Generation of Epstein-Barr Virus-specific T Cell Receptorengineered T Cells for Cancer Treatment

Die adoptive T-Zell-Therapie (ATT) ist eine sich schnell entwickelnde Immuntherapie, die bei Patienten, die an verschiedenen Krebsarten leiden, eine positive klinische Reaktion anzeigt. Eine Variante der ATT ist eine T-Zellen-Rezeptor (TCR)-Gentherapie, bei der Patienten-T-Zellen mit krebsspezifischen TCRs ausgestattet werden. Die Herstellung der TCR-erzeugten T-Zellen ist schnell und robust und erfordert eine geringe Anfangsmenge an Patienten-T-Zellen. Der Mangel an verfügbaren krebsspezifischen TCRs, die auf verschiedene Moleküle des menschlichen Leukozytenantigens (HLA) der Klasse I beschränkt sind, schließt jedoch viele Patienten von der Krebsbehandlung aus. Die Generierung einer krebsspezifischen TCR-Bibliothek, die aus gut definierten TCRs besteht, könnte die Zahl der Patienten, die an klinischen Studien teilnehmen, erhöhen. Das Ziel dieser Doktorarbeit war es, Epstein-Barr-Virus (EBV)-spezifische TCRs zu identifizieren und zu isolieren, um eine EBV-spezifische TCR-Bibliothek als ein nützliches Werkzeug der TCR-Gentherapie bei der Behandlung von EBV-bedingten Krebserkrankungen zu generieren. Insgesamt wurden neun EBV-spezifische TCRs von EBV-positiven Spendern isoliert und charakterisiert, die verschiedene pHLA-Komplexe von EBV-Latentmembranproteinen (LMP1, LMP2A) und Kernprotein (EBNA3C) erkannten. Zusätzlich wurde ein neuartiges immunogenes LMP1-Epitop (QQNWWTLLV) entdeckt, das auf HLA-C*15:02 beschränkt ist. Definierte EBV-spezifische TCRs können als Grundlage für die EBV-spezifische TCR-Bibliothek verwendet werden, die eine wertvolle Quelle von TCRs für die schnelle Generierung von EBV-spezifischen T-Zellen zur Behandlung von Krebspatienten mit verschiedenen HLA-Typen darstellt.Adoptive T cell therapy (ATT) is a fast developing immunotherapy indicating positive clinical response in patients suffering from different type of cancers. One type of the ATT is a T cell receptor (TCR) gene therapy, which involves endowing patient T cells with cancer-specific TCRs. Manufacturing of the TCR-engineered T cells is fast and robust, requiring small initial amount of patient T cells. However, lack of available cancer-specific TCRs restricted to various human leukocyte antigen (HLA) class I molecules eliminates many patients from cancer treatment. Generation of a cancer-specific TCR library consisting of well-defined TCRs could increase the number of patients enrolled in clinical trials. The aim of this PhD thesis was to identify and isolate Epstein-Barr virus (EBV)-specific TCRs in order to generate the EBV-specific TCR library as a useful tool of the TCR gene therapy for treatment of EBV-related malignancies. In total, nine EBV-specific TCRs of EBV-positive donors that recognized various pHLA complexes of EBV latent membrane proteins (LMP1, LMP2A) and nuclear protein (EBNA3C) were isolated and characterized. Additionally, a novel immunogenic LMP1 epitope (QQNWWTLLV) restricted to a HLA-C*15:02 was discovered. Defined EBV-specific TCRs can be used as a basis for the EBV-specific TCR library, which provides a valuable source of TCRs for rapid generation of EBV-specific T cells to treat cancer patients with different HLA types

Habitat associations of the Coastal Giant Salamander (Dicamptodon Tenebrosus) at its northern range limit

Knowledge of species-environment associations is critical for the management of threatened amphibian populations facing habitat fragmentation and a restricted range. The Coastal Giant Salamander (Dicamptodon tenebrosus) is subject to habitat degradation from logging and human development and is classified as Threatened at its northern range limit in British Columbia, Canada. We examined habitat associations for D. tenebrosus in relation to relative abundance and presence/absence for 32 streams sampled across the approximately 100 km range of the species in British Columbia. Of 12 environmental variables we measured at 100-m stream reaches and the adjacent riparian zone, D. tenebrosus relative abundance was positively associated with stream elevation, forest age, and the percentage of boulders within streams. A higher stream gradient was the best predictor of D. tenebrosus presence within a stream reach, with present sites having a 91% higher gradient than absent sites. When excluding sites with low relative abundance, D. tenebrosus presence was also predicted by greater forest age surrounding streams and higher site elevation. Our study highlights that conservation planning for stream-associated amphibians with patchy distributions may be improved by an understanding of species-specific habitat associations at the stream-reach scale

Taxonomic Shifts in <em>Philornis</em> Larval Behaviour and Rapid Changes in <em>Philornis downsi</em> Dodge & Aitken (Diptera: Muscidae): An Invasive Avian Parasite on the Galápagos Islands

The parasitic larvae of Philornis downsi Dodge & Aitken (Diptera: Muscidae) were first discovered in Darwin’s finch nests on the Galápagos Islands in 1997. Larvae of P. downsi consume the blood and tissue of developing birds, causing high in-nest mortality in their Galápagos hosts. The fly has been spreading across the archipelago and is considered the biggest threat to the survival of Galápagos land birds. Here, we review (1) Philornis systematics and taxonomy, (2) discuss shifts in feeding habits across Philornis species comparing basal to more recently evolved groups, (3) report on differences in the ontogeny of wild and captive P. downsi larvae, (4) describe what is known about adult P. downsi behaviour, and (5) discuss changes in P. downsi behaviour since its discovery on the Galápagos Islands. From 1997 to 2010, P. downsi larvae have been rarely detected in Darwin’s finch nests with eggs. Since 2012, P. downsi larvae have regularly been found in the nests of incubating Darwin’s finches. Exploring P. downsi ontogeny and behaviour in the larger context of taxonomic relationships provides clues about the breadth of behavioural flexibility that may facilitate successful colonisation

Do group dynamics affect colour morph clines during a range shift?

Funded by Strategic Research Area Biodiversity and Ecosystem Services in a Changing Climate (BECC) Lund and Gothenburg Universities Wenner-Gren Foundation EU FP7 Swedish Research Council Royal Swedish Academy of Sciences (KVA) Stiftelsen Anna-Greta and Holger Crafoords Fund Crafoord FoundationPeer reviewedPostprin

Signatures of local adaptation along environmental gradients in a range-expanding damselfly (Ischnura elegans)

ACKNOWLEDGEMENTSThis work was supported by an EU FP7, Marie Curie International Incoming Fellowship (to RYD; project code “MOVE2ADAPT”), a Wenner-Gren Foundation Postdoctoral Stipend (to RYD), the Oscar and Lili Lamm Foundation (to RYD, BH), Biodiversity and Ecosystem Services in a Changing Climate (BECC; a joint Lund–Gothenburg University initiative) (LL), the Swedish Research Council (EIS, BH),the Crafoord Foundation (EIS, BH) and Erik Philip-Sorensens Stiftelse (E.I.S.). We would like to thank Hanna Bensch and Paul Caplat for assistance with the collection of samples in the field and the Grimso Research Station and Mikael Akesson for logistical support. Wethank Pallavi Chauhan for assistance with SNP annotation. We thank Martin Andersson for assistance with DNA extraction, Jane Jonssonfor laboratory administration, and Julian Catchen, Martin Stervander, Dag Ahren and Maren Wellenreuther for bioinformatics advice and helpful discussion.Peer reviewedPostprin

Latitudinal clines in sexual selection, sexual size dimorphism, and sex-specific genetic dispersal during a poleward range expansion

Acknowledgements This work was supported by Macquarie University (to AC, RYD), an EU FP7, Marie Curie International Incoming Fellowship (to RYD, BH; project code ‘MOVE2ADAPT’), a WennerGren Foundation Postdoctoral Stipend (to RYD, BH), the Oscar and Lili Lamm Foundation (to RYD, BH), Biodiversity and Ecosystem Services in a Changing Climate (BECC; a joint LundGothenburg University initiative) (to LL, BH), the Swedish Research Council (to EIS, BH (2014-5222, 2016-689)), the Crafoord Foundation, “Stina Werners Stiftelse” and “Erik Philip Sörensens Stiftelse” (to EIS). We thank Hanna Bensch, John Waller, Paul Caplat and Martin Andersson for field and lab assistance, the Grimsö Research Station and Mikael Åkesson for field support and Sonu Yadav for analysis advice. We thank Julian Catchen, Martin Stervander and Dag Ahren for bioinformatics advice and Maren Wellenreuther for helpful discussion.Peer reviewedPostprin

Baseline and stress-induced blood properties of male and female Darwin’s small ground finch (Geospiza fuliginosa) of the Galapagos Islands

© 2017 Elsevier. This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/Birds are renowned for exhibiting marked sex-specific differences in activity levels and reproductive investment during the breeding season, potentially impacting circulating blood parameters associated with stress and energetics. Males of many passerines often do not incubate, but they experience direct exposure to intruder threat and exhibit aggressive behaviour during the nesting phase in order to defend territories against competing males and predators. Nesting females often have long bouts of inactivity during incubation, but they must remain vigilant of the risks posed by predators and conspecific intruders approaching the nest. Here, we use 33 free-living male (n = 16) and female (n = 17) Darwin's small ground finches (Geospiza fuliginosa) on Floreana Island (Galapagos Archipelago) to better understand how sex-specific roles during the reproductive period impact baseline and stress-induced levels of plasma corticosterone (CORT), blood glucose and haematocrit. Specifically, we hypothesise that males are characterised by higher baseline values given their direct and relatively frequent exposure to intruder threat, but that a standardised stress event (capture and holding) overrides any sex-specific differences. In contrast with expectations, baseline levels of all blood parameters were similar between sexes (13.4 ± 1.9 ng ml−1 for CORT, 13.7 ± 0.4 mmol l−1 for glucose, 58.3 ± 0.8% for haematocrit). Interestingly, females with higher body condition had lower baseline haematocrit. All blood parameters changed with time since capture (range 1.2–41.3 min) in both sexes, whereby CORT increased linearly, haematocrit decreased linearly, and glucose increased to a peak at ∼20 min post-capture and declined to baseline levels thereafter. Our results do not support the hypothesis that sex-specific roles during the reproductive period translate to differences in blood parameters associated with stress and energetics, but we found some evidence that blood oxygen transport capacity may decline as finches increase in body condition

Genomic divergence and a lack of recent introgression between commercial and wild bumblebees (Bombus terrestris)

The global movement of bees for agricultural pollination services can affect local pollinator populations via hybridization. When commercial bumblebees are of the same species but of different geographic origin, intraspecific hybridization may result in beneficial integration of new genetic variation, or alternatively may disrupt locally adapted gene complexes. However, neither the existence nor the extent of genomic introgression and evolutionary divergence between wild and commercial bumblebees is fully understood. We obtained whole-genome sequencing data from wild and commercial Bombus terrestris collected from sites in Southern Sweden with and without long-term use of commercially imported B. terrestris. We search for evidence of introgression, dispersal and genome-wide differentiation in a comparative genomic analysis of wild and commercial bumblebees. Commercial B. terrestris were found in natural environments near sites where commercial bumblebees were used, as well as drifting wild B. terrestris in commercial bumblebee colonies. However, we found no evidence for widespread, recent genomic introgression of commercial B. terrestris into local wild conspecific populations. We found that wild B. terrestris had significantly higher nucleotide diversity (Nei's pi, pi), while the number of segregating sites (Watterson's theta, theta w) was higher in commercial B. terrestris. A highly divergent region on chromosome 11 was identified in commercial B. terrestris and found to be enriched with structural variants. The genes present in this region are involved in flight muscle contraction and structure and pathogen immune response, providing evidence for differing evolutionary processes operating in wild and commercial B. terrestris. We did not find evidence for recent introgression, suggesting that co-occurring commercial B. terrestris have not disrupted evolutionary processes in wild B. terrestris populations