Virus oncogeni a dna in tumori umani: studio delle infezioni da papillomavirus e poliomavirus in neoplasie di diversa origine.

I virus tumorali inducono oncogenesi nel loro ospite naturale o in sistemi animali sperimentali, manipolando diverse vie cellulari. Ad oggi, sono stati identificati sette virus capaci di causare specifici tumori umani. Inoltre HPV, JCV ed SV40, sono stati associati con un grande numero di tumori umani in sedi corporee non convenzionali, ma, nonostante molti anni di ricerca, nessuna eziologia virale è stata ancora confermata. Lo scopo di questo studio è stato di valutare la presenza ed il significato sia di JCV ed SV40 in tumori ossei umani, e di HPV nel carcinoma della mammella (BC), galattoforectomie (GF), secrezioni mammarie patologiche (ND) e glioblastoma multiforme (GBM). Tecniche di biologia molecolare sono state impiegate per esaminare campioni di tessuto tumorale di 70 tumori ossei (20 osteosarcomi [OS], 20 tumori a cellule giganti [TCG], 30 condrosarcomi [CS]), 168 BCs , 30 GFs, 59 GBM e 30 campioni di ND. Il genoma di SV40 e JCV è stato trovato nel 70% dei CS + 20% degli OS, e nel 13% dei CS +10% dei TCG, rispettivamente. Il DNA di HPV è stato rilevato nel 30% dei pazienti con BC, nel 27% dei campioni GF e nel 13% dei NDs. HPV16 è stato il genotipo maggiormente osservato in tutti questi campioni, seguito da HPV18 e HPV35. Inoltre, il DNA di HPV è stato trovato nel 22% dei pazienti con GBM, in questo tumore HPV6 era il tipo più frequentemente rilevato, seguito da HPV16. L’ ISH ha mostrato che il DNA di HPV è situato all’interno di cellule tumorali mammarie e di GBM. I nostri risultati suggeriscono un possibile ruolo di JCV, SV40 e HPV in questi tumori, se non come induttori come promotori del processo neoplastico, tuttavia diversi criteri devono ancora essere soddisfatti prima di chiarirne il ruolo.

Cell Host-Microbe Interactions: Turning Pathogen Mechanisms Into Cell's Advantages

Host-Pathogen Interaction is a very vast field of biological sciences, indeed every year many un- known pathogens are uncovered leading to an exponential growth of this field. The present work lyes between its boundaries, touching different aspects of host-pathogen interaction: We have evaluate the permissiveness of Mesenchimal Stem cell (FM-MSC from now on) to all known human affecting herpesvirus. Our study demonstrate that FM-MSC are full permissive to HSV1, HSV2, HCMV and VZV. On the other hand HHV6, HHV7, EBV and HHV8 are susceptible, but failed to activate a lytic infection program. FM-MSC are pluripotent stem cell and have been studied intensely in last decade. FM-MSC are employed in some clinical applications. For this reason it is important to known the degree of susceptibility to transmittable pathogens. Our atten- tion has then moved to bacterial pathogens: we have performed a proteome-wide in silico analy- sis of Chlamydiaceae family, searching for putative Nuclear localization Signal (NLS). Chlamy- diaceae are a family of obligate intracellular parasites. It’s reasonably to think that its members could delivered to nucleus effector proteins via NLS sequences: if that were the case the identifi- cation of NLS carrying proteins could open the way to therapeutic approaches. Our results strengthen this hypothesis: we have identified 72 protein bearing NLS, and verified their func- tionality with in vivo assays. Finally we have conceived a molecular scissor, creating a fusion protein between HIV-1 IN protein and FokI catalytic domain (a deoxyexonuclease domain). Our aim is to obtain chimeric enzyme (trojIN) which selectively identify IN naturally occurring target (HIV LTR sites) and cleaves subsequently LTR carrying DNA (for example integrated HIV1 DNA). Our preliminary results are promising since we have identified trojIN mutated version capable to selectively recognize LTR carrying DNA in an in vitro experiments.

Mass spectrometric identification of Varicella-Zoster Virus (VZV) proteins recognized by human T cells

Primary varicella-zoster virus (VZV) infection during childhood leads to varicella commonly known as chickenpox. After primary infection has occurred VZV establishes latency in the host. During subsequent lifetime the virus can cause reactivated infection clinically known as herpes zoster or shingles. In immunodeficient patients’ dissemination of the virus can lead to life-threatening disease. Withdrawal of acyclovir drug prophylaxis puts allogeneic hematopoietic stem-cell transplantation (HSCT) patients at increased risk for herpes zoster as long as VZV-specific cellular immunity is impaired. Although an efficient live attenuated VZV vaccine for zoster prophylaxis exists, it is not approved in immunocompromised patients due to safety reasons. Knowledge of immunogenic VZV proteins would allow designing a noninfectious nonhazardous subunit vaccine suitable for patients with immunodeficiencies. The objective of this study was to identify T cell defined virus proteins of a VZV-infected Vero cell extract that we have recently described as a reliable antigen format for interferon-gamma (IFN-γ) enzyme-linked immunosorbent spot (ELISpot) assays (Distler et al. 2008). We first separated the VZV-infected/-uninfected Vero cell extracts by size filtration and reverse-phase high performance liquid chromatography (RP-HPLC). The collected fractions were screened for VZV reactivity with peripheral blood mononuclear cells (PBMCs) of VZV-seropositive healthy individuals in the sensitive IFN-γ ELISpot assay. Using this strategy, we successfully identified bioactive fractions that contained immunogenic VZV material. VZV immune reactivity was mediated by CD4+ memory T lymphocytes (T cells) of VZV-seropositive healthy individuals as demonstrated in experiments with HLA blockade antibodies and T cell subpopulations already published by Distler et al. We next analyzed the bioactive fractions with electrospray ionization mass spectrometry (ESI-MS) techniques and identified the sequences of three VZV-derived proteins: glycoprotein E (gE); glycoprotein B (gB), and immediate early protein 62 (IE62). Complementary DNA of these identified proteins was used to generate in vitro transcribed RNA for effective expression in PBMCs by electroporation. We thereby established a reliable and convenient IFN-γ ELISPOT approach to screen PBMCs of healthy donors and HSCT patients for T cell reactivity to single full-length VZV proteins. Application in 10 VZV seropositive healthy donors demonstrated much stronger recognition of glycoproteins gE and gB compared to IE62. In addition, monitoring experiments with ex vivo PBMCs of 3 allo-HSCT patients detected strongly increased CD4+ T cell responses to gE and gB for several weeks to months after zoster onset, while IE62 reactivity remained moderate. Overall our results show for the first time that VZV glycoproteins gE and gB are major targets of the post-transplant anti-zoster CD4+ T cell response. The screening approach introduced herein may help to select VZV proteins recognized by memory CD4+ T cells for inclusion in a subunit vaccine, which can be safely used for zoster prophylaxis in immunocompromised HSCT patients.

An interferon regulatory factor element controls the major immune modulator of murine cytomegalovirus

Immune modulation by herpesviruses, such as cytomegalovirus, is critical for the establishment of acute and persistent infection confronting a vigorous antiviral immune response of the host. Therefore, the action of immune-modulatory proteins has long been the subject of research, with the final goal to identify new strategies for antiviral therapy.rnIn the case of murine cytomegalovirus (mCMV), the viral m152 protein has been identified to play a major role in targeting components of both the innate and the adaptive immune system in terms of infected host-cell recognition in the effector phase of the antiviral immune response. On the one hand, it inhibits cell surface expression of RAE-1 and thereby prevents ligation of the activating natural killer (NK)-cell receptor NKG2D. On the other hand, it decreases cell surface expression of peptide-loaded MHC class I molecules thereby preventing antigen presentation to CD8 T cells. Ultimately, the outcome of CMV infection is determined by the interplay between viral and cellular factors.rnIn this context, the work presented here has revealed a novel and intriguing connection between viral m152 and cellular interferon (IFN), a key cytokine of the immune system: rnthe m152 promoter region contains an interferon regulatory factor element (IRFE) perfectly matching the consensus sequence of cellular IRFEs.rnThe biological relevance of this regulatory element was first suggested by sequence comparisons revealing its evolutionary conservation among various established laboratory strains of mCMV and more recent low-passage wild-derived virus isolates. Moreover, search of the mCMV genome revealed only three IRFE sites in the complete sequence. Importantly, the functionality of the IRFE in the m152 promoter was confirmed with the use of a mutant virus, representing a functional deletion of the IRFE, and its corresponding revertant virus. In particular, m152 gene expression was found to be inhibited in an IRFE-dependent manner in infected cells. Essentially, this inhibition proved to have a severe impact on the immune-modulatory function of m152, first demonstrated by a restored direct antigen presentation on infected cells for CD8 T-cell activation. Even more importantly, this effect of IRFE-mediated IFN signaling was validated in vivo by showing that the protective antiviral capacity of adoptively-transferred, antigen-specific CD8 T cells is also significantly restored by the IRFE-dependent inhibition of m152. Somewhat curious and surprising, the decrease in m152 protein simultaneously prevented an enhanced activation of NK cells in acute-infected mice, apparently independent of the RAE-1/NKG2D ligand/receptor interaction but rather due to reduced ‘missing-self’ recognition.rnTaken together, this work presents a so far unknown mechanism of IFN signaling to control mCMV immune modulation in acute infection.rnrn

Characterization of West Nile virus strains isolated in Italy

West Nile virus (WNV) is a neurotropic flavivirus that is maintained in an enzootic cycle between mosquitoes and birds, but can also infect and cause disease in humans and other vertebrate species. Most of WNV infections in humans are asymptomatic, but approximately 20% of infected people develop clinical symptoms, although severe neurological diseases are observed in less than 1% of them. WNV is the most widely distributed arbovirus in the world and has been recently associated with outbreaks of meningo-encephalitis in Europe, including Italy, caused by different viral strains belonging to distinct lineages 1 and 2. The hypothesis is that genetic divergence among viral strains currently circulating in Italy might reflect on their pathogenic potential and that the rapid spread of WNV with increased pathogenicity within naïve population suggest that epidemic forms of the virus may encode mechanisms to evade host immunity. Infection with WNV triggers a delayed host response that includes a delay in the production of interferon-α (IFN-α). IFNs are a family of immuno-modulatory cytokines that are produced in response to virus infection and serve as integral signal initiators of host intracellular defenses. The increased number of human cases and the lack of data about virulence of European WNV isolates highlight the importance to achieve a better knowledge on this emerging viral infection. In the present study, we investigate the phenotypic and IFN-α-regulatory properties of different WNV lineage 1 and 2 strains that are circulating in Europe/Italy in two cell lines: Vero and 1321N1. We demonstrate that: Vero and 1321N1 cells are capable of supporting WNV replication where different WNV strains show similar growth kinetics; WNV lineage 2 strain replicated in Vero and 1321N1 cells as efficiently as WNV lineage 1 strains; and both lineages 1 and 2 were highly susceptible to the antiviral actions of IFN-α.

Exploring host-pathogen interactions through protein microarray. Large-scale protein microarray analysis revealed novel human receptors for the staphylococcal immune evasion protein FLIPr and for the neisserial adhesin NadA

Adhesion, immune evasion and invasion are key determinants during bacterial pathogenesis. Pathogenic bacteria possess a wide variety of surface exposed and secreted proteins which allow them to adhere to tissues, escape the immune system and spread throughout the human body. Therefore, extensive contacts between the human and the bacterial extracellular proteomes take place at the host-pathogen interface at the protein level. Recent researches emphasized the importance of a global and deeper understanding of the molecular mechanisms which underlie bacterial immune evasion and pathogenesis. Through the use of a large-scale, unbiased, protein microarray-based approach and of wide libraries of human and bacterial purified proteins, novel host-pathogen interactions were identified. This approach was first applied to Staphylococcus aureus, cause of a wide variety of diseases ranging from skin infections to endocarditis and sepsis. The screening led to the identification of several novel interactions between the human and the S. aureus extracellular proteomes. The interaction between the S. aureus immune evasion protein FLIPr (formyl-peptide receptor like-1 inhibitory protein) and the human complement component C1q, key players of the offense-defense fighting, was characterized using label-free techniques and functional assays. The same approach was also applied to Neisseria meningitidis, major cause of bacterial meningitis and fulminant sepsis worldwide. The screening led to the identification of several potential human receptors for the neisserial adhesin A (NadA), an important adhesion protein and key determinant of meningococcal interactions with the human host at various stages. The interaction between NadA and human LOX-1 (low-density oxidized lipoprotein receptor) was confirmed using label-free technologies and cell binding experiments in vitro. Taken together, these two examples provided concrete insights into S. aureus and N. meningitidis pathogenesis, and identified protein microarray coupled with appropriate validation methodologies as a powerful large scale tool for host-pathogen interactions studies.

Diversity of baculoviruses isolated from cutworms (Agrotis spp.)

Larven der Eulenfalter, Gattung Agrotis (Lepidoptera: Noctuidae), sind Schädlinge in der Landwirtschaft, welche gravierende Fraßschäden an bodennahen Pflanzenteilen verursachen. Häufig kommt es zum Absterben der noch jungen Pflanzen oder zu Beschädigungen der pflanzlichen Produkte, was zu finanziellen Ertragsverlusten führt. Zwei der wichtigsten landwirtschaftlichen Schädlinge der Gattung Agrotis sind die Larven der Saateule (Agrotis segetum) und der Ypsiloneule (Agrotis ipsilon), welche bisher überwiegend mittels chemischer Pestizide bekämpft werden. Als eine umweltfreundliche, nachhaltige und vielversprechende Alternative in der Bekämpfung wird der Einsatz von Baculoviren berücksichtigt. Baculoviren zeichnen sich durch eine hohe Virulenz und einem sehr engen Wirtsbereich aus. Häufig werden nur wenige nah verwandte Arten der gleichen Gattung infiziert. Aus der Gattung Agrotis wurden bisher mindestens vier Baculoviren isoliert und charakterisiert, welche als potentielle biologische Pflanzenschutzmittel in Frage kommen; sie gehören zu zwei Gattungen der Baculoviren: rnAlphabaculovirusrn(i) Agrotis segetum nucleopolyhedrovirus A (AgseNPV-A)rn(ii) Agrotis segetum nucleopolyhedrovirus B (AgseNPV-B)rn(iii) Agrotis ipsilon nucleopolyhedrovirus (AgipNPV)rnBetabaculovirusrn(i) Agrotis segetum granulovirus (AgseGV).rnDie Genome der AgseNPV-A, AgipNPV sowie des AgseGV wurden in vorherigen Studien bereits vollständig sequenziert und publiziert. In der vorgelegten Dissertation wurde das AgseNPV-B sequenziert und umfassend mit AgseNPV-A und AgipNPV verglichen. Das Genom von AgseNPV-B ist 148981 Kbp groß und kodiert ….. offene Leseraster. Phylogenetische Analysen zeigen eine enge Verwandtschaft dieser drei Viren und klassifizieren AgseNPV-B als eine neue Art innerhalb der Gattung Alphabaculovirus. Auf Basis der vorhandenen Genomsequenzen konnte eine PCR-basierende Methode zur Detektion und Quantifizierung on AgseNPV-A, AgseNPV-B, AgipNPV und AgseGV etabliert werden. Dises Verfahren ermöglichte die Quantifizierung von AgseNPV-B und AgseGV in Larven von A. segetum, die von beiden Viren zeitgleichinfiziert waren. Durch das gemeinsame Auftreten dieser beiden Wiren innerhalb eines Wirtsindividuums stellte sich die Frage, welche Art der Interaktion bei einer Ko-Infektion vorliegt. Durch Mischinfektionsversuche von AgseNPV-B und AgseGV konnte gezeigt werden, dass beide Viren um die Ressourcen der Larven konkurrieren. Eine für landwirtschaftliche Zwecke vorteilige Interaktion, wie das vorzeitige Verenden der Larven, das bereits für andere interagierende Baculoviren nachgewiesen wurde, konnte ausgeschlossen werden. Neben den Mischinfektionsversuchen wurden auch AgseGV und AgseNPV-B einzeln auf ihre Eignung als biologisches Pflanzenschutzmittel getestet. AgseGV zeigte in den Laborversuchen eine relativ langsame Wirkung, während AgseNPV-B durchaus Potential für ein rasche Abtötung besitzt. rnDie durchgeführten Aktivitätsstudien und die Charakterisierung von AgseNPV-B als neue Art erlauben ein vertieftes biologisches und molekulares Verständnis des Virus legen den Grundstein für und eine mögliche spätere Zulassung als Pflanzenschutzmittel. Die Methode zur Identifizierung und Quantifizierung der Agrotis-Baculoviren stellt ein wichtiges Instrument in der Qualitätskontrolle für Produzenten dar und ermöglicht zudem weitere Untersuchungen von Agrotis-Baculoviren in Mischinfektionen.

The interaction of Leishmania major parasites with human myeloid cells and its consequence for adaptive immunity

In der vorliegenden Arbeit fokussierten wir uns auf drei verschiedene Aspekte der Leishmanien-Infektion. Wir charakterisierten den Prozess des Zelltods „Apoptose“ bei Parasiten (1), untersuchten die Eignung von Makrophagen und dendritischen Zellen als Wirtszelle für die Entwicklung der Parasiten (2) und analysierten die Konsequenzen der Infektion für die Entstehung einer adaptiven Immunantwort im humanen System. Von zentraler Bedeutung für dieses Projekt war die Hypothese, dass apoptotische Leishmanien den Autophagie-Mechanismus ihrer Wirtszellen ausnutzen, um eine T-Zell-vermittelte Abtötung der Parasiten zu vermindern.rnWir definierten eine apoptotische Leishmanien-Population, welche durch eine rundliche Morphologie und die Expression von Phosphatidylserin auf der Parasitenoberfläche charakterisiert war. Die apoptotischen Parasiten befanden sich zudem in der SubG1-Phase und wiesen weniger und fragmentierte DNA auf, welche durch TUNEL-Assay nachgewiesen werden konnte. Bei der Interaktion der Parasiten mit humanen Makrophagen und dendritischen Zellen zeigte sich, dass die anti-inflammatorischen Makrophagen anfälliger für Infektionen waren als die pro-inflammatorischen Makrophagen oder die dendritischen Zellen. Interessanterweise wurde in den dendritischen Zellen jedoch die effektivste Umwandlung zur krankheitsauslösenden, amastigoten Lebensform beobachtet. Da sowohl Makrophagen als auch dendritische Zellen zu den antigenpräsentierenden Zellen gehören, könnte dies zur Aktivierung der T-Zellen des adaptiven Immunsystems führen. Tatsächlich konnte während der Leishmanien-Infektion die Proliferation von T-Zellen beobachtet werden. Dabei stellten wir fest, dass es sich bei den proliferierenden T-Zellen um CD3+CD4+ T-Zellen handelte, welche sich überraschenderweise als Leishmanien-spezifische CD45RO+ T-Gedächtniszellen herausstellten. Dies war unerwartet, da ein vorheriger Kontakt der Spender mit Leishmanien als unwahrscheinlich gilt. In Gegenwart von apoptotischen Parasiten konnte eine signifikant schwächere T-Zell-Proliferation in Makrophagen, jedoch nicht in dendritischen Zellen beobachtet werden. Da sich die T-Zell-Proliferation negativ auf das Überleben der Parasiten auswirkt, konnten die niedrigsten Überlebensraten in dendritischen Zellen vorgefunden werden. Innerhalb der Zellen befanden sich die Parasiten in beiden Zelltypen im Phagosom, welches allerdings nur in Makrophagen den Autophagie-Marker LC3 aufwies. Chemische Induktion von Autophagie führte, ebenso wie die Anwesenheit von apoptotischen Parasiten, zu einer stark reduzierten T-Zell-Proliferation und dementsprechend zu einem höheren Überleben der Parasiten.rnZusammenfassend lässt sich aus unseren Daten schließen, dass Apoptose in Einzellern vorkommt. Während der Infektion können sowohl Makrophagen, als auch dendritische Zellen mit Leishmanien infiziert und das adaptive Immunsystem aktivert werden. Die eingeleitete T-Zell-Proliferation nach Infektion von Makrophagen ist in Gegenwart von apoptotischen Parasiten reduziert, weshalb sie im Vergleich zu dendritischen Zellen die geeigneteren Wirtszellen für Leishmanien darstellen. Dafür missbrauchen die Parasiten den Autophagie-Mechanismus der Makrophagen als Fluchtstrategie um das adaptive Immunsystem zu umgehen und somit das Überleben der Gesamtpopulation zu sichern. Diese Ergebnisse erklären den Vorteil von Apoptose in Einzellern und verdeutlichen, dass der Autophagie-Mechanismus als potentielles therapeutisches Ziel für die Behandlung von Leishmaniose dienen kann.rn

Design, realization and characterization of automated millifluidic bioreactors for investigating the molecular evolution of lytic or lysogenic vector phages infecting engineered host e. Coli

In questa tesi viene presentato un bioreattore in grado di mantenere nel tempo condizioni biologiche tali che consentano di massimizzare i cicli di evoluzione molecolare di vettori di clonazione fagici: litico (T7) o lisogeno (M13). Verranno quindi introdtti concetti legati alla Teoria della Quasispecie e alla relazione tra errori di autoreplicazione e pressioni selettive naturali o artificiali su popolazioni di virus: il modello naturale del sistema evolutivo. Tuttavia, mantenere delle popolazioni di virus significa formire loro un substrato dove replicare. Per fare ciò, altri gruppi di ricerca hanno giá sviluppato complessi e costosi prototipi di macchinari per la crescita continua di popolazioni batteriche: i compartimenti dei sistemi evolutivi. Il bioreattore, oggetto di questo lavoro, fa parte del progetto europeo Evoprog: general purpose programmable machine evolution on a chip (Jaramillo’s Lab, University of Warwick) che, utilizzando tecnologie fagiche e regolazioni sintetiche esistenti, sará in grado di produrre funzionalità biocomputazionali di due ordini di grandezza più veloci rispetto alle tecniche convenzionali, riducendo allo stesso tempo i costi complessivi. Il primo prototipo consiste in uno o piú fermentatori, dove viene fatta crescere la cultura batterica in condizioni ottimizzate di coltivazione continua, e in un cellstat, un volume separato, dove avviene solo la replicazione dei virus. Entrambi i volumi sono di pochi millilitri e appropriatamente interconnessi per consentire una sorta di screening continuo delle biomolecole prodotte all’uscita. Nella parte finale verranno presentati i risultati degli esperimenti preliminari, a dimostrazione dell’affidabilità del prototipo costruito e dei protocolli seguiti per la sterilizzazione e l’assemblaggio del bioreattore. Gli esperimenti effettuati dimostrano il successo di due coltivazioni virali continue e una ricombinazione in vivo di batteriofagi litici o lisogeni ingegnerizzati. La tesi si conclude valutando i futuri sviluppi e i limiti del sistema, tenendo in considerazione, in particolare, alcune applicazioni rivolte agli studi di una terapia batteriofagica.

Human TOP1 residues implicated in species specificity of HIV-1 infection are required for interaction with BTBD2, and RNAi of BTBD2 in old world monkey and human cells increases permissiveness to HIV-1 infection

Host determinants of HIV-1 viral tropism include factors from producer cells that affect the efficiency of productive infection and factors in target cells that block infection after viral entry. TRIM5 restricts HIV-1 infection at an early post-entry step through a mechanism associated with rapid disassembly of the retroviral capsid. Topoisomerase I (TOP1) appears to play a role in HIV-1 viral tropism by incorporating into or otherwise modulating virions affecting the efficiency of a post-entry step, as the expression of human TOP1 in African Green Monkey (AGM) virion-producing cells increased the infectivity of progeny virions by five-fold. This infectivity enhancement required human TOP1 residues 236 and 237 as their replacement with the AGM counterpart residues abolished the infectivity enhancement. Our previous studies showed that TOP1 interacts with BTBD1 and BTBD2, two proteins which co-localize with the TRIM5 splice variant TRIM5 in cytoplasmic bodies. Because BTBD1 and BTBD2 interact with one HIV-1 viral tropism factor, TOP1, and co-localize with a splice variant of another, we investigated the potential involvement of BTBD1 and BTBD2 in HIV-1 restriction.

Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load

HIV virulence, i.e. the time of progression to AIDS, varies greatly among patients. As for other rapidly evolving pathogens of humans, it is difficult to know if this variance is controlled by the genotype of the host or that of the virus because the transmission chain is usually unknown. We apply the phylogenetic comparative approach (PCA) to estimate the heritability of a trait from one infection to the next, which indicates the control of the virus genotype over this trait. The idea is to use viral RNA sequences obtained from patients infected by HIV-1 subtype B to build a phylogeny, which approximately reflects the transmission chain. Heritability is measured statistically as the propensity for patients close in the phylogeny to exhibit similar infection trait values. The approach reveals that up to half of the variance in set-point viral load, a trait associated with virulence, can be heritable. Our estimate is significant and robust to noise in the phylogeny. We also check for the consistency of our approach by showing that a trait related to drug resistance is almost entirely heritable. Finally, we show the importance of taking into account the transmission chain when estimating correlations between infection traits. The fact that HIV virulence is, at least partially, heritable from one infection to the next has clinical and epidemiological implications. The difference between earlier studies and ours comes from the quality of our dataset and from the power of the PCA, which can be applied to large datasets and accounts for within-host evolution. The PCA opens new perspectives for approaches linking clinical data and evolutionary biology because it can be extended to study other traits or other infectious diseases.

The recent breakthroughs in the understanding of host genomics in hepatitis C

Hepatitis C Virus (HCV) infection is spontaneously resolved in about 30% of acutely infected individuals. In those who progress to chronic hepatitis C, HCV therapy permanently eradicates infection in about 40% of cases. It has long been suspected that host genetic factors are key determinants for the control of HCV infection.

Destruction of lymphoid organ architecture and hepatitis caused by CD4+ T cells

Immune responses have the important function of host defense and protection against pathogens. However, the immune response also causes inflammation and host tissue injury, termed immunopathology. For example, hepatitis B and C virus infection in humans cause immunopathological sequel with destruction of liver cells by the host's own immune response. Similarly, after infection with lymphocytic choriomeningitis virus (LCMV) in mice, the adaptive immune response causes liver cell damage, choriomeningitis and destruction of lymphoid organ architecture. The immunopathological sequel during LCMV infection has been attributed to cytotoxic CD8(+) T cells. However, we now show that during LCMV infection CD4(+) T cells selectively induced the destruction of splenic marginal zone and caused liver cell damage with elevated serum alanin-transferase (ALT) levels. The destruction of the splenic marginal zone by CD4(+) T cells included the reduction of marginal zone B cells, marginal zone macrophages and marginal zone metallophilic macrophages. Functionally, this resulted in an impaired production of neutralizing antibodies against LCMV. Furthermore, CD4(+) T cells reduced B cells with an IgM(high)IgD(low) phenotype (transitional stage 1 and 2, marginal zone B cells), whereas other B cell subtypes such as follicular type 1 and 2 and germinal center/memory B cells were not affected. Adoptive transfer of CD4(+) T cells lacking different important effector cytokines and cytolytic pathways such as IFNγ, TNFα, perforin and Fas-FasL interaction did reveal that these cytolytic pathways are redundant in the induction of immunopathological sequel in spleen. In conclusion, our results define an important role of CD4(+) T cells in the induction of immunopathology in liver and spleen. This includes the CD4(+) T cell mediated destruction of the splenic marginal zone with consecutively impaired protective neutralizing antibody responses.

Subcellular Localization of the Non-Structural Proteins 3C and 3CD of the Honeybee Virus Deformed Wing Virus

Apis mellifera L., the European honeybee, is a crucial pollinator of many important agricultural crops in the United States. Recently, honeybee colonies have been affected by Colony Collapse Disorder (CCD), a disorder in which the colony fails due to the disappearance of a key functional group of worker bees. Though no direct causalrelationship has been confirmed, hives that experience CCD have been shown to have a high incidence of Deformed Wing Virus (DWV), a common honeybee virus. While the genome sequence and gene-order of DWV has been analyzed fairly recently, few other studies have been performed to understand the molecular characterization of the virus.Since little is known about where DWV proteins localize in infected host cells, the objective of this project was to determine the subcellular localization of two of the important non-structural proteins that are encoded in the DWV genome. This project focused on the protein 3C, an autocatalytic protease which cleaves itself from a longer polyprotein and helps to cut all of the other proteins apart from one another so that they can become functional, and 3D, the RNA-dependent RNA polymerase (RdRp) which is critical for replication of the virus because it copies the viral genome. By tagging nested constructs containing these two proteins and tracking where they localized in living cells, this study aimed to better understand the replication of DWV and to elicit possible targetsfor further research on how to control the virus. Since DWV is a picorna-like virus, distantly related to human viruses such as polio, and picornavirus non-structural proteins aggregate at cellular membranes during viral replication, the major hypothesis was that the 3C and 3CD proteins would localize at cellular organelle membranes as well. Using confocal microscopy, both proteins were found to localize in the cytoplasm, but the 3CDprotein was found to be mostly diffuse cytoplasmic, and the 3C protein was found to localize more specifically on membranous structures just outside of the nucleus.

IL28B alleles associated with poor hepatitis C virus (HCV) clearance protect against inflammation and fibrosis in patients infected with non-1 HCV genotypes

Genetic polymorphisms near IL28B are associated with spontaneous and treatment-induced clearance of hepatitis C virus (HCV), two processes that require the appropriate activation of the host immune responses. Intrahepatic inflammation is believed to mirror such activation, but its relationship with IL28B polymorphisms has yet to be fully appreciated. We analyzed the association of IL28B polymorphisms with histological and follow-up features in 2335 chronically HCV-infected Caucasian patients. Assessable phenotypes before any antiviral treatment included necroinflammatory activity (n = 1,098), fibrosis (n = 1,527), fibrosis progression rate (n = 1,312), and hepatocellular carcinoma development (n = 1,915). Associations of alleles with the phenotypes were evaluated by univariate analysis and multivariate logistic regression, accounting for all relevant covariates. The rare G allele at IL28B marker rs8099917-previously shown to be at risk of treatment failure-was associated with lower activity (P = 0.04), lower fibrosis (P = 0.02) with a trend toward lower fibrosis progression rate (P = 0.06). When stratified according to HCV genotype, most significant associations were observed in patients infected with non-1 genotypes (P = 0.003 for activity, P = 0.001 for fibrosis, and P = 0.02 for fibrosis progression rate), where the odds ratio of having necroinflammation or rapid fibrosis progression for patients with IL28B genotypes TG or GG versus TT were 0.48 (95% confidence intervals 0.30-0.78) and 0.56 (0.35-0.92), respectively. IL28B polymorphisms were not predictive of the development of hepatocellular carcinoma.