Refined Gelfand models for some finite complex reflection groups

In 'Involutory reflection groups and their models' (F. Caselli, 2010), a uniform Gelfand model is constructed for all complex reflection groups G(r,p,n) satisfying GCD(p,n)=1,2 and for all their quotients modulo a scalar subgroup. The present work provides a refinement for this model. The final decomposition obtained is compatible with the Robinson-Schensted generalized correspondence.

Influence of genetic variants and post transcriptional factors on imatinib transporters as determinants of the pharmacological response

Introduction – Although imatinib (IM) is a recognized gold standard in chronic myeloid leukemia (CML) therapy, resistance has emerged in a significant proportion of patients. Aim – The aim of this study was: (1) to investigate the role of genetic variants in genes encoding for IM transporters, as candidate of IM responsiveness and (2) to test the influence of miRNAs on IM response, focusing on efflux transporters. Methods – As a first step, a panel of polymorphisms (SNPs) was genotyped in a subgroup population of 189 patients enrolled in the Tyrosine Kinase Inhibitor Optimization and Selectivity (TOPS) trial. The association with cytogenetic response and molecular response (MR) was assessed for each SNP. As a second step, an in vitro IM-resistant model (K-562 CML cell line) was established. miRNAs profiles were analyzed using Taqman arrays and in silico search was performed for miRNAs deregulated after IM treatment. mRNA and protein expression were quantified using TaqMan realtime PCR and Western blotting, respectively. Results – (1) Among Caucasian patients, ABCB1 rs60023214 significantly correlated with complete MR (P = 0.005). Concerning SNPs combination in IM uptake transporters, the associations with treatment outcomes were statistically significant for both major and complete MR (P = 0.005 and P = 0.01, respectively). (2) ABCB1 protein was not expressed under any conditions of treatment, differently from ABCG2. Two deregulated miRNAs, namely miR-212 and miR-328, were identified to be inversely correlated with ABCG2 (r2= 0.57; p=0.03 and r2=0.47; p=0.06, respectively). Experiments of loss and gain of function confirmed the functional influence of these miRNAs on ABCG2. Conclusion – The multiple candidate gene approach identified single and combination of SNPs that can be proposed as predictor of IM response. The in vitro study suggested that IM resistance could be mediated by miRNA-dependent mechanism. Further studies are needed to validate these preliminary findings.

International cooperation in endourology: percutaneous and flexible ureteroscopic treatment of lower pole kidney stones

Introduction Lower pole kidney stones represent at time a challenge for the urologist. The gold standard treatment for intrarenal stones <2 cm is Extracorporeal Shock Wave Lithotripsy (ESWL) while for those >2 cm is Percutaneous Nephrolithotomy (PCNL). The success rate of ESWL, however, decreases when it is employed for lower pole stones, and this is particularly true in the presence of narrow calices or acute infundibular angles. Studies have proved that ureteroscopy (URS) is an efficacious alternative to ESWL for lower pole stones <2 cm, but this is not reflected by either the European or the American guidelines. The aim of this study is to present the results of a large series of flexible ureteroscopies and PCNLs for lower pole kidney stones from high-volume centers, in order to provide more evidences on the potential indications of the flexible ureteroscopy for the treatment of kidney stones. Materials and Methods A database was created and the participating centres retrospectively entered their data relating to the percutaneous and flexible ureteroscopic management of lower pole kidney stones. Patients included were treated between January 2005 and January 2010. Variables analyzed included case load number, preoperative and postoperative imaging, stone burden, anaesthesia (general vs. spinal), type of lithotripter, access location and size, access dilation type, ureteral access sheath use, visual clarity, operative time, stone-free rate, complication rate, hospital stay, analgesic requirement and follow-up time. Stone-free rate was defined as absence of residual fragments or presence of a single fragment <2 mm in size at follow-up imaging. Primary end-point was to test the efficacy and safety of flexible URS for the treatment of lower pole stones; the same descriptive analysis was conducted for the PCNL approach, as considered the gold standard for the treatment of lower pole kidney stones. In this setting, no statistical analysis was conducted owing to the different selection criteria of the patients. Secondary end-point consisted in matching the results of stone-free rates, operative time and complications rate of flexible URS and PCNL in the subgroup of patients harbouring lower pole kidney stones between 1 and 2 cm in the higher diameter. Results A total 246 patients met the criteria for inclusion. There were 117 PCNLs (group 1) and 129 flexible URS (group 2). Ninety-six percent of cases were diagnosed by CT KUB scan. Mean stone burden was 175±160 and 50±62 mm2 for groups 1 and 2, respectively. General anaesthesia was induced in 100 % and 80% of groups 1 and 2, respectively. Pneumo-ultrasonic energy was used in 84% of cases in the PCNL group, and holmium laser in 95% of the cases in the flexible URS group. The mean operative time was 76.9±44 and 63±37 minutes for groups 1 and 2 respectively. There were 12 major complications (11%) in group 1 (mainly Grade II complications according to Clavidien classification) and no major complications in group 2. Mean hospital stay was 5.7 and 2.6 days for groups 1 and 2, respectively. Ninety-five percent of group 1 and 52% of group 2 required analgesia for a period longer than 24 hours. Intraoperative stone-free rate after a single treatment was 88.9% for group 1 and 79.1% for group 2. Overall, 6% of group 1 and 14.7% of group 2 required a second look procedure. At 3 months, stone-free rates were 90.6% and 92.2% for groups 1 and 2, respectively, as documented by follow-up CT KUB (22%) or combination of intra-venous pyelogram, regular KUB and/or kidney ultrasound (78%). In the subanalysis conducted comparing 82 vs 65 patients who underwent PCNL and flexible URS for lower pole stones between 1 and 2 cm, intreoperative stone-free rates were 88% vs 68% (p= 0.03), respectively; anyway, after an auxiliary procedure which was necessary in 6% of the cases in group 1 and 23% in group 2 (p=0.03), stone-free rates at 3 months were not statistically significant (91.5% vs 89.2%; p=0.6). Conversely, the patients undergoing PCNL maintained a higher risk of complications during the procedure, with 9 cases observed in this group versus 0 in the group of patients treated with URS (p=0.01) Conclusions These data highlight the value of flexible URS as a very effective and safe option for the treatment of kidney stones; thanks to the latest generation of flexible devices, this new technical approach seems to be a valid alternative in particular for the treatment of lower pole kidney stones less than 2 cm. In high-volume centres and in the hands of skilled surgeons, this technique can approach the stone-free rates achievable through PCNL in lower pole stones between 1 and 2 cm, with a very low risk of complications. Furthermore, the results confirm the high success rate and relatively low morbidity of modern PCNL for lower pole stones, with no difference detectable between the prone and supine position.

Identificazione dei fenotipi clinici dell’insufficienza renale cronica che predicono la progressione della malattia. Un’applicazione della tecnica degli alberi decisionali

The primary aim of this dissertation to identify subgroups of patients with chronic kidney disease (CKD) who have a differential risk of progression of illness and the secondary aim is compare 2 equations to estimate the glomerular filtration rate (GFR). To this purpose, the PIRP (Prevention of Progressive Kidney Disease) registry was linked with the dialysis and mortality registries. The outcome of interest is the mean annual variation of GFR, estimated using the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation. A decision tree model was used to subtype CKD patients, based on the non-parametric procedure CHAID (Chi-squared Automatic Interaction Detector). The independent variables of the model include gender, age, diabetes, hypertension, cardiac diseases, body mass index, baseline serum creatinine, haemoglobin, proteinuria, LDL cholesterol, tryglycerides, serum phoshates, glycemia, parathyroid hormone and uricemia. The decision tree model classified patients into 10 terminal nodes using 6 variables (gender, age, proteinuria, diabetes, serum phosphates and ischemic cardiac disease) that predict a differential progression of kidney disease. Specifically, age <=53 year, male gender, proteinuria, diabetes and serum phosphates >3.70 mg/dl predict a faster decrease of GFR, while ischemic cardiac disease predicts a slower decrease. The comparison between GFR estimates obtained using MDRD4 and CKD-EPI equations shows a high percentage agreement (>90%), with modest discrepancies for high and low age and serum creatinine levels. The study results underscore the need for a tight follow-up schedule in patients with age <53, and of patients aged 54 to 67 with diabetes, to try to slow down the progression of the disease. The result also emphasize the effective management of patients aged>67, in whom the estimated decrease in glomerular filtration rate corresponds with the physiological decrease observed in the absence of kidney disease, except for the subgroup of patients with proteinuria, in whom the GFR decline is more pronounced.

Weathering of Fe-bearing minerals under extraterrestrial conditions, investigated by Mössbauer spectroscopy

The weathering of Fe-bearing minerals under extraterrestrial conditions was investigated by Mössbauer (MB) spectroscopy to gain insights into the role of water on the planet Mars. The NASA Mars Exploration Rovers Spirit and Opportunity each carry a miniaturized Mössbauer spectrometer MIMOS II for the in situ investigation of Martian soils and rocks as part of their payload. The MER flight instruments had to be modified in order to work over the Martian diurnal temperature range (180 K – 290 K) and within the unique electronic environment of the rovers. The modification required special calibration procedures. The integration time necessary to obtain a good quality Mössbauer spectrum with the MIMOS II flight instruments was reduced by 30 % through the design of a new collimator. The in situ investigation of rocks along the rover Spirit's traverse in Gusev crater revealed weakly altered olivine basalt on the plains and pervasively altered basalt in the Columbia Hills. Correlation plots of primary Fe-bearing minerals identified by MB spectroscopy such as olivine versus secondary Fe-bearing phases such as nanophase Fe oxides showed that olivine is the mineral which is primarily involved in weathering reactions. This argues for a reduced availability of water. Identification of the Fe-oxyhydroxide goethite in the Columbia Hills is unequivocal evidence for aqueous weathering processes in the Columbia Hills. Experiments in which mineral powders were exposed to components of the Martian atmosphere showed that interaction with the atmosphere alone, in the absence of liquid water, is sufficient to oxidize Martian surface materials. The fine-grained dust suspended in the Martian atmosphere may have been altered solely by gas-solid reactions. Fresh and altered specimens of Martian meteorites were investigated with MIMOS II. The study of Martian meteorites in the lab helped to identify in Bounce Rock the first rock on Mars which is similar in composition to basaltic shergottites, a subgroup of the Martian meteorites. The field of astrobiology includes the study of the origin, evolution and distribution of life in the universe. Water is a prerequisite for life. The MER Mössbauer spectrometers identified aqueous minerals such as jarosite and goethite. The identification of jarosite was crucial to evaluate the habitability of Opportunity's landing site at Meridiani Planum during the formation of the sedimentary outcrop rocks, because jarosite puts strong constrains on pH levels. The identification of olivine in rocks and soils on the Gusev crater plains provide evidence for the sparsity of water under current conditions on Mars. Ratios of Fe2+/Fe3+ were obtained with Mössbauer spectroscopy from basaltic glass samples which were exposed at a deep sea hydrothermal vent. The ratios were used as a measure of potential energy for use by a microbial community. Samples from Mars analogue field sites on Earth exhibiting morphological biosignatures were also investigated.

Human papillomavirus (HPV) and associated diseases: between applied diagnostic and basic research

Human Papillomavirus (HPV) is the cause of cervical cancers (among these, adenocarcinoma, AdCa) and is associated to a subgroup of oropharyngeal carcinomas (OPSCCs). Even if the risk for cancer development is linked to the infection by some viral genotypes, mainly HPV16 and 18, viral DNA alone seems not to be sufficient for diagnosis. Moreover, the role of the virus in OPSCCs has not been totally clarified yet. In the first part of the thesis, the performances concerning viral genotyping in clinical cervical samples of a new pyrosequencing-based test and a well-known hybridization-based assay have been compared. Similar results between the methods have been obtained. However, the former showed advantages in detecting intratype variants, higher specificity and a broader spectrum of detectable HPV types. The second part deals with the evaluation of virological markers (genotyping, viral oncoproteins expression, viral load, physical state and CpG methylation of HPV16 genome) in the diagnosis/prognosis of cervical AdCa and HPV-associated OPSCCs. HPV16 has been confirmed the most prevalent genotype in both the populations. Interestingly, the mean methylation frequency of viral DNA at the early promoter showed the tendency to be associated to invasion for cervical AdCa and to a worse prognosis for OPSCCs, suggesting a promising role as diagnostic/prognostic biomarker. The experiments of the third part were performed at the DKFZ in Heidelberg (Germany) and dealt with the analysis of the response to IFN-k transfection in HPV16-positive cervical cancer and head&neck carcinoma cell lines to evaluate its potential role as new treatment. After 24h, we observed increased IFN-b expression which lead to the up-regulation of genes involved in the antigens presentation pathway (MHC class I and immunoproteasome) and antiviral response as well, in particular in cervical cancer cell lines. This fact suggested also the presence of different HPV-mediated carcinogenic pathways between the two anatomical districts.

Decorso delle coliti severe: un confronto tra colite ulcerosa e di Crohn

Pochi sono i dati disponibili sul decorso clinico della malattia di Crohn del colon severa(CD). L'obiettivo è quello di descrivere il decorso clinico della colite di Crohn severa (CC) in una coorte di pazienti isolata con CD del colon o ileocolica, e di confrontarlo con il decorso clinico di pazienti affetti da colite ulcerosa severa (UC). 34 pazienti con CC severa sono stati identificati retrospettivamente nella nostra coorte di 593 pazienti ricoverati (2003-2012) attraverso la valutazione di CDAI score e HBI. 169 pazienti con UC severa sono stati identificati retrospettivamente in una coorte di 449 pazienti ricoverati (2003-2012) attraverso la valutazione del score di Lichtiger e di Truelove-Witts. Abbiamo valutato questi risultati: risposta agli steroidi, risposta ai farmaci biologici, tasso di colectomia acuta, tasso di colectomia durante il follow-up, megacolon e tasso di infezione da citomegalovirus. Non abbiamo trovato differenze significative nella risposta agli steroidi e biologici, della percentuale di infezione da citomegalovirus e di megacolon, mentre il tasso di colectomia in acuto è risultato essere maggiore nei pazienti con CC rispetto ai pazienti con UC; anche la differenza tra i tassi di colectomia alla fine del follow-up è risultata non significativa. Con l'analisi univariata la giovane età alla diagnosi è associata ad un aumentato rischio di colectomia in assoluto (p = 0,024) e in elezione (p = 0.022), ma non in acuto. Il tasso globale di colectomia nei pazienti con CC severa è superiore a quella dei pazienti con UC severa , ma questo dato non è supportato da una diversa risposta clinica alla terapia steroidea o terapia di salvataggio con biologici. Il vero decorso clinico della colite di Crohn severa necessita di essere chiarito da studi prospettici che includano un numero maggiore di pazienti con questo sottogruppo di malattia.

Aussagekraft einer quantitativen, PC-unterstützten PCNA-Bestimmung an Leiomyosarkomen und Leiomyomen

Ziel der Studie war die Untersuchung inwieweit PCNA als immunhistochemisches Hilfsmittel eine Verbesserung der Abgrenzung von uterinen LM gegenüber uterinen LMS und eine Hilfe bei der Prognoseaussage bei uterinen und gastrointestinalen LMS darstellt. Dabei wurden auch weitere, herkömmliche, in einer Reihe von Studien untersuchte Prognoseparameter mit in Betracht gezogen.rnDie Auswertung der Färbungen erfolgte quantitativ mittels einer PC-gesteuerten Bildverarbeitung, die neben der positiven Zellfläche und Zellzahl auch die Kernfläche berechnet. Vorteil der quantitativen Messung ist die Möglichkeit der Reproduzierbarkeit unabhängig vom Benutzer, im Gegensatz zu semiquantitativen Analysen, die häufiger angewendet werden.rnEs fällt dabei auf, dass sowohl die Zellkerngröße generell als auch die Zellkerngröße der positiv gefärbten Zellen signifikant größer bei LMS als bei LM ist. (p< 0,0001). Zwischen den Zellkerngrößen der uterinen und der gastrointestinalen LMS fanden sich keine signifikanten Unterschiede.rnBezüglich der Abgrenzung zwischen uterinen LM und LMS zeigten sich signifikant höhere PCNA-Meßwerte für LMS (mittlere positive Zellkernzahl 15,08%, mittlere positive Zellkernzahl 16,67%) gegenüber LM (mittlere positive Zellkernzahl 1,95%, mittlere positive Zellkernzahl 2,02%). Zu den gastrointestinalen LMS-PCNA Messwerten gab es keinen signifikanten Unterschied (mittlere positive Zellkernfläche 19,07%, mittlere positive Zellkernzahl 16,43).rnKein signifikanter Zusammenhang zeigte sich bei der Höhe der PCNA-Meßwerte und der Prognose sowohl der uterinen als auch der gastrointestinalen LMS.rnIn dieser Studie stellten sich als signifikant prognoserelevant lediglich das Alter sowohl bei den uterinen und gastrointestinalen LMS heraus. Bei den uterinen LMS war auch noch ein schlechteres Grading und das Vorhandensein von Nekrosen signifikant mit der Prognose korreliert.rnNicht signifikant prognoserelevant waren sowohl bei den uterinen wie den gastrointestinalen LMS die Tumorgröße und die PCNA-Meßwerthöhe. Bei den gastrointestinalen Leiomyosarkomen zusätzlich noch das Vorhandensein von Nekrosen.rnEin signifikanter Zusammenhang wurde zwischen PCNA-Meßwerten und der Uterusgröße bzw. auch der Myomgröße bei den uterinen Leiomyomen sowie analog der Tumorgröße der uterinen und der gastrointestinalen LMS festgestellt. Innerhalb der Gruppe der uterinen Myome zeigten sich für zellreiche Myome zwar höhere Messwerte, die jedoch nicht signifikant waren.rnKein Zusammenhang zeigte sich dagegen für die Höhe der PNCA-Meßwerte und dem Grading der uterinen sowohl als auch der gastrointestinalen Leiomyosarkome, dem Alter der Patientinnen bei den uterinen LMS, dem Vorhandensein von Nekrosen bei den uterinen sowohl als auch bei gastrointestinalen LMS und dem Geschlecht bei den gastrointestinalen LMS.rnDie Ergebnisse stehen bezüglich der Aussage der Prognose teilweise in Widerspruch, teilweise in Einklang mit den bisherigen Veröffentlichungen. Ein großes Hemmnis ist die geringe Fallzahl, die vor allem durch die Seltenheit der Tumore bedingt ist, desweiteren die ungenügende Nachverfolgung der Patienten, die auch daraus resultiert, dass es sich um eine retrospektive Studie handelt. Hier bedarf es größerer Studien, möglicherweise als multizentrische Studien mit genauer Verlaufsbeobachtung, um auch im deutschsprachigen Raum eine weitere Erforschung dieser seltenen, umsomehr sehr interessanten und an den untersuchenden Pathologen besondere Ansprüche stellende Tumore zu geben.rn

La farmacogenetica della narcolessia: comorbidità psichiatriche e risvolti in sanità pubblica

La farmacogenetica fornisce un importante strumento utile alla prescrizione farmacologica, migliorando l’efficacia terapeutica ed evitando le reazioni avverse. Il citocromo P450 gioca un ruolo centrale nel metabolismo di molti farmaci utilizzati nella pratica clinica e il suo polimorfismo genetico spiega in gran parte le differenze interindividuali nella risposta ai farmaci. Con riferimento alla terapia della narcolessia, occorre premettere che la narcolessia con cataplessia è una ipersonnia del Sistema Nervoso Centrale caratterizzata da eccessiva sonnolenza diurna, cataplessia, paralisi del sonno, allucinazioni e sonno notturno disturbato. Il trattamento d’elezione per la narcolessia include stimolanti dopaminergici per la sonnolenza diurna e antidepressivi per la cataplessia, metabolizzati dal sistema P450. Peraltro, poiché studi recenti hanno attestato un’alta prevalenza di disturbi alimentari nei pazienti affetti da narcolessia con cataplessia, è stata ipotizzata una associazione tra il metabolismo ultrarapido del CYP2D6 e i disturbi alimentari. Lo scopo di questa ricerca è di caratterizzare il polimorfismo dei geni CYP2D6, CYP2C9, CYP2C19, CYP3A4, CYP3A5 e ABCB1 coinvolti nel metabolismo e nel trasporto dei farmaci in un campione di 108 pazienti affetti da narcolessia con cataplessia, e valutare il fenotipo metabolizzatore in un sottogruppo di pazienti che mostrano un profilo psicopatologico concordante con la presenza di disturbi alimentari. I risultati hanno mostrato che il fenotipo ultrarapido del CYP2D6 non correla in maniera statisticamente significativa con i disturbi alimentari, di conseguenza il profilo psicopatologico rilevato per questo sottogruppo di pazienti potrebbe essere parte integrante del fenotipo sintomatologico della malattia. I risultati della tipizzazione di tutti i geni analizzati mostrano un’alta frequenza di pazienti con metabolismo intermedio, elemento potenzialmente in grado di influire sulla risposta terapeutica soprattutto in caso di regime politerapico, come nel trattamento della narcolessia. In conclusione, sarebbe auspicabile l’esecuzione del test farmacogenetico in pazienti affetti da narcolessia con cataplessia.

Carcinoma polmonare non a piccole cellule T1aN0M0: Ruolo prognostico della Microvessel Density

Obiettivi. Valutare l’angiogenesi tumorale mediante la Microvessel density (MVD) come fattore predittivo di mortalità per tumore polmonare non a piccole cellule (NSCLC) pT1aN0M0 trattato chirurgicamente. Metodi. I dati demografici, clinici e istopatologici sono stati registrati per 82 pazienti (60 maschi, 22 femmine) sottoposti a resezione chirurgica in due diverse Chirurgie Toraciche tra gennaio 2002 e dicembre 2007 per tumori polmonari non a piccole cellule pT1AN0M0. La MVD è stata valutata mediante il conteggio visivo dei microvasi positivi alla colorazione immunoistochimica con anticorpo monoclonale anti-CD31 e definita come il numero medio di microvasi per 1 mm2 di campo ottico. Risultati. Sono state eseguite 59 lobectomie (72%) e 23 resezioni sublobari (28%). Reperti istopatologici: 43 adenocarcinomi (52%) e 39 neoplasie non- adenocarcinoma (48%) pT1aN0M0; MVD media: 161 (CD31/mm2); mediana: 148; range 50-365, cut-off=150. Una MVD elevata (> 150 CD31/mm2) è stata osservata in 40 pazienti (49%), una MVD ridotta ( ≤ 150 CD31/mm2 ) in 42 pazienti (51%). Sopravvivenze a 5 anni: 70 % e 95%, rispettivamente per il gruppo ad elevata MVD vs il gruppo a ridotta MVD con una p = 0,0041, statisticamente significativa. Il tipo di resezione chirurgica, il diametro del tumore, le principali comorbidità e l’istotipo nono sono stati fattori predittivi significativi di mortalità correlata alla malattia. La MVD è risultata essere superiore nel gruppo “Adenocarcinoma” (MVD mediana=180) rispetto al gruppo “Non-Adenocarcinoma (MVD mediana=125), con un test di Mann-Whitney statisticamente significativo (p < 0,0001). Nel gruppo “Adenocarcinoma” la sopravvivenza a 5 anni è stata del 66% e 93 %, rispettivamente per i pazienti con MVD elevata e ridotta (p = 0.043. Conclusioni. Il nostro studio ha mostrato che la Microvessel density valutata con la colorazione immunoistochimica per CD31 ha un valore prognostico rilevante nel carcinoma polmonare in stadio precoce pT1aN0M0.

Evolutionary genetics of lactase persistence in Eurasian human populations

Although ability to digest lactose generally declines after weaning in all mammals, in some human populations it persists also in adult individuals, a condition named lactase persistence (LP). Studies on the prevalence of the LP phenotype in worldwide human populations have shown that the frequency of this trait is highly variable in different ethnic groups, appearing to be positively correlated with the importance of milk in the diet. In particular, several single-nucleotide polymorphisms (SNPs) in the proximity of the LCT gene have been proved to be associated with LP. Nevertheless, few studies have till now analyzed genetic variation underlying LP in a wide set of Eurasian populations and, especially, in the Italian one. In the present study, we thus typed 40 SNPs surrounding the LCT gene in more than 1,000 samples from Italian and Arabic peninsulas to investigate patterns of LP-related genetic diversity in two regions which have played a pivotal role in the recent human evolutionary history according to their geographical position and historical/archaeological records. Our results underline a high and complex variability of the explored genomic region in both studied populations. In particular, a clear diversification of Northern Italian groups from the rest of the peninsula, was observed, with the formers being genetically more similar to Northern European populations than to Southern Italians. These observation are consistent with known decreasing pattern of LP from Northern to Southern Italy and suggest the possibility of an independent evolution of LP-associated genotypes in Northern Italy. A similar scenario was observed in the Arabian peninsula, with Dhofari Arabs from Southern Oman and Yemeni clustering together with respect to Arabs from Northern Oman and the subgroup of Omanis of Asian origin which appeared instead to be genetically closer to Europeans than to the rest of Arabic groups.

Identification and genetic diversity in phytoplasmas associated with diseases of cassava and other agronomic relevant crops in south-east Asia and Latin America

Identification and genetic diversity of phytoplasmas infecting tropical plant species, selected among those most agronomically relevant in South-east Asia and Latin America were studied. Correlation between evolutionary divergence of relevant phytoplasma strains and their geographic distribution by comparison on homologous genes of phytoplasma strains detected in the same or related plant species in other geographical areas worldwide was achieved. Molecular diversity was studied on genes coding ribosomal proteins, groEL, tuf and amp besides phytoplasma 16S rRNA. Selected samples infected by phytoplasmas belonging to diverse ribosomal groups were also studied by in silico RFLP followed by phylogenetic analyses. Moreover a partial genome annotation of a ‘Ca. P. brasiliense’ strain was done towards future application for epidemiological studies. Phytoplasma presence in cassava showing frog skin (CFSD) and witches’ broom (CWB) diseases in Costa Rica - Paraguay and in Vietnam – Thailand, respectively, was evaluated. In both cases, the diseases were associated with phytoplasmas related to aster yellows, apple proliferation and “stolbur” groups, while only phytoplasma related to X-disease group in CFSD, and to hibiscus witches’ broom, elm yellows and clover proliferation groups in CWB. Variability was found among strains belonging to the same ribosomal group but having different geographic origin and associated with different disease. Additionally, a dodder transmission assay to elucidate the role of phytoplasmas in CWB disease was carried out, and resulted in typical phytoplasma symptoms in periwinkle plants associated with the presence of aster yellows-related strains. Lethal wilt disease, a severe disease of oil palm in Colombia that is spreading throughout South America was also studied. Phytoplasmas were detected in symptomatic oil palm and identified as ‘Ca. P. asteris’, ribosomal subgroup 16SrI-B, and were distinguished from other aster yellows phytoplasmas used as reference strains; in particular, from an aster yellows strain infecting corn in the same country.

Identification of novel genetic alterations in pediatric cytogenetically normal acute myeloid leukemia by next-generation sequencing

Pediatric acute myeloid leukemia (AML) is a molecularly heterogeneous disease that arises from genetic alterations in pathways that regulate self-renewal and myeloid differentiation. While the majority of patients carry recurrent chromosomal translocations, almost 20% of childhood AML do not show any recognizable cytogenetic alteration and are defined as cytogenetically normal (CN)-AML. CN-AML patients have always showed a great variability in response to therapy and overall outcome, underlining the presence of unknown genetic changes, not detectable by conventional analyses, but relevant for pathogenesis, and outcome of AML. The development of novel genome-wide techniques such as next-generation sequencing, have tremendously improved our ability to interrogate the cancer genome. Based on this background, the aim of this research study was to investigate the mutational landscape of pediatric CN-AML patients negative for all the currently known somatic mutations reported in AML through whole-transcriptome sequencing (RNA-seq). RNA-seq performed on diagnostic leukemic blasts from 19 pediatric CN-AML cases revealed a considerable incidence of cryptic chromosomal rearrangements, with the identification of 21 putative fusion genes. Several of the fusion genes that were identified in this study are recurrent and might have a prognostic and/or therapeutic relevance. A paradigm of that is the CBFA2T3-GLIS2 fusion, which has been demonstrated to be a common alteration in pediatric CN-AML, predicting poor outcome. Important findings have been also obtained in the identification of novel therapeutic targets. On one side, the identification of NUP98-JARID1A fusion suggests the use of disulfiram; on the other, here we describe alteration-activating tyrosine kinases, providing functional data supporting the use of tyrosine kinase inhibitors to specifically inhibit leukemia cells. This study provides new insights in the knowledge of genetic alterations underlying pediatric AML, defines novel prognostic markers and putative therapeutic targets, and prospectively ensures a correct risk stratification and risk-adapted therapy also for the “all-neg” AML subgroup.

Methods and strategies to identify the mode of action of phytoactive compounds

Small molecules affecting biological processes in plants are widely used in agricultural practice as herbicides or plant growth regulators and in basic plant sciences as probes to study the physiology of plants. Most of the compounds were identified in large screens by the agrochemical industry, as phytoactive natural products and more recently, novel phytoactive compounds originated from academic research by chemical screens performed to induce specific phenotypes of interest. The aim of the present PhD thesis is to evaluate different approaches used for the identification of the primary mode of action (MoA) of a phytoactive compound. Based on the methodologies used for MoA identification, three approaches are discerned: a phenotyping approach, an approach based on a genetic screen and a biochemical screening approach.rnFour scientific publications resulting from my work are presented as examples of how a phenotyping approach can successfully be applied to describe the plant MoA of different compounds in detail.rnI. A subgroup of cyanoacrylates has been discovered as plant growth inhibitors. A set of bioassays indicated a specific effect on cell division. Cytological investigations of the cell division process in plant cell cultures, studies of microtubule assembly with green fluorescent protein marker lines in vivo and cross resistant studies with Eleusine indica plants harbouring a mutation in alpha-tubulin, led to the description of alpha-tubulin as a target site of cyanoacrylates (Tresch et al., 2005).rnII. The MoA of the herbicide flamprop-m-methyl was not known so far. The studies described in Tresch et al. (2008) indicate a primary effect on cell division. Detailed studies unravelled a specific effect on mitotic microtubule figures, causing a block in cell division. In contrast to other inhibitors of microtubule rearrangement such as dinitroanilines, flamprop-m-methyl did not influence microtubule assembly in vitro. An influence of flamprop-m-methyl on a target within the cytoskeleton signalling network could be proposed (Tresch et al., 2008).rnIII. The herbicide endothall is a protein phosphatase inhibitor structurally related to the natural product cantharidin. Bioassay studies indicated a dominant effect on dark-growing cells that was unrelated to effects observed in the light. Cytological characterisation of the microtubule cytoskeleton in corn tissue and heterotrophic tobacco cells showed a specific effect of endothall on mitotic spindle formation and ultrastructure of the nucleus in combination with a decrease of the proliferation index. The observed effects are similar to those of other protein phosphatase inhibitors such as cantharidin and the structurally different okadaic acid. Additionally, the observed effects show similarities to knock-out lines of the TON1 pathway, a protein phosphatase-regulated signalling pathway. The data presented in Tresch et al. (2011) associate endothall’s known in vitro inhibition of protein phosphatases with in vivo-effects and suggest an interaction between endothall and the TON1 pathway.rnIV. Mefluidide as a plant growth regulator induces growth retardation and a specific phenotype indicating an inhibition of fatty acid biosynthesis. A test of the cuticle functionality suggested a defect in the biosynthesis of very-long-chain fatty acids (VLCFA) or waxes. Metabolic profiling studies showed similarities with different groups of VLCFA synthesis inhibitors. Detailed analyses of VLCFA composition in tissues of duckweed (Lemna paucicostata) indicated a specific inhibition of the known herbicide target 3 ketoacyl-CoA synthase (KCS). Inhibitor studies using a yeast expression system established for plant KCS proteins verified the potency of mefluidide as an inhibitor of plant KCS enzymes. It could be shown that the strength of inhibition varied for different KCS homologues. The Arabidopsis Cer6 protein, which induces a plant growth phenotype similar to mefluidide when knocked out, was one of the most sensitive KCS enzymes (Tresch et al., 2012).rnThe findings of my own work were combined with other publications reporting a successful identification of the MoA and primary target proteins of different compounds or compound classes.rnA revised three-tier approach for the MoA identification of phytoactive compounds is proposed. The approach consists of a 1st level aiming to address compound stability, uniformity of effects in different species, general cytotoxicity and the effect on common processes like transcription and translation. Based on these findings advanced studies can be defined to start the 2nd level of MoA characterisation, either with further phenotypic characterisation, starting a genetic screen or establishing a biochemical screen. At the 3rd level, enzyme assays or protein affinity studies should show the activity of the compound on the hypothesized target and should associate the in vitro effects with the in vivo profile of the compound.