (3-OHB) is the main physiological ketone body, whose concentration can reach plasma levels of 2–6 mM during KDs or fasting. The impact of 3-OHB on the biology of tumor cells described so far is contradictory. Therefore, we investigated the effect of a physiological concentration of 3 mM 3-OHB on metabolism, proliferation, and viability of breast cancer (BC) cells in vitro.
Methods:
Seven different human BC cell lines (BT20, BT474, HBL100, MCF-7, MDA-MB 231, MDA-MB 468, and T47D) were cultured in medium with 5 mM glucose in the presence of 3 mM 3-OHB at mild hypoxia (5% oxygen) or normoxia (21% oxygen). Metabolic profiling was performed by quantification of the turnover of glucose, lactate, and 3-OHB and by Seahorse metabolic flux analysis. Expression of key enzymes of ketolysis as well as the main monocarboxylic acid transporter MCT2 and the glucose-transporter GLUT1 was analyzed by RT-qPCR and Western blotting. The effect of 3-OHB on short- and long-term cell proliferation as well as chemo- and radiosensitivity were also analyzed.
Results:
3-OHB significantly changed the oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) in BT20 cells resulting in a more oxidative energetic phenotype. MCF-7 and MDA-MB 468 cells had increased ECAR only in response to 3-OHB, while the other three cell types remained uninfluenced. All cells expressed MCT2 and GLUT1, thus being able to uptake the metabolites. The consumption of 3-OHB was not strongly linked to mRNA overexpression of key enzymes of ketolysis and did not correlate with lactate production and glucose consumption. Neither 3-OHB nor acetoacetate did interfere with proliferation. Further, 3-OHB incubation did not modify the response of the tested BC cell lines to chemotherapy or radiation.
Conclusions:
We found that a physiological level of 3-OHB can change the energetic profile of some BC cell lines. However, 3-OHB failed to influence different biologic processes in these cells, e.g., cell proliferation and the response to common breast cancer chemotherapy and radiotherapy. Thus, we have no evidence that 3-OHB generally influences the biology of breast cancer cells in vitro.
The neurodegenerative disorder Alzheimer's disease (AD) is the cause of approximately 60% of the world's 35 million patients suffering from dementia. Current research focuses here are on association with other diseases such as diabetes type 2 (T2DM), possible genetic markers, specific signal transduction pathways within the brain and potential protein modification, because the pathogenesis and etiology of AD are still not fully understood. Specifically association of T2DM with AD came to the focus with the so-called "Rotterdam study" in 1999, indicating that T2DM doubles the risk of developing AD. In the meantime, it is known that the prevalence rate in patients with T2DM is 30%. Drugs commonly used in the treatment of T2DM such as peroxisome proliferator-activated receptors gamma (PPARγ) agonists show improvement of the cognitive abilities in patients with early stage of dementia, with potential therapeutically relevance. Therefore it is important not only to investigate a link between these diseases, but also to investigate the insulin signaling pathway in the brain of AD patients. In order to investigate this complex issue in more details and demonstrate additional links between T2DM and AD, the present study used several basic biological methods to clarify the question: "Is impaired insulin signaling pathway within the brain crucial for the development of AD?" from several points of view. The methods used in this work have been i) an analysis of single nucleotide (SNP) polymorphism of the insulin-degrading enzyme gene (IDE) in relation to risk of AD and / or of T2DM, ii) post-mortem histochemical studies of brain tissue of patients with only AD, with AD combined with T2DM and with only T2DM compared with an age-matched control group, and iii.) investigations of neurochemical pathways and gene/protein expression changes of a human cell culture as a consequences of amyloid β (Aβ) treatment. After analysis of the IDE SNP polymorphism in the selected VITA (Vienna Trans Danube Aging) cohort disease-specific effects were discovered. The upstream polymorphism (IDE2) was found to influence AD risk in a protective manner, while the downstream polymorphism (IDE7) modified the T2DM risk. Based on the SNP results, the presented study delineate the model that IDE promoter and 3‟ untranslated region/downstream variation can have different effects on IDE expression, maybe a relevant endophenotype with disorder-specific effects on AD and T2DM susceptibility. Furthermore, the human post-mortem studies could show that both AD as well as T2DM patients had a significantly lower density of the insulin receptor (IR) in the hippocampus, whereas a significantly increased density of inactive phosphorylated PPARγ has been found and this persisted even in patients with both diseases. Summarizing the histological study, it was possible to reveal common histological features of AD and T2DM, but no direct connection between the two diseases. Although AD is nowadays not only characterized by amyloid-containing plaque deposits and by the hyperphosphorylation of tau protein, the excessive Aβ42 presence in the brains of AD patients is still playing a key role. Up to date it is still not entirely clear which physical form of Aβ42 is responsible for the development of AD. The present work investigated, what impact has the state of aggregation of Aβ42 on genes and proteins of the insulin signaling pathway and the amyloid cascade. It could be shown that the oligomeric variant enhanced specifically the gene and protein expression of glycogen synthase kinase (GSK) 3β and also the enzyme activity was significantly increased, but has in turn strongly inhibited the IR gene and protein expression. Additionally, the effect of Aβ42 on monoamine oxidase B (MAO-B) was examined. An effect of both aggregated forms of Aβ42 had on enzyme activity was discovered. However, the fibrillar variants led to significantly increased activity of MAO-B while the oligomeric variants inhibited the enzyme activity. Several previous studies have demonstrated the involvement of increased MAO-B activity in AD, but the present work provides for the first time a direct link between the states of aggregation of Aβ42 to enzyme activity. Finally the results of the presented thesis can be summarized to following conclusion: Although AD and T2DM sharing some degrees of common features, still there is a lack of direct association, and therefore the diseases must be considered more independent rather than linked. But the impaired cerebral insulin signaling pathway seems to be another manifested hallmark of AD.
Study of the properties of channel-forming proteins of the cell walls of different Corynebacteriae
(2008)
The genus Corynebacterium belongs, together with Mycobacterium, Nocardia, Rhodococcus and further closely related genera, to the distinctive suprageneric taxon mycolata. Many species within this diverse group of mycolic acid containing actinomycetes are known either because of their medical or biotechnological relevance. For instance, Mycobacterium tuberculosis, Mycobacterium leprae, Corynebacterium diphtheriae and Nocardia farcinica, causer of most dangerous bacterial infectious diseases world-wide, are among this exceptional group of Gram-positive bacteria. Likewise of importance are some harmless mycolata species which find use in industrial settings. Corynebacterium glutamicum and Corynebacterium efficiens are, e.g., potent producers of the flavour enhancer glutamate and the animal feed additive lysine, while several Rhodococcus species are applied in the production of acrylic acids. The cell wall of mycolata species, compared with that of Gram-positive bacteria, exhibits an unusual composition and organization. Besides an arabinogalactan-peptidoglycan complex, the cell walls of most actinomycetes contain large amounts of mycolic acids. Comparable to the outer membrane of Gram-negative bacteria, these long-chained branched fatty acids form a highly impermeable hydrophobic outer layer which provides the basis of the exceptional drug resistance of mycolata species. Like the outer membrane of Gram-negative bacteria, the cell wall of mycolata contains channel-forming proteins that allow the passage of hydrophilic solutes. By permitting and controlling the exchange and communication between the interior of the cell and the environment in which the bacterium lives, the channels play an important role for the function of the bacterial cell envelope. This thesis aimed to extend our knowledge about cell wall channels in corynebacteria. For this purpose, we examined PorA and PorH proteins that have been associated by previous studies with cell wall pores in C. glutamicum, C. efficiens and Corynebacterium callunae in order to resolve unanswered questions and to gain structural knowledge. We also investigated cell walls of pathogenic corynebacteria, in particular of Corynebacterium diphtheriae and Corynebacterium jeikeium, to investigate if these species possessed channels as is the case with their harmless relatives. In this work we provided evidence for the existence of large and water-filled cell wall channels in C. diphtheriae and C. jeikeium. Moreover, we demonstrated that the major cell wall channels of C. glutamicum, C. efficiens and C. diphtheriae consist of two distinctive polypeptides; one of whom belongs to the class of PorH proteins and the other to the class of PorA proteins. This heteromeric structure of channels of corynebacteria represents a novelty for channels of the mycolata. In contrast, the C. jeikeium channel is solely constituted by a single protein, CjPorA, arranged as an oligomer. Although the molecular mass of this protein (4kDa) is comparable to those of PorH and PorA proteins (5-7 kDa), it shares no distinctive homology in its primary sequence with them. However, there is evidence for relationship between CjPorA and PorH/PorA proteins because the gene jk0268, coding for CjPorA, is localized in a chromosomal region of C. jeikeium that corresponds to the genomic region containing the porH/porA genes in the other corynebacteria. This suggests that jk0268 (coding for the homomeric cell wall channel in C. jeikeium) and the porH/porA genes of C. glutamicum, C. efficiens and C. diphtheriae (coding for heteromeric cell wall channels) are presumably descendants of a common ancestor gene. This assumption gets support from data on phylogenetic analysis of the genus Corynebacterium. Moreover, these data suggest that the here investigated cell wall channels are presumably widespread within this genus. A profound knowledge of cell wall channels, building the main passage of solutes through the outer mycolate membrane in corynebacteria and other members of the mycolata, can be of great economical and medical value.
Connecting lysosomes and mitochondria – a novel role for lipid metabolism in cancer cell death
(2019)
Background
The understanding of lysosomes has been expanded in recent research way beyond their view as cellular trash can. Lysosomes are pivotal in regulating metabolism, endocytosis and autophagy and are implicated in cancer. Recently it was discovered that the lysosomal V-ATPase, which is known to induce apoptosis, interferes with lipid metabolism in cancer, yet the interplay between these organelles is poorly understood.
Methods
LC-MS/MS analysis was performed to investigate lipid distribution in cells. Cell survival and signaling pathways were analyzed by means of cell biological methods (qPCR, Western Blot, flow cytometry, CellTiter-Blue). Mitochondrial structure was analyzed by confocal imaging and electron microscopy, their function was determined by flow cytometry and seahorse measurements.
Results
Our data reveal that interfering with lysosomal function changes composition and subcellular localization of triacylglycerids accompanied by an upregulation of PGC1α and PPARα expression, master regulators of energy and lipid metabolism. Furthermore, cardiolipin content is reduced driving mitochondria into fission, accompanied by a loss of membrane potential and reduction in oxidative capacity, which leads to a deregulation in cellular ROS and induction of mitochondria-driven apoptosis. Additionally, cells undergo a metabolic shift to glutamine dependency, correlated with the fission phenotype and sensitivity to lysosomal inhibition, most prominent in Ras mutated cells.
Conclusion
This study sheds mechanistic light on a largely uninvestigated triangle between lysosomes, lipid metabolism and mitochondrial function. Insight into this organelle crosstalk increases our understanding of mitochondria-driven cell death. Our findings furthermore provide a first hint on a connection of Ras pathway mutations and sensitivity towards lysosomal inhibitors.
Synaptophysin: a substrate for the protein tyrosine kinase pp60c-src in intact synaptic vesicles
(1990)
Expression of pp60 c-src, the first well defined proto-oncogene product, is developmentally regulated and tissue-specific, with neuronal tissues displaying high amounts of the c-src encoded pp60 c-src kinase activity. In the central nervous system pp60 s-src is preferentially expressed in regions characterized by a high content of grey matter and elevated density of nerve terminals. In this study we show for the first time a direct interaction between pp60 c-src and synaptophysin as a physiological target protein in neurons by demonstrating that endogenous pp60 c-src is able to phosphorylate synaptophysin (p38). p38 is a major constituent of the synaptic vesicle membrane protein and is thought to play a key role in the exocytosis of small synaptic vesicles and possibly small clear vesicles in neuroendocrine cells.
Activation of the pp60\(^{c-src}\) kinase during differentiation of monomyelocytic cells in vitro
(1986)
Tbe proto-oncogene c-src, the cellular homolog of the Rous sarcoma virus (RSV) transforming gene v-src, is expressed in a tissue-specific and age-dependent manner. Its physiological function, although still unknown, appears to be more closely related to differentiation processes than to proliferation processes. To obtain more information about the physiological role of the c-src gene in cells, we have studied differentiation-dependent alterations using the human HL-60 leukaemia cell line as a model system. Induction of monocytic and granulocytic differentiation of HL-60 cells by 12-0-tetradecanoylphorbol-13-acetate (TPA) and dimethylsulfoxide (DMSO) is associated with an activation of the pp60<sup>c-src</sup> tyrosine kinase, but not with increased c-src gene expression. Control experiments exclude an interaction of TPA and DMSO themselves with the pp60<sup>c-src</sup> kinase.
Characterization of motility and erythrocyte adherence as virulence factors in African trypanosomes
(2018)
Pathogens causing African animal trypanosomiasis (AAT), the major livestock disease in sub-Saharan Africa, belong to the salivarian group of the African trypanosomes, which are transmitted by the bite of the tsetse fly (Glossina spec.). T. vivax, T. congolense and T. brucei brucei are major pathogens of cattle in particular, causing nagana, with dramatic socio-economic consequences for the affected regions. The parasites additionally have a huge reservoir of other livestock and wild animal hosts. T. brucei, the species which also includes the subspecies pathogenic to humans causing sleeping sickness, has been extensively studied as the cultivatable model trypanosome. But less is known about the other salivarian species, which are not routinely held in culture, if at all possible. A hallmark of trypanosomal lifestyle is the protozoan flagellates incessant motility, which enables them to populate an enormous range of habitats in very diverse hosts. We were now able to characterize, for the first time with high spatiotemporal resolution microscopy, the swimming behaviour and mechanism of the most relevant salivarian species isolated directly from blood. We show the influence of viscosity on the motility of bloodstream form (BSF) cells and simulate their movement between erythrocytes, giving a clear picture of how all analyzed species move under varying environmental conditions. We show that although the basic mechanism of flagellar motility applies to all analyzed species, there are clear morphological differences that produce different reactions to the physical environment. We could define specific conditions for highly increased swimming persistence and speed for compared to the behaviour in standard culture. These results have important implications for the parasites survival strategies in the host, e.g. regarding the capacity for antibody clearance. Although we show all species to effectively remove antibodies from the cell surface, T. congolense differed markedly in its motility behaviour, which gives rise to interesting questions about this species behaviour in the bloodstream. Most of the T. congolense parasites (and to a lesser extent T. vivax) adhere to sheep erythrocytes. Further in vitro studies showed that T. congolense and T. vivax adhered to rabbit, goat, pig and cattle erythrocytes- but binding behaviour was absent in murine blood. Notably, both T. brucei and T. evansi lacked adherence to all studied host erythrocytes. Generally, attachment to blood cells caused reduction of swimming velocities. Judging from its cell architecture, as well as the motility studies in higher media viscosity and in micropillar arrays, T. congolense is not adapted to swim at high speeds in the mammalian bloodstream. Low swimming speeds could allow these purely intravascular parasites to remain bound to the host erythrocytes.
African trypanosomes thrive in the bloodstream and tissue spaces of a wide range of mammalian hosts. Infections of cattle cause an enormous socio-economic burden in sub-Saharan Africa. A hallmark of the trypanosome lifestyle is the flagellate’s incessant motion. This work details the cell motility behavior of the four livestock-parasites Trypanosoma vivax, T. brucei, T. evansi and T. congolense. The trypanosomes feature distinct swimming patterns, speeds and flagellar wave frequencies, although the basic mechanism of flagellar propulsion is conserved, as is shown by extended single flagellar beat analyses. Three-dimensional analyses of the trypanosomes expose a high degree of dynamic pleomorphism, typified by the ‘cellular waveform’. This is a product of the flagellar oscillation, the chirality of the flagellum attachment and the stiffness of the trypanosome cell body. The waveforms are characteristic for each trypanosome species and are influenced by changes of the microenvironment, such as differences in viscosity and the presence of confining obstacles. The distinct cellular waveforms may be reflective of the actual anatomical niches the parasites populate within their mammalian host. T. vivax displays waveforms optimally aligned to the topology of the bloodstream, while the two subspecies T. brucei and T. evansi feature distinct cellular waveforms, both additionally adapted to motion in more confined environments such as tissue spaces. T. congolense reveals a small and stiff waveform, which makes these parasites weak swimmers and destined for cell adherence in low flow areas of the circulation. Thus, our experiments show that the differential dissemination and annidation of trypanosomes in their mammalian hosts may depend on the distinct swimming capabilities of the parasites.
Cancer cells frequently escape from immune surveillance by down-regulating two important components of the immune defence: antigen-presenting MHC and costimulatory molecules. Therefore several novel anti-tumour compounds that aim to assist the immune system in recognising and fighting cancer are currently under development. Recombinant bispecific antibodies represent one group of such novel therapeutics. They target two different antigens and recruit cytotoxic effector cells to tumour cells. For cancer immunotherapy, bispecific T cell-engaging antibodies are already well characterised. These antibodies target a tumour-associated antigen and CD3ε, the constant molecule of the T cell receptor complex.
On the one hand, this study presents the development of a bispecific antibody targeting CD3ε and the rhabdomyosarcoma-associated fetal acetylcholine receptor. On the other hand, it describes a novel two-part trispecific antibody format for the treatment of leukaemia and other haematological malignancies in the context of haematopoietic stem cell transplantation (HSCT).
For HSCT, an HLA-identical donor is preferred, but very rarely available. In an HLA-mismatched setting, the HLA disparity could be exploited for targeted cancer treatment. In the present study, a two-part trispecific HLA-A2 × CD45 × CD3 antibody was developed for potential cases in which the patient is HLA-A2-positive, but the donor is not. This holds true for about half the cases in Germany, since HLA-A2 is the most common HLA molecule found here. Combinatorial targeting of HLA-A2 and the leucocyte-common antigen CD45 allows for highly specific dual-antigen restricted tumour targeting.
More precisely, two single-chain antibody constructs were developed: i) a single-chain variable fragment (scFv) specific for HLA-A2, and ii) a scFv against CD45, both linked to the VL and the VH domain of a CD3ε-specific antibody, respectively. It turned out that, after the concomitant binding of these constructs to the same HLA-A2- and CD45-expressing cell, the unpaired variable domains of a CD3ε-specific antibody assembled to a functional scFv. In a therapeutic situation, this assembly should exclusively occur on the recipient’s blood cancer cells, leading to T cell-mediated cancer cell destruction. In this way, a relapse of disease might be prevented, and standard therapy (radiation and chemotherapy) might be omitted.
For both approaches, the antibody constructs were periplasmically expressed in E. coli, purified via His tag, and biochemically characterised. Their binding to the respective targets was proven by flow cytometry. The stimulatory properties of the antibodies were assayed by measuring IL-2 release after incubation with T cells and antigen-expressing target cells. Both the bispecific antibody against rhabdomyosarcoma and the assembled trispecific antibody against blood cancer mediated T-cell activation in a concentration-dependent manner at nanomolar concentrations. For the trispecific antibody, this effect indeed proved to be dual antigen-restricted, as it could be blocked by prior incubation of either HLA-A2- or CD45-specific scFv and did not occur on single-positive (CD45+) or double-negative (HLA-A2- CD45-) target cells. Furthermore, antibodies from both approaches recruited T cells for tumour cell destruction in vitro.
Comparison of the central human and mouse platelet signaling cascade by systems biological analysis
(2020)
Background
Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is involved in major responses to exogenous factors. This is defined by systemsbiological pathway analysis as the central regulating signaling cascade of platelets (CC).
Results
The CC is systematically compared here between mouse and human and major differences were found. Genetic differences were analysed comparing orthologous human and mouse genes. We next analyzed different expression levels of mRNAs. Considering 4 mouse and 7 human high-quality proteome data sets, we identified then those major mRNA expression differences (81%) which were supported by proteome data. CC is conserved regarding genetic completeness, but we observed major differences in mRNA and protein levels between both species. Looking at central interactors, human PLCB2, MMP9, BDNF, ITPR3 and SLC25A6 (always Entrez notation) show absence in all murine datasets. CC interactors GNG12, PRKCE and ADCY9 occur only in mice. Looking at the common proteins, TLN1, CALM3, PRKCB, APP, SOD2 and TIMP1 are higher abundant in human, whereas RASGRP2, ITGB2, MYL9, EIF4EBP1, ADAM17, ARRB2, CD9 and ZYX are higher abundant in mouse. Pivotal kinase SRC shows different regulation on mRNA and protein level as well as ADP receptor P2RY12.
Conclusions
Our results highlight species-specific differences in platelet signaling and points of specific fine-tuning in human platelets as well as murine-specific signaling differences.
G-protein-coupled receptors (GPCRs) are hypothesized to possess molecular mobility over a wide temporal range. Until now the temporal range has not been fully accessible due to the crucially limited temporal range of available methods. This in turn, may lead relevant dynamic constants to remain masked. Here, we expand this dynamic range by combining fluorescent techniques using a spot confocal setup. We decipher mobility constants of β\(_{2}\)-adrenergic receptor over a wide time range (nanosecond to second). Particularly, a translational mobility (10 µm\(^{2}\)/s), one order of magnitude faster than membrane associated lateral mobility that explains membrane protein turnover and suggests a wider picture of the GPCR availability on the plasma membrane. And a so far elusive rotational mobility (1-200 µs) which depicts a previously overlooked dynamic component that, despite all complexity, behaves largely as predicted by the Saffman-Delbrück model.
The biosynthesis of ribosomes is a complex cellular process involving ribosomal RNA, ribosomal proteins and several further trans-acting factors. DExD/H box proteins constitute the largest family of trans-acting protein factors involved in this process. Several members of this protein family have been directly implicated in ribosome biogenesis in yeast. In trypanosomes, ribosome biogenesis differs in several features from the process described in yeast. Here, we have identified the DExD/H box helicase Hel66 as being involved in ribosome biogenesis. The protein is unique to Kinetoplastida, localises to the nucleolus and its depletion via RNAi caused a severe growth defect. Loss of the protein resulted in a decrease of global translation and accumulation of rRNA processing intermediates for both the small and large ribosomal subunits. Only a few factors involved in trypanosome rRNA biogenesis have been described so far and our findings contribute to gaining a more comprehensive picture of this essential process.
The variant surface glycoprotein (VSG) of African trypanosomes plays an essential role in protecting the parasites from host immune factors. These trypanosomes undergo antigenic variation resulting in the expression of a single VSG isoform out of a repertoire of around 2000 genes. The molecular mechanism central to the expression and regulation of the VSG is however not fully understood.
Gene expression in trypanosomes is unusual due to the absence of typical RNA polymerase II promoters and the polycistronic transcription of genes. The regulation of gene expression is therefore mainly post-transcriptional. Regulatory sequences, mostly present in the 3´ UTRs, often serve as key elements in the modulation of the levels of individual mRNAs. In T. brucei VSG genes, a 100 % conserved 16mer motif within the 3´ UTR has been shown to modulate the stability of VSG transcripts and hence their expression. As a stability-associated sequence element, the absence of nucleotide substitutions in the motif is however unusual. It was therefore hypothesised that the motif is involved in other essential roles/processes besides stability of the VSG transcripts.
In this study, it was demonstrated that the 100 % conservation of the 16mer motif is not essential for cell viability or for the maintenance of functional VSG protein levels. It was further shown that the intact motif in the active VSG 3´ UTR is neither required to promote VSG silencing during switching nor is it needed during differentiation from bloodstream forms to procyclic forms. Crosstalk between the VSG and procyclin genes during differentiation to the insect vector stage is also unaffected in cells with a mutated 16mer motif. Ectopic overexpression of a second VSG however requires the intact motif to trigger silencing and exchange of the active VSG, suggesting a role for the motif in transcriptional VSG switching. The 16mer motif therefore plays a dual role in VSG in situ switching and stability of VSG transcripts. The additional role of the 16mer in the essential process of antigenic variation appears to be the driving force for the 100 % conservation of this RNA motif.
A screen aimed at identifying candidate RNA-binding proteins interacting with the 16mer motif, led to the identification of a DExD/H box protein, Hel66. Although the protein did not appear to have a direct link to the 16mer regulation of VSG expression, the DExD/H family of proteins are important players in the process of ribosome biogenesis. This process is relatively understudied in trypanosomes and so this candidate was singled out for detailed characterisation, given that the 16mer story had reached a natural end point. Ribosome biogenesis is a major cellular process in eukaryotes involving ribosomal RNA, ribosomal proteins and several non-ribosomal trans-acting protein factors. The DExD/H box proteins are the most important trans-acting protein factors involved in the biosynthesis of ribosomes. Several DExD/H box proteins have been directly implicated in this process in yeast. In trypanosomes, very few of this family of proteins have been characterised and therefore little is known about the specific roles they play in RNA metabolism. Here, it was shown that Hel66 is involved in rRNA processing during ribosome biogenesis. Hel66 localises to the nucleolus and depleting the protein led to a severe growth defect. Loss of the protein also resulted in a reduced rate of global translation and accumulation of rRNA processing intermediates of both the small and large ribosomal subunits. Hel66 is therefore an essential nucleolar DExD/H protein involved in rRNA processing during ribosome biogenesis. As very few protein factors involved in the processing of rRNAs have been described in trypanosomes, this finding represents an important platform for future investigation of this topic.
Die Meiose ist eine besondere Art der Zellteilung, die während der Keimzellreifung stattfindet. Sie umfasst zwei aufeinander folgende Zellteilungen mit nur einer DNA-Repli-kationsrunde, wodurch aus einer diploiden Ausgangszelle vier haploide Gameten entstehen. In der ersten meiotischen Teilung werden die homologen Chromosomen miteinander rekombiniert und voneinander getrennt, in der Meiose II findet die Trennung der Schwesterchromatiden statt. Für den korrekten Ablauf dieser Prozesse musste sich eine spezielle molekulare Architektur des meiotischen Chromosoms entwickeln welche die Synapse der homologen Chromosomen durch den Synaptonemalkomplex (SC) beinhaltet. SCs sind evolutionär hochkonservierte, meiosespezifische Proteinkomplexe, die eine zentrale Bedeutung für Synapse, Rekombination und Segregation der homologen Chromosomen haben. Ein SC besteht aus zwei lateralen Elementen (LEs), die den Achsen der homologen Chromosomen aufgelagert sind, einer zentralen Region (CR) und einem zentralen Element (CE). Eine Hauptstrukturkomponente der LEs in Vertebraten ist das Synaptonemalkomplexprotein, SYCP3. Um die molekulare Architektur des SC besser zu verstehen und die Bedeutung von SYCP3 für die Zusammenlagerung der LE aufzudecken, wurden die Polymerisationseigenschaften von SYCP3, exprimiert in somatischen Zellen, erforscht. In diesem experimentellen Ansatz polymerisierte SYCP3 autonom zu stabilen, höher geordneten, filamentösen Strukturen. Die „Coiled-Coil“-Domäne und die flankierenden, evolutionär konservierten Motive sind dabei notwenig, und nach Deletion des weniger konservierten N-terminalen Bereichs auch ausreichend für die Bildung der höher geordneten Strukturen. Der N-Terminus hingegen spielt eine Rolle in der Stabilität der Polymärstrukturen, welche durch Phosphorylierung zweier Serinreste im N-terminalen Bereich beeinflusst werden könnte. Obwohl die Struktur des SC in der Evolution hochkonserviert ist, sind die Protein-komponenten auf Aminosäuresequenzebene sehr unterschiedlich und weisen wenn überhaupt eine strukturelle Homologie in ihrer Domänenorganisation auf. Um den SC-Aufbau und dessen Funktion besser verstehen zu können, wurden die orthologen SC-Proteine zwischen taxonomisch entfernten Spezies Ratte und Medaka verglichen. Es konnte gezeigt werden, dass trotz der Unterschiede in den Aminosäuresequenzen die sich in den letzen 450 Millionen Jahren zwischen Fisch- und Säugern-SYCP3 akkumuliert haben, die Eigenschaften der Proteine vergleichbar sind, und das sie unter experimentellen Bedingungen miteinander interagieren und zu höher geordneten Strukturen kopolymerisieren können.
Usher syndrome, the most prevalent cause of combined hereditary vision and hearing impairment, is clinically and genetically heterogeneous. Moreover, several conditions with phenotypes overlapping Usher syndrome have been described. This makes the molecular diagnosis of hereditary deaf-blindness challenging. Here, we performed exome sequencing and analysis on 7 Mexican and 52 Iranian probands with combined retinal degeneration and hearing impairment (without intellectual disability). Clinical assessment involved ophthalmological examination and hearing loss questionnaire. Usher syndrome, most frequently due to biallelic variants in MYO7A (USH1B in 16 probands), USH2A (17 probands), and ADGRV1 (USH2C in 7 probands), was diagnosed in 44 of 59 (75%) unrelated probands. Almost half of the identified variants were novel. Nine of 59 (15%) probands displayed other genetic entities with dual sensory impairment, including Alström syndrome (3 patients), cone-rod dystrophy and hearing loss 1 (2 probands), and Heimler syndrome (1 patient). Unexpected findings included one proband each with Scheie syndrome, coenzyme Q10 deficiency, and pseudoxanthoma elasticum. In four probands, including three Usher cases, dual sensory impairment was either modified/aggravated or caused by variants in distinct genes associated with retinal degeneration and/or hearing loss. The overall diagnostic yield of whole exome analysis in our deaf-blind cohort was 92%. Two (3%) probands were partially solved and only 3 (5%) remained without any molecular diagnosis. In many cases, the molecular diagnosis is important to guide genetic counseling, to support prognostic outcomes and decisions with currently available and evolving treatment modalities.
Quantifying tree defoliation by insects over large areas is a major challenge in forest management, but it is essential in ecosystem assessments of disturbance and resistance against herbivory. However, the trajectory from leaf-flush to insect defoliation to refoliation in broadleaf trees is highly variable. Its tracking requires high temporal- and spatial-resolution data, particularly in fragmented forests.
In a unique replicated field experiment manipulating gypsy moth Lymantria dispar densities in mixed-oak forests, we examined the utility of publicly accessible satellite-borne radar (Sentinel-1) to track the fine-scale temporal trajectory of defoliation. The ratio of backscatter intensity between two polarizations from radar data of the growing season constituted a canopy development index (CDI) and a normalized CDI (NCDI), which were validated by optical (Sentinel-2) and terrestrial laser scanning (TLS) data as well by intensive caterpillar sampling from canopy fogging.
The CDI and NCDI strongly correlated with optical and TLS data (Spearman's ρ = 0.79 and 0.84, respectively). The ΔNCDII\(_{Defoliation(A−C)}\) significantly explained caterpillar abundance (R\(^{2}\) = 0.52). The NCDI at critical timesteps and ΔNCDI related to defoliation and refoliation well discriminated between heavily and lightly defoliated forests.
We demonstrate that the high spatial and temporal resolution and the cloud independence of Sentinel-1 radar potentially enable spatially unrestricted measurements of the highly dynamic canopy herbivory. This can help monitor insect pests, improve the prediction of outbreaks and facilitate the monitoring of forest disturbance, one of the high priority Essential Biodiversity Variables, in the near future.
Aim: Despite increasing interest in β-diversity, that is the spatial and temporal turnover of species, the mechanisms underlying species turnover at different spatial scales are not fully understood, although they likely differ among different functional groups. We investigated the relative importance of dispersal limitations and the environmental filtering caused by vegetation for local, multi-taxa forest communities differing in their dispersal ability, trophic position and body size.
Location: Temperate forests in five regions across Germany.
Methods: In the inter-region analysis, the independent and shared effects of the regional spatial structure (regional species pool), landscape spatial structure (dispersal limitation) and environmental factors on species turnover were quantified with a 1-ha grain across 11 functional groups in up to 495 plots by variation partitioning. In the intra-region analysis, the relative importance of three environmental factors related to vegetation (herb and tree layer composition and forest physiognomy) and spatial structure for species turnover was determined.
Results: In the inter-region analysis, over half of the explained variation in community composition (23% of the total explained 35%) was explained by the shared effects of several factors, indicative of spatially structured environmental filtering. Among the independent effects, environmental factors were the strongest on average over 11 groups, but the importance of landscape spatial structure increased for less dispersive functional groups. In the intra-region analysis, the independent effect of plant species composition had a stronger influence on species turnover than forest physiognomy, but the relative importance of the latter increased with increasing trophic position and body size.
Main conclusions: Our study revealed that the mechanisms structuring assemblage composition are associated with the traits of functional groups. Hence, conservation frameworks targeting biodiversity of multiple groups should cover both environmental and biogeographical gradients. Within regions, forest management can enhance β-diversity particularly by diversifying tree species composition and forest physiognomy.
Formic acid is the main component of the ant’s major weapon against enemies. Being mainly used as a chemical defense, the acid is also exploited for recruitment and trail marking. The repelling effect of the organic acid is used by some mammals and birds which rub themselves in the acid to eliminate ectoparasites. Beekeepers across the world rely on this effect to control the parasitic mite Varroa destructor. Varroa mites are considered the most destructive pest of honey bees worldwide and can lead to the loss of entire colonies. Formic acid is highly effective against Varroa mites but can also kill the honeybee queen and worker brood. Whether formic acid can also affect the behavior of honey bees is unknown. We here study the effect of formic acid on sucrose responsiveness and cognition of honey bees treated at different live stages in field-relevant doses. Both behaviors are essential for survival of the honey bee colony. Rather unexpectedly, formic acid clearly improved the learning performance of the bees in appetitive olfactory conditioning, while not affecting sucrose responsiveness. This exciting side effect of formic acid certainly deserves further detailed investigations.
Drilus beetle larvae (Coleoptera: Elateridae) are specialized predators of land snails. Here, we describe various aspects of the predator-prey interactions between multiple Drilus species attacking multiple Albinaria (Gastropoda: Clausiliidae) species in Greece. We observe that Drilus species may be facultative or obligate Albinaria-specialists. We map geographically varying predation rates in Crete, where on average 24% of empty shells carry fatal Drilus bore holes. We also provide first-hand observations and video-footage of prey entry and exit strategies of the Drilus larvae, and evaluate the potential mutual evolutionary impacts. We find limited evidence for an effect of shell features and snail behavioral traits on inter-and intraspecifically differing predation rates. We also find that Drilus predators adjust their predation behavior based on specific shell traits of the prey. In conclusion, we suggest that, with these baseline data, this interesting predator-prey system will be available for further, detailed more evolutionary ecology studies.
We have studied the responses of honey bees at different life stages (Apis mellifera) to controlled infection with acute bee paralysis virus and have identified the haemolymph of infected larvae and adult worker bees as the compartment where massive propagation of ABPV occurs. Insects respond with a broad spectrum of induced innate immune reactions to bacterial infections, whereas defence mechanisms based on RNA interference play a major role in antiviral immunity. In this study, we have determined that honey bee larvae and adult workers do not produce a humoral immune reaction upon artificial infection with ABPV, in contrast to control individuals challenged with Escherichia coli. ABPV-infected bees produced neither elevated levels of specific antimicrobial peptides (AMPs), such as hymenoptaecin and defensin, nor any general antimicrobial activity, as revealed by inhibition-zone assays. Additionally, adult bees did not generate melanised nodules upon ABPV infection, an important cellular immune function activated by bacteria and viruses in some insects. Challenge of bees with both ABPV and E. coli showed that innate humoral and cellular immune reactions are induced in mixed infections, albeit at a reduced level.
Das angeborene Immunsystem von Insekten besteht aus einer humoralen Komponente, einer zellulären Komponente und dem Prophenoloxidase-aktivierenden System. Fast alle Erkenntnisse über das angeborene Immunsystem stammen von Arbeiten mit Modellorganismen wie z.B. Drosophila oder Anopheles gambiae. Wie genau das Immunsystem der Honigbiene (Apis mellifera) funktioniert, ist jedoch noch relativ unbekannt. In der vorliegenden Arbeit wurden die unterschiedlichen Immunreaktionen aller drei Entwicklungsstadien der Honigbiene nach artifizieller Infektion mit Gram-negativen und Gram-positiven Bakterien (Escherichia coli und Micrococcus flavus) und dem Akuten Bienen Paralyse Virus (ABPV) untersucht und verglichen. Eine E. coli-Injektion zeigt bei Larven und adulten Arbeiterinnen nur wenig Auswirkung auf das äußere Erscheinungsbild und die Überlebensrate. In beiden Entwicklungsstadien wird die humorale Immunantwort stark induziert, erkennbar an der Expression der antimikrobiellen Peptide (AMPs) Hymenoptaecin, Defensin1 und Abaecin. Zusätzlich werden allein in Jungbienen nach bakterieller Infektion vier weitere immunspezifische Proteine exprimiert. Unter anderem eine Carboxylesterase (CE1) und das Immune-Responsive Protein 30 (IRp30). Die Expression von CE1 und IRp30 zeigt dabei den gleichen zeitlichen Verlauf wie die der AMPs. In Jungbienen kommt es zudem nach E. coli-Injektion zu einer raschen Abnahme an lebenden Bakterien in der Hämolymphe, was auf eine Aktivierung der zellulären Immunantwort schließen lässt. Ältere Bienen und Winterbienen zeigen eine stärkere Immunkompetenz als Jungbienen. Selbst nicht-infizierte Winterbienen exprimieren geringe Mengen der immunspezifischen Proteine IRp30 und CE1. Die Expression von IRp30 kann dabei durch Verwundung oder Injektion von E. coli noch gesteigert werden. Eine weitere Besonderheit ist die im Vergleich zu Jungbienen raschere Abnahme an lebenden Bakterien in der Hämolymphe bis hin zur vollständigen Eliminierung. Die Reaktion von Puppen auf eine bakterielle Infektion war völlig unerwartet. Nach Injektion von E. coli-Zellen kommt es innerhalb von 24 h p.i. zu einem tödlichen Kollaps, der sich in einer Graufärbung des gesamten Puppenkörpers äußert. Da keine Expression von AMPs nachzuweisen war, wird die humorale Immunantwort offensichtlich nicht induziert. Auch die zelluläre Immunantwort scheint nicht aktiviert zu werden, denn es konnte keine Abnahme an lebenden E. coli-Zellen beobachtet werden. Aufgrund dieser fehlenden Immunreaktionen vermehrt sich E. coli im Hämocoel infizierter Puppen und scheint damit deren Tod herbeizuführen. Nach viraler Infektion wurden in allen drei Entwicklungsstadien der Honigbiene gänzlich andere Reaktionen beobachtet als nach bakterieller Infektion. Bei dem verwendeten Akuten Bienen Paralyse Virus (ABPV) handelt es sich um ein Picorna-ähnliches Virus, dessen Vermehrung in der Hämolymphe über die massive Synthese der Capsidproteine verfolgt werden kann. Eine Injektion von sehr wenigen ABPV-Partikeln ins Hämocoel hat dramatische Auswirkungen auf Larven. Nach Virusinjektion kommt es innerhalb weniger Stunden zu einer raschen Virusvermehrung und schon 24 h p.i. zum Tod, häufig begleitet von einer Schwarzfärbung der gesamten Larve. Kurz vor dem Ableben kommt es neben dem Abbau hochmolekularer Speicherproteine zur Expression zahlreicher Proteine, die u.a. an der Translation oder dem Schutz vor oxidativem Stress beteiligt sind. Auf Jungbienen hat eine ABPV-Infektion keine so dramatischen Auswirkungen wie auf Larven. Sie zeigen lediglich Zeichen von Paralyse, zudem überleben sie länger bei höheren injizierten Partikelzahlen, die Virusvermehrung ist langsamer und es kommt zu keiner starken Veränderung des Hämolymph-Proteinmusters. Es konnte gezeigt werden, dass es in ABPV-infizierten Larven oder adulten Bienen zu keiner erkennbaren Aktivierung des humoralen Immunsystems in Form von exprimierten AMPs kommt. Zudem scheint die humorale Immunantwort auch nicht unterdrückt zu werden, denn nach gleichzeitiger Injektion von E. coli und ABPV kommt es neben der Expression viraler Capsidproteine auch zur Expression von AMPs. Zusätzlich konnte in Jungbienen nach Infektion mit ABPV eine zelluläre Immunantwort in Form von Nodulation ausgeschlossen werden. Ältere Bienen scheinen nicht nur mit bakteriellen Infektionen, sondern auch mit einer ABPV-Infektion besser zurechtzukommen. Bei einer Menge an ABPV-Partikeln, die in Jungbienen spätestens 72 h p.i. zum Tod führt, ist in Winterbienen eine Virusvermehrung erst ab 96 h p.i. erkennbar und diese beeinträchtigt die Überlebensrate kaum. Puppen sind einer Virusinfektion genauso schutzlos ausgeliefert wie einer Bakterieninfektion. Es kommt zwar zu keiner starken Änderung des äußeren Erscheinungsbildes, jedoch bleiben Puppen in ihrer Entwicklung komplett stehen. Das Virus muss sich daher stark vermehren, allerdings nicht überwiegend - wie bei Larven und adulten Bienen - in der Hämolymphe.
Nucleic acid motifs consist of conserved and variable nucleotide regions. For functional action, several motifs are combined to modules. The tool AIModules allows identification of such motifs including combinations of them and conservation in several nucleic acid stretches. AIModules recognizes conserved motifs and combinations of motifs (modules) allowing a number of interesting biological applications such as analysis of promoter and transcription factor binding sites (TFBS), identification of conserved modules shared between several gene families, e.g. promoter regions, but also analysis of shared and conserved other DNA motifs such as enhancers and silencers, in mRNA (motifs or regulatory elements e.g. for polyadenylation) and lncRNAs. The tool AIModules presented here is an integrated solution for motif analysis, offered as a Web service as well as downloadable software. Several nucleotide sequences are queried for TFBSs using predefined matrices from the JASPAR DB or by using one’s own matrices for diverse types of DNA or RNA motif discovery. Furthermore, AIModules can find TFBSs common to two or more sequences. Demanding high or low conservation, AIModules outperforms other solutions in speed and finds more modules (specific combinations of TFBS) than alternative available software. The application also searches RNA motifs such as polyadenylation site or RNA–protein binding motifs as well as DNA motifs such as enhancers as well as user-specified motif combinations (https://bioinfo-wuerz.de/aimodules/; alternative entry pages: https://aimodules.heinzelab.de or https://www.biozentrum.uni-wuerzburg.de/bioinfo/computing/aimodules). The application is free and open source whether used online, on-site, or locally.
Die Regulation der Genexpression steht am Anfang vieler zellbiologischer Prozesse wie beispielsweise dem Zellwachstum oder der Differenzierung. Gene werden an Promotoren transkribiert, wobei ein Promotor selbst aus vielen logischen Einheiten aufgebaut ist, den Transkriptionsfaktorbindestellen (TFBSs). Diese können sehr nah beieinander liegen, aber auch weit entfernt voneinander sein. Sie werden spezifisch von Transkriptionsfaktoren (TFs) gebunden, die die Transkritptionsrate z.B. verstärken (Enhancer) oder schwächen (Silencer) können. Zwei oder mehr dieser TFBSs mit bestimmtem Abstand werden als "Module" zusammengefasst, die über Spezies hinweg konserviert sein können. Typischerweise findet man Module in Zellen mit einem Zellkern. Spezies mit gemeinsamen Modulen können ein Hinweis auf die gemeinsame phylogenetische Abstammung darstellen, aber auch gemeinsame Funktionsmechanismen von TFs über Gene hinweg aufdecken. Heutzutage sind verschiedene Anwendungen verfügbar, mit denen nach TFBSs in DNA gesucht werden kann. Zum Zeitpunkt des Verfassens dieser Arbeit sind aber nur zwei kommerzielle Produkte bekannt, die nicht nur TFBSs, sondern auch Module erkennen. Deshalb stellen wir hier die freie und quelloffene Lösung "AIModules" vor, die diese Lücke füllt und einen Webservice zur Verfügung stellt, der es erlaubt nach TFBSs sowie nach Modulen auf DNA- und auf RNA-Abschnitten zu suchen. Für die Motivesuche werden entweder Matrizen aus der Jaspar Datenbank oder Matrizen vom Anwender verwendet. Darüberhinaus zeigen wir, dass unser Tool für die TF Suche nur Sekunden benötigt, wohingegen conTraV3 mindestens eine Stunde für dieselbe Analyse braucht. Zusätzlich kann der Anwender bei unserem Tool den Grad der Konserviertheit für TFs mit angeben und wir zeigen, dass wir mit unserer Lösung, die die Jaspar Datenbank heranzieht, mehr Module finden, als ein kommerziell verfügbares Produkt. Weiterhin kann mit unserer Lösung auch auf RNA-Sequenzen nach regulatorischen Motiven gesucht werden, wenn der Anwender die dafür nötigen Matrizen liefert. Wir zeigen dies am Beispiel von Polyadenylierungsstellen. Zusammenfassend stellen wir ein Werkzeug vor, das erstens frei und quelloffen ist und zweitens entweder auf Servern veröffentlicht werden kann oder On-Site auf einem Notebook läuft. Unser Tool erlaubt es Promotoren zu analysieren und nach konservierten Modulen sowie TFBSs in Genfamilien sowie nach regulatorischen Elementen in mRNA wie z.B. Polyadenylierungsstellen oder andere regulatorische Elemente wie beispielsweise Enhancern oder Silencern in genomischer DNA zu suchen.
Die Identifikation der Bindungsspezifitäten von Proteininteraktionsdomänen und damit letztlich auch die Fähigkeit potentielle Bindungspartner dieser in vivo vorherzusagen bildet ein grundlegendes Element für das Verständnis der biologischen Funktionen dieser Domänen. In dieser Arbeit wurde untersucht, inwieweit solche Vorhersagen bezüglich der SH3-Domäne – als Beispiel für eine Proteininteraktionsdomäne – mithilfe von Support-Vector-Machines (SVMs) möglich sind, wenn diesen als Informationsquelle ausschließlich die innerhalb der Aminosäuresequenz der Domäne konservierten Informationen zur Verfügung stehen. Um den SVM-basierten Klassifikator zu trainieren und zu validieren, wurde ein Satz aus 51 SH3-Domänen verwendet, die zuvor entsprechend ihrer Ligandenpräferenz in ein System aus acht verschiedenen Klassen eingeteilt worden waren. Da die innerhalb der Aminosäuresequenzen konservierten Informationen in abstrakte Zahlenwerte konvertiert werden mussten (Voraussetzung für mathematisch basierte Klassifikatoren wie SVMs), wurde jede Aminosäuresequenz durch ihren jeweiligen Fisher-Score-Vektor ausgedrückt. Die Ergebnisse erbrachten einen Klassifikationserror, welcher weit unterhalb des Zufallsniveaus lag, was darauf hindeutet, dass sich die Bindungsspezifität (Klasse) einer SH3-Domäne in der Tat von seiner Aminosäuresequenz ableiten lassen dürfte. Mithilfe klassenspezifisch emittierter, artifizieller Sequenzen, implementiert in den Trainingsprozess des Klassifikators, um etwaigen nachteiligen Auswirkungen von Overfitting zu entgegenzuwirken, sowie durch Berücksichtigung taxonomischer Informationen des Klassensystems während Training und Validierung, ließ sich der Klassifikationserror sogar noch weiter senken und lag schließlich bei lediglich 35,29% (vergleiche Zufall: 7/8 = 87.50%). Auch die Nutzung von Feature Selections zur Abmilderung Overfitting-bedingter, negativer Effekte lieferte recht vielversprechende Ergebnisse, wenngleich ihr volles Potential aufgrund von Software-Beschränkungen nicht ausgenutzt werden konnte.
Die Analyse der Positionen im Sequence-Alignment, welche für den SVM- basierten Klassifikator am relevantesten waren, zeigte, dass diese häufig mit Positionen korrelierten, von denen angenommen wird auch in vivo eine Schlüsselrolle bei der Determination der Bindungsspezifität (Klasse) zu spielen. Dies unterstreicht nicht nur die Reliabilität des präsentierten Klassifikators, es gibt auch Grund zur Annahme, dass das Verfahren möglicherweise auch als Supplement anderer Ansätze genutzt werden könnte, welche zum Ziel haben die Positionen zu identifizieren, die die Ligandenpräferenz in vivo determinieren. Informationen, die nicht nur für ein besseres Verständnis der SH3-Domäne (und möglicherweise auch anderer Proteininteraktionsdomänen) von grundlegender Bedeutung sind, sondern auch aus pharmakologischer Sicht von großem Interesse sein dürften.
Copy number variations (CNVs) of the KITLG gene seem to be involved in the oncogenesis of digital squamous cell carcinoma (dSCC). The aims of this study were (1) to investigate KITLG CNV in giant (GS), standard (SS), and miniature (MS) schnauzers and (2) to compare KITLG CNV between black GS with and without dSCC. Blood samples from black GS (22 with and 17 without dSCC), black SS (18 with and 4 without dSSC; 5 unknown), and 50 MS (unknown dSSC status and coat colour) were analysed by digital droplet PCR. The results are that (1) most dogs had a copy number (CN) value > 4 (range 2.5–7.6) with no significant differences between GS, SS, and MS, and (2) the CN value in black GS with dSCC was significantly higher than in those without dSCC (p = 0.02). CN values > 5.8 indicate a significantly increased risk for dSCC, while CN values < 4.7 suggest a reduced risk for dSCC (grey area: 4.7–5.8). Diagnostic testing for KITLG CNV may sensitise owners to the individual risk of their black GS for dSCC. Further studies should investigate the relevance of KITLG CNV in SS and the protective effects in MS, who rarely suffer from dSCC.
The interaction of synaptic proteins orchestrate the function of one of the most complex organs, the brain. The multitude of molecular elements influencing neurological correlations makes imaging processes complicated since conventional fluorescence microscopy methods are unable to resolve structures beyond the diffraction-limit.
The implementation of super-resolution fluorescence microscopy into the field of neuroscience allows the visualisation of the fine details of neural connectivity. The key element of my thesis is the super-resolution technique dSTORM (direct Stochastic Optical Reconstruction Microscopy) and its optimisation as a multi-colour approach. Capturing more than one target, I aim to unravel the distribution of synaptic proteins with nanometer precision and set them into a structural and quantitative context with one another. Therefore dSTORM specific protocols are optimized to serve the peculiarities of particular neural samples.
In one project the brain derived neurotrophic factor (BDNF) is investigated in primary, hippocampal neurons. With a precision beyond 15 nm, preand post-synaptic sites can be identified by staining the active zone proteins bassoon and homer. As a result, hallmarks of mature synapses can be exhibited. The single molecule sensitivity of dSTORM enables the measurement of endogenous BDNF and locates BDNF granules aligned with glutamatergic pre-synapses. This data proofs that hippocampal neurons are capable of enriching BDNF within the mature glutamatergic pre-synapse, possibly influencing synaptic plasticity.
The distribution of the metabotropic glutamate receptor mGlu4 is investigated in physiological brain slices enabling the analysis of the receptor in its natural environment. With dual-colour dSTORM, the spatial arrangement of the mGlu4 receptor in the pre-synaptic sites of parallel fibres in the molecular layer of the mouse cerebellum is visualized, as well as a four to six-fold increase in the density of the receptor in the active zone compared to the nearby environment. Prior functional measurements show that metabotropic glutamate receptors influence voltage-gated calcium channels and proteins that are involved in synaptic vesicle priming. Corresponding dSTORM data indeed suggests that a subset of the mGlu4 receptor is correlated with the voltage-gated calcium channel Cav2.1 on distances around 60 nm.
These results are based on the improvement of the direct analysis of localisation data. Tools like coordinated based correlation analysis and nearest neighbour analysis of clusters centroids are used complementary to map protein connections of the synapse. Limits and possible improvements of these tools are discussed to foster the quantitative analysis of single molecule localisation microscopy data.
Performing super-resolution microscopy on complex samples like brain slices benefits from a maximised field of view in combination with the visualisation of more than two targets to set the protein of interest in a cellular context. This challenge served as a motivation to establish a workflow for correlated structured illumination microscopy (SIM) and dSTORM. The development of the visualisation software coSIdSTORM promotes the combination of these powerful super-resolution techniques even on separated setups. As an example, synapses in the cerebellum that are affiliated to the parallel fibres and the dendrites of the Purkinje cells are identified by SIM and the protein bassoon of those pre-synapses is visualised threedimensionally with nanoscopic precision by dSTORM.
In this work I placed emphasis on the improvement of multi-colour super-resolution imaging and its analysing tools to enable the investigation of synaptic proteins. The unravelling of the structural arrangement of investigated proteins supports the building of a synapse model and therefore helps to understand the relation between structure and function in neural transmission processes.
Chlamydia trachomatis is the main cause of sexually transmitted diseases worldwide. As obligate intracellular bacteria Chlamydia replicate in a membrane bound vacuole called inclusion and acquire nutrients for growth and replication from their host cells. However, like all intracellular bacteria, Chlamydia have to prevent eradication by the host's cell autonomous system. The chlamydial deubiquitinase Cdu1 is secreted into the inclusion membrane, facing the host cell cytosol where it deubiquitinates cellular proteins. Here we show that inactivation of Cdu1 causes a growth defect of C. trachomatis in primary cells. Moreover, ubiquitin and several autophagy receptors are recruited to the inclusion membrane of Cdu1‐deficient Chlamydia . Interestingly, the growth defect of cdu1 mutants is not rescued when autophagy is prevented. We find reduced recruitment of Golgi vesicles to the inclusion of Cdu1 mutants indicating that vesicular trafficking is altered in bacteria without active deubiquitinase (DUB). Our work elucidates an important role of Cdu1 in the functional preservation of the chlamydial inclusion surface.
The human pathogen Chlamydia trachomatis is the main cause of sexually transmitted infections worldwide. The obligate intracellular bacteria are the causative agent of several diseases that reach from conjunctivitis causing trachoma and blindness as well as salpingitis and urethritis which can lead to infertility if left untreated.
In order to gain genetically engineered Chlamydia that inducible knock down specific gene expression, the CRISPRi system was established in C. trachomatis. In a proof of principle experiment it was shown that C. trachomatis pCRISPRi:gCdu1III target ChlaDUB1 expression and reduce the protein amount up to 50 %. Knock-down of the DUB did not influence protein levels of anti-apoptotic Mcl-1 and did not make cells susceptible for apoptosis. However, reduced dCas9 protein size, bacterial growth impairment and off target effects interfering with the GFP signal, form obstacles in CRISPRi system in Chlamydia. For routinely use of the CRISPRi method in C. trachomatis further investigation is needed.
Since the bacterial life cycle includes two morphological and functional distinct forms, it is essential for chlamydial spread to complete the development cycle and form infectious progeny. Therefore, Chlamydia has evolved strategies to evade the host immune system in order to stay undetected throughout the developmental cycle. The bacteria prevent host cell apoptosis via stabilization of anti-apoptotic proteins like Mcl-1, Survivin and HIF-1α and activate pro-survival pathways, inhibiting invasion of immune cells to the site of infection. The host cell itself can destroy intruders via cell specific defense systems that involve autophagy and recruitment of professional immune cells. In this thesis the role of the chlamydial deubiuqitinase ChlaDUB1 upon immune evasion was elucidated. With the mutant strain Ctr Tn-cdu1 that encodes for a truncated DUB due to transposon insertion, it was possible to identify ChlaDUB1 as a potent opponent of the autophagic system. Mutant inclusions were targeted by K48 and K63 chain ubiquitination. Subsequently the inclusion was recognized by autophagic receptors like p62, NBR1 and NDP52 that was reversed again by complementation with the active DUB. Xenophagy was promoted so far as LC3 positive phagosomes formed around the inclusion of Ctr Tn-cdu1, which did not fuse with the lysosome. The detected growth defect in human primary cells of Chlamydia missing the active DUB was not traced back to autophagy, but was due to impaired development and replication. It was possible to identify Ankib1, the E3 ligase, that ubiquitinates the chlamydial inclusion in a siRNA based screen. The activating enzyme Ube1 and the conjugating enzyme Ube2L3 are also essential in this process. Chlamydia have a reduced genome and depend on lipids and nutrients that are translocated from the host cell to the inclusion to proliferate. Recruitment of fragmented Golgi stacks to the inclusion surface was prevented when ChlaDUB1 was inactive, probably causing diminished bacterial growth. Additionally, the modification of the inclusion by Ankib1 and subsequent decoration by autophagic markers was not only present in human but also murine cells. Comparison of other Chlamydia strains and species revealed Ankib1 to be located at the proximity of the inclusion in C. trachomatis strains only but not in C. muridarum or C. pneumoniae, indicating that Ankib1 is specifically the E3 ligase of C. trachomatis. Moreover, the role of ChlaDUB1 in infected tissue was of interest, since ChlaDUB1 protein was also found in early EB stage and so might get in contact with invading immune cells after cell lysis. While bacteria spread and infect new host cells, Chlamydia can also infect immune cells. Infection of human neutrophils with Ctr Tn-cdu1 shows less bacterial survival and affirms the importance of the DUB for bacterial fitness in these cells.
Stapylococcus aureus colonises the nose of healthy individuals but can also cause a wide range of infections. Amino acid (AA) synthesis and their availability is crucial to adapt to conditions encountered in vivo. Most S. aureus genomes comprise all genes required for AA biosynthesis. Nevertheless, different strains require specific sets of AAs for growth. In this study we show that regulation inactivates pathways under certain conditions which result in these observed auxotrophies. We analyzed in vitro and modeled in silico in a Boolean semiquantitative model (195 nodes, 320 edges) the regulatory impact of stringent response (SR) on AA requirement in S. aureus HG001 (wild-type) and in mutant strains lacking the metabolic regulators RSH, CodY and CcpA, respectively. Growth in medium lacking single AAs was analyzed. Results correlated qualitatively to the in silico predictions of the final model in 92% and quantitatively in 81%. Remaining gaps in our knowledge are evaluated and discussed. This in silico model is made fully available and explains how integration of different inputs is achieved in SR and AA metabolism of S. aureus. The in vitro data and in silico modeling stress the role of SR and central regulators such as CodY for AA metabolisms in S. aureus.
Animals acquire predictive values of sensory stimuli through reinforcement. In the brain of Drosophila melanogaster, activation of two types of dopamine neurons in the PAM and PPL1 clusters has been shown to induce aversive odor memory. Here, we identified the third cell type and characterized aversive memories induced by these dopamine neurons. These three dopamine pathways all project to the mushroom body but terminate in the spatially segregated subdomains. To understand the functional difference of these dopamine pathways in electric shock reinforcement, we blocked each one of them during memory acquisition. We found that all three pathways partially contribute to electric shock memory. Notably, the memories mediated by these neurons differed in temporal stability. Furthermore, combinatorial activation of two of these pathways revealed significant interaction of individual memory components rather than their simple summation. These results cast light on a cellular mechanism by which a noxious event induces different dopamine signals to a single brain structure to synthesize an aversive memory.
This thesis consists of three major chapters, each of which has been separately published or under the process for publication. The first chapter is about anatomical characterization of the mushroom body of adult Drosophila melanogaster. The mushroom body is the center for olfactory learning and many other functions in the insect brains. The functions of the mushroom body have been studied by utilizing the GAL4/UAS gene expression system. The present study characterized the expression patterns of the commonly used GAL4 drivers for the mushroom body intrinsic neurons, Kenyon cells. Thereby, we revealed the numerical composition of the different types of Kenyon cells and found one subtype of the Kenyon cells that have not been described. The second and third chapters together demonstrate that the multiple types of dopaminergic neurons mediate the aversive reinforcement signals to the mushroom body. They induce the parallel memory traces that constitute the different temporal domains of the aversive odor memory. In prior to these chapters, “General introduction and discussion” section reviews and discuss about the current understanding of neuronal circuit for olfactory learning in Drosophila.
The human gut is home for thousands of microbes that are important for human life. As most of these cannot be cultivated, metagenomics is an important means to understand this important community. To perform comparative metagenomic analysis of the human gut microbiome, I have developed SMASH (Simple metagenomic analysis shell), a computational pipeline. SMASH can also be used to assemble and analyze single genomes, and has been successfully applied to the bacterium Mycoplasma pneumoniae and the fungus Chaetomium thermophilum. In the context of the MetaHIT (Metagenomics of the human intestinal tract) consortium our group is participating in, I used SMASH to validate the assembly and to estimate the assembly error rate of 576.7 Gb metagenome sequence obtained using Illumina Solexa technology from fecal DNA of 124 European individuals. I also estimated the completeness of the gene catalogue containing 3.3 million open reading frames obtained from these metagenomes. Finally, I used SMASH to analyze human gut metagenomes of 39 individuals from 6 countries encompassing a wide range of host properties such as age, body mass index and disease states. We find that the variation in the gut microbiome is not continuous but stratified into enterotypes. Enterotypes are complex host-microbial symbiotic states that are not explained by host properties, nutritional habits or possible technical biases. The concept of enterotypes might have far reaching implications, for example, to explain different responses to diet or drug intake. We also find several functional markers in the human gut microbiome that correlate with a number of host properties such as body mass index, highlighting the need for functional analysis and raising hopes for the application of microbial markers as diagnostic or even prognostic tools for microbiota-associated human disorders.
African trypanosomes are unicellular parasites that cause nagana and sleeping sickness in livestock and man, respectively. The major pathogens for the animal disease include Trypanosoma vivax, T. congolense, and T. brucei brucei, whereas T. b. gambiense and T. b. rhodesiense are responsible for human infections. Given that the bloodstream form (BSF) of African trypanosomes is exclusively extracellular, its cell surface forms a critical boundary with the host environment. The cell surface of the BSF African trypanosomes is covered by a dense coat of immunogenic variant surface glycoproteins (VSGs). This surface protein acts as an impenetrable shield that protects the cells from host immune factors and is also involved in antibody clearance and antigenic variation, which collectively ensure that the parasite stays ahead of the host immune system. Gene expression in T. brucei is markedly different from other eukaryotes: most genes are transcribed as long polycistronic units, processed by trans-splicing a 39-nucleotide mini exon at the 5′ and polyadenylation at the 3′ ends of individual genes to generate the mature mRNA.
Therefore, gene expression in T. brucei is regulated post-transcriptionally, mainly by the action of RNA binding proteins (RBPs) and conserved elements in the 3′ untranslated regions (UTR) of transcripts. The expression of VSGs is highly regulated, and only a single VSG gene is expressed at a time from one of the ~15 subtelomeric domains termed bloodstream expression sites (BES). When cells are engineered to simultaneously express two VSGs, the total VSG mRNA do not exceed the wild type amounts. This suggests that a robust VSG mRNA balancing mechanism exists in T. brucei. The present study uses inducible and constitutive expression of ectopic VSG genes to show that the endogenous VSG mRNA is regulated only if the second VSG is properly targeted to the ER. Additionally, the endogenous VSG mRNA response is triggered when high amounts of the GFP reporter with a VSG 3′UTR is targeted to the ER. Further evidence that non-VSG ER import signals can efficiently target VSGs to the ER is presented. This study suggests that a robust trans-regulation of the VSG mRNA is elicited at the ER through a feedback loop to keep the VSG transcripts in check and avoid overshooting the secretory pathway capacity.
Further, it was shown that induction of expression of the T. vivax VSG ILDat1.2 in T. brucei causes a dual cell cycle arrest, with concomitant upregulation of the protein associated with differentiation (PAD1) expression. It could be shown that T. vivax VSG ILDat1.2 can only be sufficiently expressed in T. brucei after replacing its native GPI signal peptide with that of a T. brucei VSG. Taken together, these data indicate that inefficient VSG GPI anchoring and expression of low levels of the VSG protein can trigger differentiation from slender BSF to stumpy forms. However, a second T. vivax VSG, ILDat2.1, is not expressed in T. brucei even after similar modifications to its GPI signals. An X-ray crystallography approach was utilized to solve the N-terminal domain (NTD) structure of VSG ILDat1.2. This is first structure of a non-T. brucei VSG, and the first of a surface protein of T. vivax to be solved. VSG ILDat1.2 NTD maintains the three-helical bundle scaffold conserved in T. brucei surface proteins. However, it is likely that there are variations in the architecture of the membrane proximal region of the ILDat1.2 NTD and its CTD from T. brucei VSGs. The tractable T. brucei system is presented as a model that can be used to study surface proteins of related trypanosome species, thus creating avenues for further characterization of trypanosome surface coats.
Nucleotide sequence of the cloned mRNA and gene of the ADP/ATP carrier from Neurospora crassa
(1984)
A cDNA complementary to the mRNA of the ADPIATP carrier from Neurospora crassa was identified among ordered cDNA clones by hybridizing total polyadenylated RNA to pools of 96 cDNA recombinant plasmids and subsequent cellfree translation of hybridization-selected mRNA. Further carrier cDNAs were found by colony fdter hybridization at a frequency of 0.2-0.3%. The gene of the carrier was cloned and isolated on a 4.6-kbp EcoRl fragment of total Neurospora DNA, and the start of the mRNA was determined by Sl nuclease mapping. From the nucleotide sequence of the cDNA and the genomic DNA, the primary structure of the gene, of the mRNA and of the ADP I ATP carrier protein could be deduced. The gene occurs in a single copy in the genome and related genes are absent. It contains two short introns, and a pyrimidine-rieb promoter region. The mRNA has a 46-bp 5 1 end and a 219-bp 3 1 end. There is an open reading frame coding for the 313 amino acid residues of the Neurospora carrier protein. The amino acid sequence is homologous in 148 positions with the established primary structure of the beef heart carrier.