T cell receptor modification by alpha and beta chain domain cross-over for adoptive T cell therapy

Adoptive T cell transfer is a novel approach for cancer treatment in which patient’s T lymphocytes are extracted and genetically modified to redirect these against the cancer cell. However, there are still a number of risks and limitations to this approach. One is the formation of autoreactive T cell: The antigen-recognizing part of the T cell receptor is a dimer of an α- and a β-chain. Accordingly, transduced T cells can express ‘mispaired’ T cell receptors that comprise a native and an exogenous chain. These heterodimers can cause autoimmunity if they target self-antigens. The aim of this study was to investigate a novel approach against mispairing by transferring either the variable or the constant domain of one chain across to the other chain. This concept is already successfully employed in the design of bispecific antibodies to avoid mispairing and may be transferable due to a high degree of homology between T cell receptors and antibodies. The transduction of crossed receptors into murine T cells did not result in any surface expression. We observed an intracellular accumulation of α-chains. After a redesign eliminating an interference with the linker sequence, we found a temporary surface expression of α-chains in one of our constructs. However, when transducing only the single chain, we could not detect surface expression. We concluded that, while undetectable, the β-chain must be expressed when transducing with the bicistronic vector and that the crossed T cell receptor assembles correctly with the CD3 subunits. Finally, we aimed at stabilizing surface expression of the crossed receptor. We added an additional disulfide bond between both chains at different locations and changed the exact location of the domain cross-over in the so-called elbow region, which links the variable and the constant domain of each chain. Yet, a sustained surface expression of crossed T cell receptors could not be achieved. Alternative strategies are thus needed to prevent TCR mispairing.Adoptiver T-Zelltransfer ist ein Therapieverfahren, bei dem Patienten-eigene T-Lymphozyten mit einem tumorspezifischen Rezeptor transduziert werden, um eine anti-tumorale Aktivität zu induzieren Trotz vieler Fortschritte birgt dieses Verfahren auch Risiken. Eines ist die Bildung autoreaktiver T-Zellen: Die Erkennungsdomäne des T-Zellrezeptors ist ein Dimer aus α- und β-Kette. Daher kann, durch Hinzufügen eines zweiten T-Zellrezeptors in eine T-Zelle, ein weiteres Dimer aus einer nativen und einer exogenen Kette entstehen. Ein solcher, fehlgepaarter (’mispaired’) Rezeptor kann potenziell neue Antigene erkennen und Autoimmunreaktionen auslösen. Gegenstand der vorliegenden Arbeit ist es eine neuartige T-Zellrezeptormodifikation zum Unterbinden von Mispairing zu untersuchen. Dazu vertauschten wir die konstante oder die variable Domäne zwischen den Ketten (’domain crossover’). Dieses Prinzip wird bereits erfolgreich beim Design von bispezifischen Antikörpern eingesetzt, um Mispairing zu vermeiden und könnte sich dank großer Homologie auf T-Zellrezeptoren übertragen lassen. Bei Transduktion der gekreuzten Rezeptorketten in murine T-Zellen, stellten wir zunächst keine Oberflächenexpression, jedoch eine intrazellulä̈re Akkumulation von gekreuzten α-Ketten fest. Nach Beseitigung einer Interferenz durch die Linkersequenz stellte sich eine temporäre Oberfä̈chenexpression der α-Kette des gekreuzten Rezeptors ein. Transduzierten wir jedoch nur eine einzelne Kette, so war keine Oberflächenexpression nachweisbar. Wir folgerten, dass auch die grundsätzlich nicht mehr detektierbare β-Kette exprimiert wird und sich gekreuzten Ketten erfolgreich mit CD3 Untereinheiten zusammensetzen. Um eine stabile Oberflächenexpression zu ermöglichen, fügten wir Disulfidbrücken ein und veranderten die genaue Kreuzungsstelle innerhalb der Ellbogenregion, welche die variable und konstante Domäne verbindet. Es ließ sich jedoch keine dauerhafte Oberflächenexpression erzielen. Somit sind andere Strategien erforderlich um Mispairing zu verhindern oder zu reduzieren

On the Complexity of Reconstructing Chemical Reaction Networks

The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network properties are typically made on standard graphs derived from the full hypergraph description, e.g.\ on the so-called species and reaction graphs. However, a reconstruction of the underlying hypergraph from these graphs is not necessarily unique. In this paper, we address the problem of reconstructing a hypergraph from its species and reaction graph and show NP-completeness of the problem in its Boolean formulation. Furthermore we study the problem empirically on random and real world instances in order to investigate its computational limits in practice

Robust Tests on Fractional Cointegration

Cointegration describes the pattern that pairs of time series keep together in long run, although they diverge in short run. A generalisation of this behaviour is the fractional cointegration. Two statistical tests, the M– and ML–test are formulated for fractional cointegration in different situations. It turns out that the robust M–test reaches almost the same power as the maximum likelihood test under certain assumptions. In contrast to this, the power of the M–test is much higher than that of the ML–test if the examined time series is contaminated following the general replacement model

Introduction: Special Issue ‘Complexity and Truth’

If not even earlier, then at the latest when Oxford Dictionaries selected ‘post-truth’ as Word of the Year 2016, did the global public become aware that ‘truth’ is not an uncontested and finite concept but a social construct. Are we, then, standing on the threshold of a new ‘post-truth age’ as – for instance – The Independent has claimed? (Norman 2016) Certainly, the Word of the Year 2016 has cast a bright light onto the case that there is not ‘one truth only’ but that there are facts that can be interpreted – or rejected – in different ways. This means that truth is ‘produced’, but is it produced as scientific or religious truth or as political truth? Just think of `fake news´ and its strategic use in influencing elections, as in the case of the latest presidential elections in the US or Brazil, or the leave campaign in the case of the Brexit referendum. Thus, the production of truth is undertaken by society, at least on the level of concrete actions. This situation becomes more complicated if we consider modern complex society. The increasing globalization of economies and societies has made the world more complex than it has ever before been

Low-cost Sensor Glove with Force Feedback for Learning from Demonstrations using Probabilistic Trajectory Representations

Sensor gloves are popular input devices for a large variety of applications including health monitoring, control of music instruments, learning sign language, dexterous computer interfaces, and tele-operating robot hands. Many commercial products as well as low-cost open source projects have been developed. We discuss here how low-cost (approx. 250 EUROs) sensor gloves with force feedback can be build, provide an open source software interface for Matlab and present first results in learning object manipulation skills through imitation learning on the humanoid robot iCub.Comment: 3 pages, 3 figures. Workshop paper of the International Conference on Robotics and Automation (ICRA 2015

Motivations, concerns and selection biases when posting preprints: A survey of bioRxiv authors

Since 2013, the usage of preprints as a means of sharing research in biology has rapidly grown, in particular via the preprint server bioRxiv. Recent studies have found that journal articles that were previously posted to bioRxiv received a higher number of citations or mentions/shares on other online platforms compared to articles in the same journals that were not posted. However, the exact causal mechanism for this effect has not been established, and may in part be related to authors' biases in the selection of articles that are chosen to be posted as preprints. We aimed to investigate this mechanism by conducting a mixed-methods survey of 1,444 authors of bioRxiv preprints, to investigate the reasons that they post or do not post certain articles as preprints, and to make comparisons between articles they choose to post and not post as preprints. We find that authors are most strongly motivated to post preprints to increase awareness of their work and increase the speed of its dissemination; conversely, the strongest reasons for not posting preprints centre around a lack of awareness of preprints and reluctance to publicly post work that has not undergone a peer review process. We additionally find evidence that authors do not consider quality, novelty or significance when posting or not posting research as preprints, however, authors retain an expectation that articles they post as preprints will receive more citations or be shared more widely online than articles not posted.Seit 2013 hat die Nutzung von Preprints als Mittel zur Verbreitung von Forschungsergebnissen in der Biologie stark zugenommen, insbesondere über den Preprint-Server bioRxiv. Jüngste Studien haben ergeben, dass Zeitschriftenartikel, die zuvor auf bioRxiv veröffentlicht wurden, auf anderen Online-Plattformen häufiger zitiert oder erwähnt/geteilt wurden als Artikel derselben Zeitschriften, die nicht veröffentlicht wurden. Der genaue kausale Mechanismus für diesen Effekt ist jedoch nicht geklärt und könnte zum Teil mit der Voreingenommenheit der Autor*innen bei der Auswahl der Artikel, die als Preprints veröffentlicht werden, zusammenhängen. Die Autor*innen wollten diesen Mechanismus untersuchen, indem sie eine mixed-methods-Umfrage unter 1.444 Autor*innen von bioRxiv-Preprints durchführten, um die Gründe zu untersuchen, aus denen sie bestimmte Artikel als Preprints veröffentlichen oder nicht veröffentlichen, und um Vergleiche zwischen Artikeln anzustellen, die sie als Preprints veröffentlichen oder nicht veröffentlichen. Sie stellen fest, dass Autor*innen am stärksten motiviert sind, Preprints zu veröffentlichen, um den Bekanntheitsgrad ihrer Arbeit zu erhöhen und deren Verbreitung zu beschleunigen. Umgekehrt liegen die stärksten Gründe für die Nichtveröffentlichung von Preprints in der mangelnden Bekanntheit von Preprints und der Abneigung, eine Arbeit zu veröffentlichen, die keinen Peer-Review-Prozess durchlaufen hat