RNA-Strukturen im Hepatitis-C-Virus und ihre Bedeutung für Translation und Replikation

Das Hepatitis C Virus (HCV) ist ein umhülltes Virus aus der Familie der Flaviviridae. Es besitzt ein Plusstrang-RNA Genom von ca. 9600 Nukleotiden Länge, das nur ein kodierendes Leseraster besitzt. Das Genom wird am 5’ und 3’ Ende von nicht-translatierten Sequenzen (NTRs) flankiert, welche für die Translation und vermutlich auch Replikation von Bedeutung sind. Die 5’ NTR besitzt eine interne Ribosomeneintrittsstelle (IRES), die eine cap-unabhängige Translation des ca. 3000 Aminosäure langen viralen Polyproteins erlaubt. Dieses wird ko- und posttranslational von zellulären und viralen Proteasen in 10 funktionelle Komponenten gespalten. Inwieweit die 5’ NTR auch für die Replikation der HCV RNA benötigt wird, war zu Beginn der Arbeit nicht bekannt. Die 3’ NTR besitzt eine dreigeteilte Struktur, bestehend aus einer variablen Region, dem polyU/UC-Bereich und der sogenannten X-Sequenz, eine hochkonservierte 98 Nukleotide lange Region, die vermutlich für die RNA-Replikation und möglicherweise auch für die Translation benötigt wird. Die genuae Rolle der 3’ NTR für diese beiden Prozesse war zu Beginn der Arbeit jedoch nicht bekannt. Ziel der Dissertation war deshalb eine detaillierte genetische Untersuchung der NTRs hinsichtlich ihrer Bedeutung für die RNA-Translation und -Replikation. In die Analyse mit einbezogen wurden auch RNA-Strukturen innerhalb der kodierenden Region, die zwischen verschiedenen HCV-Genotypen hoch konserviert sind und die mit verschiedenen computer-basierten Modellen vorhergesagt wurden. Zur Kartierung der für RNA-Replikation benötigten Minimallänge der 5’ NTR wurde eine Reihe von Chimären hergestellt, in denen unterschiedlich lange Bereiche der HCV 5’ NTR 3’ terminal mit der IRES des Poliovirus fusioniert wurden. Mit diesem Ansatz konnten wir zeigen, dass die ersten 120 Nukleotide der HCV 5’ NTR als Minimaldomäne für Replikation ausreichen. Weiterhin ergab sich eine klare Korrelation zwischen der Länge der HCV 5’ NTR und der Replikationseffizienz. Mit steigender Länge der 5’ NTR nahm auch die Replikationseffizienz zu, die dann maximal war, wenn das vollständige 5’ Element mit der Poliovirus-IRES fusioniert wurde. Die hier gefundene Kopplung von Translation und Replikation in der HCV 5’ NTR könnte auf einen Mechanismus zur Regulation beider Funktionen hindeuten. Es konnte allerdings noch nicht geklärt werden, welche Bereiche innerhalb der Grenzen des IRES-Elements genau für die RNA-Replikation benötigt werden. Untersuchungen im Bereich der 3’ NTR ergaben, dass die variable Region für die Replikation entbehrlich, die X-Sequenz jedoch essentiell ist. Der polyU/UC-Bereich musste eine Länge von mindestens 11-30 Uridinen besitzen, wobei maximale Replikation ab einer Länge von 30-50 Uridinen beobachtet wurde. Die Addition von heterologen Sequenzen an das 3’ Ende der HCV-RNA führte zu einer starken Reduktion der Replikation. In den hier durchgeführten Untersuchungen zeigte keines der Elemente in der 3’ NTR einen signifikanten Einfluss auf die Translation. Ein weiteres cis aktives RNA-Element wurde im 3’ kodierenden Bereich für das NS5B Protein beschrieben. Wir fanden, dass Veränderungen dieser Struktur durch stille Punktmutationen die Replikation hemmten, welche durch die Insertion einer intakten Version dieses RNA-Elements in die variable Region der 3’ NTR wieder hergestellt werden konnte. Dieser Versuchsansatz erlaubte die genaue Untersuchung der für die Replikation kritischen Strukturelemente. Dadurch konnte gezeigt werden, dass die Struktur und die Primärsequenz der Loopbereiche essentiell sind. Darüber hinaus wurde eine Sequenzkomplementarität zwischen dem Element in der NS5B-kodierenden Region und einem RNA-Bereich in der X-Sequenz der 3’ NTR gefunden, die eine sog. „kissing loop“ Interaktion eingehen kann. Mit Hilfe von gezielten Mutationen konnten wir zeigen, dass diese RNA:RNA Interaktion zumindest transient stattfindet und für die Replikation des HCV essentiell ist.

Test of Lorentz symmetry with a 3 He,129 Xe clock-comparison experiment

In case of violation of CPT- and Lorentz Symmetry, the minimal Standard Model Extension (SME) of Kostelecky and coworkers predicts sidereal modulations of atomic transition frequencies as the Earth rotates relative to a Lorentz-violating background field. One method to search for these modulations is the so-called clock-comparison experiment, where the frequencies of co-located clocks are compared as they rotate with respect to the fixed stars. In this work an experiment is presented where polarized 3He and 129Xe gas samples in a glass cell serve as clocks, whose nuclear spin precession frequencies are detected with the help of highly sensitive SQUID sensors inside a magnetically shielded room. The unique feature of this experiment is the fact that the spins are precessing freely, with transverse relaxation times of up to 4.4 h for 129Xe and 14.1 h for 3He. To be sensitive to Lorentz-violating effects, the influence of external magnetic fields is canceled via the weighted difference of the 3He and 129Xe frequencies or phases. The Lorentz-violating SME parameters for the neutron are determined out of a fit on the phase difference data of 7 spin precession measurements of 12 to 16 hours length. The result of the fit gives an upper limit for the equatorial component of the neutron parameter b_n of 3.7×10^(−32) GeV at the 95% confidence level. This value is not limited by the signal-to-noise ratio, but by the strong correlations between the fit parameters. To reduce the correlations and therewith improve the sensitivity of future experiments, it will be necessary to change the time structure of the weighted phase difference, which can be realized by increasing the 129Xe relaxation time.

Generation of FLT3-ITD-reactive T-cell populations from different sources

Approximately 25% of acute myeloid leukemias (AMLs) carry internal tandem duplications (ITD) of various lengths within the gene encoding the FMS-like tyrosine kinase receptor 3 (FLT3). Although varying duplication sites exist, most of these length mutations affect the protein´s juxtamembrane domain. FLT3-ITDs support leukemic transformation by constitutive phosphorylation resulting in uncontrolled activation, and their presence is associated with worse prognosis. As known form previous work, they represent leukemia- and patient-specific neoantigens that can be recognized by autologous AML-reactive CD8+ T cells (Graf et al., 2007; Graf et al., unpublished). Herein, in patient FL, diagnosed with FLT3-ITD+ AML and in first complete remission after induction chemotherapy, T cells against her leukemia´s individual FLT3-ITD were detected at a frequency up to 1.7x10-3 among peripheral blood CD8+ T lymphocytes. This rather high frequency suggested, that FLT3-ITD-reactive T cells had been expanded in vivo due to the induction of an anti-leukemia response.rnrnCell material from AML patients is limited, and the patients´ anti-leukemia T-cell repertoire might be skewed, e.g. due to complex previous leukemia-host interactions and chemotherapy. Therefore, allogeneic sources, i.e. buffy coats (BCs) from health donors and umbilical cord blood (UCB) donations, were exploited for the presence and the expansion of FLT3-ITD-reactive T-cell populations. BC- and UCB-derived CD8+ T cells, were distributed at 105 cells per well on microtiter plates and, were stimulated with antigen-presenting cells (APCs) transfected with in vitro-transcribed mRNA (IVT-mRNA) encoding selected FTL3-ITDs. APCs were autologous CD8- blood mononuclear cells, monocytes or FastDCs.rnrnBuffy coat lymphocytes from 19 healthy individuals were analyzed for CD8+ T-cell reactivity against three immunogenic FLT3-ITDs previously identified in patients VE, IN and QQ and designated as VE_, IN_ and QQ_FLT3-ITD, respectively. These healthy donors carried at least one of the HLA I alleles known to present an ITD-derived peptide from one of these FLT3-ITDs. Reactivities against single ITDs were observed in 8/19 donors. In 4 donors the frequencies of ITD-reactive T cells were determined and were estimated to be in the range of 1.25x10-6 to 2.83x10-7 CD8+ T cells. These frequencies were 1,000- to 10,000-fold lower than the frequency of autologous FLT3-ITD-reactive T cells observed in patient FL. Restricting HLA I molecules were identified in two donors. In one of them, the recognition of VE_FLT3-ITD was found to be restricted by HLA-C*07:02, which is different from the HLA allele restricting the anti-ITD T cells of patient VE. In another donor, the recognition of IN_FLT3-ITD was restricted by HLA-B*35:01, which also had been observed in patient IN (Graf et al., unpublished). By gradual 3´-fragmentation of the IN_FLT3-ITD cDNA, the 10-mer peptide CPSDNEYFYV was identified as the target of allogeneic T cells against IN_FLT3-ITD. rnLymphocytes in umbilical cord blood predominantly exhibit a naïve phenotype. Seven UCB donations were analyzed for T-cell responses against the FLT3-ITDs of patients VE, IN, QQ, JC and FL irrespective of their HLA phenotype. ITD-reactive responses against all stimulatory FLT3-ITDs were observed in 5/7 UCB donations. The frequencies of T cells against single FLT3-ITDs in CD8+ lymphocytes were estimated to be in the range of 1.8x10-5 to 3.6x10-6, which is nearly 15-fold higher than the frequencies observed in BCs. Restricting HLA I molecules were identified in 4 of these 5 positive UCB donations. They were mostly different from those observed in the respective patients. But in one UCB donation T cells against the JC_FLT3-ITD had exactly the same peptide specificity and HLA restriction as seen before in patient JC (Graf et al., 2007). Analyses of UCB responder lymphocytes led to the identification of the 10-mer peptide YESDNEYFYV, encoded by FL_FLT3-ITD, that was recognized in association with the frequent allele HLA-A*02:01. This peptide was able to stimulate and enrich ITD-reactive T cells from UCB lymphocytes in vitro. Peptide responders not only recognized the peptide, but also COS-7 cells co-transfected with FL_FLT3-ITD and HLA-A*02:01.rnrnIn conclusion, T cells against AML- and individual-specific FLT3-ITDs were successfully generated not only from patient-derived blood, but also from allogeneic sources. Thereby, ITD-reactive T cells were detected more readily and at higher frequencies in umbilical cord blood than in buffy coat lymphocytes. It occurred that peptide specificity and HLA restriction of allogeneic, ITD-reactive T cells were identical to autologous patient-derived T cells. As shown herein, allogeneic, FLT3-ITD-reactive T cells can be used for the identification of FLT3-ITD-encoded peptides, e.g. for future therapeutic vaccination studies. In addition, these T cells or their receptors can be applied to adoptive transfer.

Influenza di un co-sustrato sulla biodegradabilità anaerobica (mesofilica) dei fanghi di stazioni di depurazione delle acque residuali

La presente tesi di laurea magistrale si è elaborata nell'ambito del Dipartimento di Tecnologie Ambientali dell'Università di Cadice (Spagna). Tratta lo studio dell'influenza di un co-substrato sulla biodegradabilità anaerobica, in condizioni mesofiliche, dei fanghi di depurazione delle acque residuali. Il co-substrato utilizzato per il miglioramento dei trattamenti dei fanghi è il glicerolo, un sottoprodotto di lavorazione del biodiesel. Le prove realizzate mirano a ottimizzare l'eliminazione della materia organica e la produzione di biogas (idrogeno e metano). Come imminente prospettiva futura, avremo l'avviamento nelle migliori condizioni di processo dell'impianto pilota di depurazione fanghi ubicato presso la stazione di trattamento delle acque reflue urbane di Cadice - San fernando.

Switch from antagonist to agonist after addition of a DOTA chelator to a somatostatin analog

Peptide receptor targeting has become an increasingly attractive method to target tumors diagnostically and radiotherapeutically. Peptides linked to a variety of chelators have been developed for this purpose. They have, however, rarely been tested for their agonistic or antagonistic properties. We report here on a somatostatin antagonist that switched to an agonist upon coupling to a DOTA chelator.

Body mass index, hormone replacement therapy, and endometrial cancer risk: a meta-analysis

Background: Body mass index (BMI) is a risk factor for endometrial cancer. We quantified the risk and investigated whether the association differed by use of hormone replacement therapy (HRT), menopausal status, and histologic type. Methods: We searched MEDLINE and EMBASE (1966 to December 2009) to identify prospective studies of BMI and incident endometrial cancer. We did random-effects meta-analyses, meta-regressions, and generalized least square regressions for trend estimations assuming linear, and piecewise linear, relationships. Results: Twenty-four studies (17,710 cases) were analyzed; 9 studies contributed to analyses by HRT, menopausal status, or histologic type, all published since 2003. In the linear model, the overall risk ratio (RR) per 5 kg/m2 increase in BMI was 1.60 (95% CI, 1.52–1.68), P < 0.0001. In the piecewise model, RRs compared with a normal BMI were 1.22 (1.19–1.24), 2.09 (1.94–2.26), 4.36 (3.75–5.10), and 9.11 (7.26–11.51) for BMIs of 27, 32, 37, and 42 kg/m2, respectively. The association was stronger in never HRT users than in ever users: RRs were 1.90 (1.57–2.31) and 1.18 (95% CI, 1.06–1.31) with P for interaction ¼ 0.003. In the piecewise model, the RR in never users was 20.70 (8.28–51.84) at BMI 42 kg/m2, compared with never users at normal BMI. The association was not affected by menopausal status (P ¼ 0.34) or histologic type (P ¼ 0.26). Conclusions: HRT use modifies the BMI-endometrial cancer risk association. Impact: These findings support the hypothesis that hyperestrogenia is an important mechanism underlying the BMI-endometrial cancer association, whilst the presence of residual risk in HRT users points to the role of additional systems. Cancer Epidemiol Biomarkers Prev; 19(12); 3119–30.

A New Crystalline LiPON Electrolyte: Synthesis, Properties, and Electronic Structure

The new crystalline compound, Li2PO2N, was synthesized using high temperature solid state methods starting with a stoichiometric mixture of Li2O, P2O5, and P3N5. Its crystal structure was determined ab initio from powder X-ray diffraction. The compound crystallizes in the orthorhombic space group Cmc2(1) (# 36) with lattice constants a = 9.0692(4) angstrom, b = 53999(2) angstrom, and c = 4.6856(2) angstrom. The crystal structure of SD-Li2PO2N consists of parallel arrangements of anionic chains formed of corner sharing (PO2N2) tetrahedra. The chains are held together by Li+ cations. The structure of the synthesized material is similar to that predicted by Du and Holzwarth on the basis of first principles calculations (Phys. Rev. B 81,184106 (2010)). The compound is chemically and structurally stable in air up to 600 degrees C and in vacuum up to 1050 degrees C. The Arrhenius activation energy of SD-Li2PO2N in pressed pellet form was determined from electrochemical impedance spectroscopy measurements to be 0.6 eV, comparable to that of the glassy electrolyte LiPON developed at Oak Ridge National Laboratory. The minimum activation energies for Li ion vacancy and interstitial migrations are computed to be 0.4 eV and 0.8 eV, respectively. First principles calculations estimate the band gap of SD-Li2PO2N to be larger than 6 eV. (C) 2013 Elsevier B.V. All rights reserved.

Domains of physical activity and all-cause mortality: systematic review and dose-response meta-analysis of cohort studies

Background The dose–response relation between physical activity and all-cause mortality is not well defined at present. We conducted a systematic review and meta-analysis to determine the association with all-cause mortality of different domains of physical activity and of defined increases in physical activity and energy expenditure. Methods MEDLINE, Embase and the Cochrane Library were searched up to September 2010 for cohort studies examining all-cause mortality across different domains and levels of physical activity in adult general populations. We estimated combined risk ratios (RRs) associated with defined increments and recommended levels, using random-effects meta-analysis and dose–response meta-regression models. Results Data from 80 studies with 1 338 143 participants (118 121 deaths) were included. Combined RRs comparing highest with lowest activity levels were 0.65 [95% confidence interval (95% CI) 0.60–0.71] for total activity, 0.74 (95% CI 0.70–0.77) for leisure activity, 0.64 (95% CI 0.55–0.75) for activities of daily living and 0.83 (95% CI 0.71–0.97) for occupational activity. RRs per 1-h increment per week were 0.91 (95% CI 0.87–0.94) for vigorous exercise and 0.96 (95% CI 0.93–0.98) for moderate-intensity activities of daily living. RRs corresponding to 150 and 300 min/week of moderate to vigorous activity were 0.86 (95% CI 0.80–0.92) and 0.74 (95% CI 0.65–0.85), respectively. Mortality reductions were more pronounced in women. Conclusion Higher levels of total and domain-specific physical activity were associated with reduced all-cause mortality. Risk reduction per unit of time increase was largest for vigorous exercise. Moderate-intensity activities of daily living were to a lesser extent beneficial in reducing mortality.

Progressive dopamine and hypocretin deficiencies in Parkinson's disease: is there an impact on sleep and wakefulness?

Sleep-wake disturbances are frequent in patients with Parkinson's disease, but prospective controlled electrophysiological studies of sleep in those patients are surprisingly sparse, and the pathophysiology of sleep-wake disturbances in Parkinson's disease remains largely elusive. In particular, the impact of impaired dopaminergic and hypocretin (orexin) signalling on sleep and wakefulness in Parkinson's disease is still unknown. We performed a prospective, controlled electrophysiological study in patients with early and advanced Parkinson's disease, e.g. in subjects with presumably different levels of dopamine and hypocretin cell loss. We compared sleep laboratory tests and cerebrospinal fluid levels with hypocretin-deficient patients with narcolepsy with cataplexy, and with matched controls. Nocturnal sleep efficiency was most decreased in advanced Parkinson patients, and still lower in early Parkinson patients than in narcolepsy subjects. Excessive daytime sleepiness was most severe in narcolepsy patients. In Parkinson patients, objective sleepiness correlated with decrease of cerebrospinal fluid hypocretin levels, and repeated hypocretin measurements in two Parkinson patients revealed a decrease of levels over years. This suggests that dopamine and hypocretin deficiency differentially affect sleep and wakefulness in Parkinson's disease. Poorer sleep quality is linked to dopamine deficiency and other disease-related factors. Despite hypocretin cell loss in Parkinson's disease being only partial, disturbed hypocretin signalling is likely to contribute to excessive daytime sleepiness in Parkinson patients.

Treatment of soft tissue recessions at titanium implants using a resorbable collagen matrix: a pilot study

OBJECTIVES: To histologically assess the effectiveness of a porcine-derived collagen matrix (CM) and a subepithelial connective tissue graft (CTG) for the coverage of single mucosal recessions at osseointegrated dental implants. MATERIALS AND METHODS: Chronic-type mucosal Miller Class I-like recessions (mean clinical defect height: 0.67 ± 0.33-1.16 ± 0.19 mm) were established at the buccal aspect of titanium implants with platform switch in six beagle dogs. The defects were randomly allocated to either (1) coronally advanced flap surgery (CAF) + CM, (2) CAF + CTG or (3) CAF alone. At 12 weeks, histomorphometrical measurements were made (e.g.) between the implant shoulder (IS) and the mucosal margin (PM) and IS and the outer contour of the adjacent soft tissue (mucosal thickness [MT]). RESULTS: All treatment procedures investigated were associated with an almost complete soft tissue coverage of the defect area (i.e. coronal positioning of PM relative to IS). Mean IS-PM and MT values tended to be increased in both CAF + CM (1.04 ± 0.74 mm/0.71 ± 0.55 mm) and CAF + CTG (0.88 ± 1.23 mm/0.62 ± 0.66 mm) groups when compared with CAF (0.16 ± 0.28 mm/0.34 ± 0.23 mm) alone. These differences, however, did not reach statistical significance. CONCLUSIONS: Within the limits of this pilot study, it was concluded that all treatment procedures investigated were effective in covering soft tissue recessions at titanium implants.

Glomerulonephropathy in Aged Captive Key Largo Woodrats (Neotoma floridana smalli)

A retrospective review of mortality records of Key Largo woodrats (Neotoma floridana smalli) in a captive breeding program revealed chronic renal disease in 5 of 6 woodrats older than 4 years of age. Two of the 5 woodrats with chronic renal disease also had clinical evidence of diabetes mellitus. Kidneys from all 5 woodrats were examined via light microscopy, histochemical staining, immunohistochemical staining, and transmission electron microscopy. The dietary histories of the affected animals were examined as well. The most striking histopathologic abnormality in the affected kidneys was the presence of large protein casts within cortical and medullary tubules in combination with lesions of membranous glomerulopathy and glomerulosclerosis. Transmission electron microscopy revealed thickening and undulation of the tubular and glomerular mesangial basement membranes with the variable presence of electron-dense deposits within the capillary endothelial basement membrane. Patchy glomerular immunoreactivity for IgG was noted in 2 cases, but IgA and IgM immunoreactivity were not present. The pathologic changes in the kidneys of the Key Largo woodrats mirrored many of the features of chronic progressive nephropathy commonly diagnosed in laboratory rats. Woodrats in the captive population were fed an ad libitum high-protein diet similar to diets that have been shown in laboratory rats to exacerbate the development and progression of chronic progressive nephropathy. It is concluded that Key Largo woodrats develop glomerulonephropathy with features similar to chronic progressive nephropathy described in laboratory rats. Age, concomitant disease, and dietary factors may contribute to the development and severity of this potentially age-limiting disease in Key Largo woodrats.