Strategies to identify and further characterize novel and known genes involved in regulation of skeletogenesis

372 osteochondrodysplasias and genetically determined dysostoses were reported in 2007 [Superti-Furga and Unger, 2007]. For 215 of these conditions, an association with one or more genes can be stated, while the molecular changes for the remaining syndromes remain illusive to date. Thus, the present dissertation aims at the identification of novel genes involved in processes regarding cartilage/ bone formation, growth, differentiation and homeostasis, which may serve as candidate genes for the above mentioned conditions. Two different approaches were undertaken. Firstly, a high throughput EST sequencing project from a human fetal cartilage library was performed to identify novel genes in early skeletal development (20th week of gestation until 2nd year of life) that could be investigated as potential candidate genes. 5000 EST sequences were generated and analyzed representing 1573 individual transcripts, corresponding to known (1400) and to novel, yet uncharacterized genes (173). About 7% of the proteins were already described in cartilage/ bone development or homeostasis, showing that the generated library is tissue specific. The remaining profile of this library was compared to previously published libraries from different time points (8th–12th, 18th–20th week and adult human cartilage) that also showed a similar distribution, reflecting the quality of the presented library analyzed. Furthermore, three potential candidate genes (LRRC59, CRELD2, ZNF577) were further investigated and their potential involvement in skeletogenesis was discussed. Secondly, a disease-orientated approach was undertaken to identify downstream targets of LMX1B, the gene causing Nail-Patella syndrome (NPS), and to investigate similar conditions. Like NPS, Genitopatellar syndrome (GPS) is characterized by aplasia or hypoplasia of the patella and renal anomalies. Therefore, six GPS patients were enrolled in a study to investigate the molecular changes responsible for this relatively rare disease. A 3.07 Mb deletion including LMX1B and NR5A1 (SF1) was found in one female patient that showed features of both NPS and GPS and investigations revealed a 46,XY karyotype and ovotestes indicating true hermaphroditism. The microdeletion was not seen in any of the five other patients with GPS features only, but a potential regulatory element between the two genes cannot be ruled out yet. Since Lmx1b is expressed in the dorsal limb bud and in podocytes, proteomic approaches and expression profiling were performed with murine material of the limbs and the kidneys to identify its downstream targets. After 2D-gel electrophoresis with protein extracts from E13.5 fore limb buds and newborn kidneys of Lmx1b wild type and knock-out mice and mass spectrometry analysis, only two proteins, agrin and carbonic anhydrase 2, remained of interest, but further analysis of the two genes did not show a transcriptional down regulation by Lmx1b. The focus was switched to expression profiles and RNA from newborn Lmx1b wild type and knock-out kidneys was compared by microarray analysis. Potential Lmx1b targets were almost impossible to study, because of the early death of Lmx1b deficient mice, when the glomeruli, containing podocytes, are still immature. Because Lmx1b is also expressed during limb development, RNA from wild type and knock-out Lmx1b E11.5 fore limb buds was investigated by microarray, revealing four potential Lmx1b downstream targets: neuropilin 2, single-stranded DNA binding protein 2, peroxisome proliferative activated receptor, gamma, co-activator 1 alpha, and short stature homeobox 2. Whole mount in situ hybridization strengthened a potential down regulation of neuropilin 2 by Lmx1b, but further investigations including in situ hybridization and protein-protein interaction studies will be needed.

Nuovo scaffold biomimetico per il trattamento delle lesioni osteocondrali: studio clinico pilota

Nel corso degli anni diverse sono le tecniche proposte per il trattamento delle lesioni osteocondrali, da quelle mini-invasive con stimolazione midollare fino a quelle più aggressive basate sul trapianto di tessuti autologhi o eterologhi. Tutti questi metodi hanno comunque dei difetti ed è questo il motivo per cui il trattamento delle lesioni osteocondrali rappresenta tuttora una sfida per il chirurgo ortopedico, in considerazione dell’alta specializzazione e del basso potere di guarigione del tessuto cartilagineo. Buoni risultati sono stati ottenuti con innesti bioingegnerizzati o matrici polimeriche impiantati nei siti danneggiati. La quantità di scaffolds in uso per la riparazione condrale ed osteocondrale è molto ampia; essi differiscono non solo per il tipo di materiali usati per la loro realizzazione, ma anche per la presenza di promotori di una o più linee cellulari , su base condrogenica o osteogenica. Quando ci si approccia ad una lesione condrale di grandi dimensioni, l’osso sub-condrale è anch’esso coinvolto e necessita di trattamento per ottenere il corretto ripristino degli strati articolari più superficiali. La scelta più giusta sembra essere un innesto osteocondrale bioingegnerizzato, pronto per l’uso ed immediatamente disponibile, che consenta di effettuare il trattamento in un unico tempo chirurgico. Sulla base di questo razionale, dopo uno studio preclinico animale e previa autorizzazione del comitato etico locale, abbiamo condotto uno studio clinico clinico pilota utilizzando un nuovo innesto biomimetico nanostrutturato per il trattamento di lesioni condrali ed osteocondrali del ginocchio; la sua sicurezza e maneggevolezza, così come la facile riproducibilità della tecnica chirurgica ed i risultati clinici ottenuti sono stati valutati nel tempo a 6, 12, 24, 36 e 48 mesi dall’impianto in modo da testare il suo potenziale intrinseco senza l’aggiunta di alcuna linea cellulare.

Trattamento delle lesioni osteocondrali di grado I e II mediante infiltrazione intra-articolare di fattori di crescita autologhi (plasma rich in platelets)

The use of Platelet-rich plasma (PRP), a platelet concentrate made of autogenous blood, is becoming use in the treatment of some orthopaedic diseases. The aim of this study is to assess the effect of PRP on articular cartilage defects in a rabbit model (10 subjects). Twenty osteochondral defects created in the femoropatellar groove, were in ten cases left untreated and in ten cases treated with autogenous PRP. PRP was obtained using a double centrifugation of the rabbit’s blood harvested before the operation. 30 days after the lesion was made in both knee, the left one in each rabbit was treated by a PRP injection, followed by other two injection at 45 and 60 days. Tissue specimens were assessed by macroscopic examination and histological evaluation, that showed a better healing of the lesions in the knee treated with PRP injections.

A new method for continuous quality control of nsm cfrp systems

In the last decade the near-surface mounted (NSM) strengthening technique using carbon fibre reinforced polymers (CFRP) has been increasingly used to improve the load carrying capacity of concrete members. Compared to externally bonded reinforcement (EBR), the NSM system presents considerable advantages. This technique consists in the insertion of carbon fibre reinforced polymer laminate strips into pre-cut slits opened in the concrete cover of the elements to be strengthened. CFRP reinforcement is bonded to concrete with an appropriate groove filler, typically epoxy adhesive or cement grout. Up to now, research efforts have been mainly focused on several structural aspects, such as: bond behaviour, flexural and/or shear strengthening effectiveness, and energy dissipation capacity of beam-column joints. In such research works, as well as in field applications, the most widespread adhesives that are used to bond reinforcements to concrete are epoxy resins. It is largely accepted that the performance of the whole application of NSM systems strongly depends on the mechanical properties of the epoxy resins, for which proper curing conditions must be assured. Therefore, the existence of non-destructive methods that allow monitoring the curing process of epoxy resins in the NSM CFRP system is desirable, in view of obtaining continuous information that can provide indication in regard to the effectiveness of curing and the expectable bond behaviour of CFRP/adhesive/concrete systems. The experimental research was developed at the Laboratory of the Structural Division of the Civil Engineering Department of the University of Minho in Guimar\~aes, Portugal (LEST). The main objective was to develop and propose a new method for continuous quality control of the curing of epoxy resins applied in NSM CFRP strengthening systems. This objective is pursued through the adaptation of an existing technique, termed EMM-ARM (Elasticity Modulus Monitoring through Ambient Response Method) that has been developed for monitoring the early stiffness evolution of cement-based materials. The experimental program was composed of two parts: (i) direct pull-out tests on concrete specimens strengthened with NSM CFRP laminate strips were conducted to assess the evolution of bond behaviour between CFRP and concrete since early ages; and, (ii) EMM-ARM tests were carried out for monitoring the progressive stiffness development of the structural adhesive used in CFRP applications. In order to verify the capability of the proposed method for evaluating the elastic modulus of the epoxy, static E-Modulus was determined through tension tests. The results of the two series of tests were then combined and compared to evaluate the possibility of implementation of a new method for the continuous monitoring and quality control of NSM CFRP applications.

Analisi e realizzazione di un convertitore multilivello ad alta efficienza per applicazioni fotovoltaiche

Nei primi vent’anni, la ricerca in ambito fotovoltaico si è focalizzata sull’evoluzione di quelle tecnologie associate alla semplice cella ed al sistema intero, per offrire miglioramenti con particolare riguardo al fronte dell’efficienza. Negli ultimi decenni, lo studio sull’energia rinnovabile ha ampliato i propri confini, sino a quella branca denominata elettronica di potenza, che ne permette la conversione e lo sfruttamento da parte dell’utente. L’elaborato si propone quindi di apportare un contributo verso tale direzione, teorico piuttosto che pratico, esaminando dapprima il mondo che effettivamente circonda l’impianto fotovoltaico grid-connected e successivamente ponderando e pianificando le scelte che conseguono dall’analisi letteraria. Particolare attenzione sarà rivolta al concetto di multilivello relativo agli inverter e agli aspetti che ne comportano il largo utilizzo nell’elettronica di potenza. Si stima che i primi brevetti risalgano a circa trent’anni orsono e uno di questi, tracciabile, riguarderebbe la configurazione a cascata di full-bridge, alimentati separatamente in DC, per ottenere a valle una scala di tensioni AC. Per mezzo di manipolazioni, nascerà in seguito il diode-clamped, attuale predecessore del Neutral Point Clamped T-Type Inverter. Si introdurranno pertanto le principali caratteristiche che contraddistinguono il convertitore, peculiare riguardo per la configurazione single leg nonché trifase. Ardua sarà la scelta sulla tecnica di controllo dell’inverter, sia per quanto concerne la fase simulativa che quella realizzativa, in quanto il dispositivo è indubbiamente considerato innovativo nel proprio campo di appartenenza. Convalidando la letteratura per mezzo di opportune simulazioni, si potrà procedere alla progettazione e quindi all’assemblaggio della scheda che effettivamente include l’inverter. Il lavoro implicherà numerose prove, effettuate in svariate condizioni di funzionamento, al fine di sostenere le conclusioni teoriche.

Sviluppo di un framework per la gestione di documenti multimediali

Questo lavoro di tesi si propone di realizzare un sistema in grado non solo di gestire la similarità tra media di stesso tipo, in modo tale da essere al pari per potenzialità in catalogazione e ricerca dei sistemi esistenti, ma di introdurre anche il concetto di similarità tra documenti, i quali contengono media di diverso tipo. Anche se esistono già DBMS in grado di gestire tipi di media complessi, nessuno ha un modello in grado di gestire la compresenza di più tipi di dato efficientemente. Per realizzare un sistema multimediale che sia in grado di gestire non solo la similarità tra media compatibili per tipo ma in generale la ricerca tra documenti si è deciso di utilizzare sistemi per media specifici già esistenti e di integrarli in modo da farli cooperare. A tale proposito si è deciso inizialmente di creare un sistema in grado di gestire documenti che possano contenere inizialmente parti testuali, immagini, video e serie temporali. E’ chiaro intuire come le differenze tra i singoli sistemi (e tra le singole tipologie di dati) rendano quasi impossibile il confronto tra media di tipo diverso esaminandone solamente il contenuto. Per questo un sistema multimediale come quello proposto non potrà effettuare ricerca per contenuto tra media differenti (a parte tra immagini e video in cui può essere possibile confrontare l’immagine con gli screenshot che compongono un video) ma si baserà principalmente sul confronto semantico tra media di tipo diverso e lo combinerà invece con ricerche per metadati e contenuto tra media dello stesso tipo. In questa tesi verranno analizzate le tecnologie utilizzate, le modifiche apportate ai framework esistenti e le novità introdotte per realizzare il sistema generale e in seguito verrà proposta la realizzazione due applicazioni su casi reali per dimostrare l’efficacia di tale sistema.

Molecular Dynamics Simulation of a PNA·DNA·PNA Triple Helix in Aqueous Solution

Molecular dynamics simulations have been used to explore the conformational flexibility of a PNA·DNA·PNA triple helix in aqueous solution. Three 1.05 ns trajectories starting from different but reasonable conformations have been generated and analyzed in detail. All three trajectories converge within about 300 ps to produce stable and very similar conformational ensembles, which resemble the crystal structure conformation in many details. However, in contrast to the crystal structure, there is a tendency for the direct hydrogen-bonds observed between the amide hydrogens of the Hoogsteen-binding PNA strand and the phosphate oxygens of the DNA strand to be replaced by water-mediated hydrogen bonds, which also involve pyrimidine O2 atoms. This structural transition does not appear to weaken the triplex structure but alters groove widths and so may relate to the potential for recognition of such structures by other ligands (small molecules or proteins). Energetic analysis leads us to conclude that the reason that the hybrid PNA/DNA triplex has quite different helical characteristics from the all-DNA triplex is not because the additional flexibility imparted by the replacement of sugar−phosphate by PNA backbones allows motions to improve base-stacking but rather that base-stacking interactions are very similar in both types of triplex and the driving force comes from weak but definate conformational preferences of the PNA strands.

Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees

The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 900. This bend results almost entirely from two 400 kinks that occur between TG/CA base pairs at positions 5 and 6 on each side of the dyad axis of the complex. DNA sequence discrimination by CAP derives both from sequence-dependent distortion of the DNA helix and from direct hydrogen-bonding interactions between three protein side chains and the exposed edges of three base pairs in the major groove of the DNA. The structure of this transcription factor-DNA complex provides insights into possible mechanisms of transcription activation

Vibronic Spectra of Jet-Cooled 2-Aminopurine center dot H2O Clusters Studied by UV Resonant Two-Photon Ionization Spectroscopy and Quantum Chemical Calculations

For understanding the major- and minor-groove hydration patterns of DNAs and RNAs, it is important to understand the local solvation of individual nucleobases at the molecular level. We have investigated the 2-aminopurine center dot H2O. monohydrate by two-color resonant two-photon ionization and UV/UV hole-burning spectroscopies, which reveal two isomers, denoted A and B. The electronic spectral shift delta nu of the S-1 <- S-0 transition relative to bare 9H-2-aminopurine (9H-2AP) is small for isomer A (-70 cm(-1)), while that of isomer B is much larger (delta nu = 889 cm(-1)). B3LYP geometry optimizations with the TZVP basis set predict four cluster isomers, of which three are doubly H-bonded, with H2O acting as an acceptor to a N-H or -NH2 group and as a donor to either of the pyrimidine N sites. The "sugar-edge" isomer A is calculated to be the most stable form with binding energy D-e = 56.4 kJ/mol. Isomers B and C are H-bonded between the -NH2 group and pyrimidine moieties and are 2.5 and 6.9 kJ/mol less stable, respectively. Time-dependent (TD) B3LYP/TZVP calculations predict the adiabatic energies of the lowest (1)pi pi* states of A and B in excellent agreement with the observed 0(0)(0) bands; also, the relative intensities of the A and B origin bands agree well with the calculated S-0 state relative energies. This allows unequivocal identification of the isomers. The R2PI spectra of 9H-2AP and of isomer A exhibit intense low-frequency out-of-plane overtone and combination bands, which is interpreted as a coupling of the optically excited (1)pi pi* state to the lower-lying (1)n pi* dark state. In contrast, these overtone and combination bands are much weaker for isomer B, implying that the (1)pi pi* state of B is planar and decoupled from the (1)n pi* state. These observations agree with the calculations, which predict the (1)n pi* above the (1)pi pi* state for isomer B but below the (1)pi pi* for both 9H-2AP and isomer A.

Canine distemper virus infects canine keratinocytes and immune cells by using overlapping and distinct regions located on one side of the attachment protein

The morbilliviruses measles virus (MeV) and canine distemper virus (CDV) both rely on two surface glycoproteins, the attachment (H) and fusion proteins, to promote fusion activity for viral cell entry. Growing evidence suggests that morbilliviruses infect multiple cell types by binding to distinct host cell surface receptors. Currently, the only known in vivo receptor used by morbilliviruses is CD150/SLAM, a molecule expressed in certain immune cells. Here we investigated the usage of multiple receptors by the highly virulent and demyelinating CDV strain A75/17. We based our study on the assumption that CDV-H may interact with receptors similar to those for MeV, and we conducted systematic alanine-scanning mutagenesis on CDV-H throughout one side of the beta-propeller documented in MeV-H to contain multiple receptor-binding sites. Functional and biochemical assays performed with SLAM-expressing cells and primary canine epithelial keratinocytes identified 11 residues mutation of which selectively abrogated fusion in keratinocytes. Among these, four were identical to amino acids identified in MeV-H as residues contacting a putative receptor expressed in polarized epithelial cells. Strikingly, when mapped on a CDV-H structural model, all residues clustered in or around a recessed groove located on one side of CDV-H. In contrast, reported CDV-H mutants with SLAM-dependent fusion deficiencies were characterized by additional impairments to the promotion of fusion in keratinocytes. Furthermore, upon transfer of residues that selectively impaired fusion induction in keratinocytes into the CDV-H of the vaccine strain, fusion remained largely unaltered. Taken together, our results suggest that a restricted region on one side of CDV-H contains distinct and overlapping sites that control functional interaction with multiple receptors.

Development and validation of a real-time quantitative PCR assay for rapid identification of Bacillus anthracis in environmental samples

A real-time polymerase chain reaction (PCR) assay was developed for rapid identification of Bacillus anthracis in environmental samples. These samples often harbor Bacillus cereus bacteria closely related to B. anthracis, which may hinder its specific identification by resulting in false positive signals. The assay consists of two duplex real-time PCR: the first PCR allows amplification of a sequence specific of the B. cereus group (B. anthracis, B. cereus, Bacillus thuringiensis, Bacillus weihenstephanensis, Bacillus pseudomycoides, and Bacillus mycoides) within the phosphoenolpyruvate/sugar phosphotransferase system I gene and a B. anthracis specific single nucleotide polymorphism within the adenylosuccinate synthetase gene. The second real-time PCR assay targets the lethal factor gene from virulence plasmid pXO1 and the capsule synthesis gene from virulence plasmid pXO2. Specificity of the assay is enhanced by the use of minor groove binding probes and/or locked nucleic acids probes. The assay was validated on 304 bacterial strains including 37 B. anthracis, 67 B. cereus group, 54 strains of non-cereus group Bacillus, and 146 Gram-positive and Gram-negative bacteria strains. The assay was performed on various environmental samples spiked with B. anthracis or B. cereus spores. The assay allowed an accurate identification of B. anthracis in environmental samples. This study provides a rapid and reliable method for improving rapid identification of B. anthracis in field operational conditions.

Identification of key residues in virulent canine distemper virus hemagglutinin that control CD150/SLAM-binding activity

Morbillivirus cell entry is controlled by hemagglutinin (H), an envelope-anchored viral glycoprotein determining interaction with multiple host cell surface receptors. Subsequent to virus-receptor attachment, H is thought to transduce a signal triggering the viral fusion glycoprotein, which in turn drives virus-cell fusion activity. Cell entry through the universal morbillivirus receptor CD150/SLAM was reported to depend on two nearby microdomains located within the hemagglutinin. Here, we provide evidence that three key residues in the virulent canine distemper virus A75/17 H protein (Y525, D526, and R529), clustering at the rim of a large recessed groove created by beta-propeller blades 4 and 5, control SLAM-binding activity without drastically modulating protein surface expression or SLAM-independent F triggering.

eIF4E is an important determinant of adhesion and pseudohyphal growth of the yeast S. cerevisiae

eIF4E, the cytoplasmatic cap-binding protein, is required for efficient cap-dependent translation. We have studied the influence of mutations that alter the activity and/or expression level of eIF4E on haploid and diploid cells in the yeast S. cerevisiae. Temperature-sensitive eIF4E mutants with reduced levels of expression and reduced cap-binding affinity clearly show a loss in haploid adhesion and diploid pseudohyphenation upon starvation for nitrogen. Some of these mutations affect the interaction of the cap-structure of mRNAs with the cap-binding groove of eIF4E. The observed reduction in adhesive and pseudohyphenating properties is less evident for an eIF4E mutant that shows reduced interaction with p20 (an eIF4E-binding protein) or for a p20-knockout mutant. Loss of adhesive and pseudohyphenating properties was not only observed for eIF4E mutants but also for knockout mutants of components of eIF4F such as eIF4B and eIF4G1. We conclude from these experiments that mutations that affect components of the eIF4F-complex loose properties such as adhesion and pseudohyphal differentiation, most likely due to less effective translation of required mRNAs for such processes.

[Medium-term results after m. vastus medialis obliquus-plasty for lateral patellar dislocation]

Progressive retropatellar arthrosis is often seen in dated rigid distal realignment (i.e. osteotomy of tuberositas) at long-term follow-ups. Therefore, operations for lateral dislocation of the patella are still discussed controversially. Dynamic, proximal realignments seem to have lower rates of arthrosis but higher rates of redislocation. Recently, in anatomic and biomechanic studies, the m. vastus medialis obliquus (vmo) was found to be one of the most important proximal restraints to lateral dislocation of the patella.A total of 28 patients (mean age 21.5 years) were treated between 1994 and 2003 with a plasty of the vmo for lateral patellar dislocation. The technique was performed for most etiologies of femoropatellar instability.For this proximal soft tissue technique, the muscle tendon is detached from its patellar insertion. Subsequently, the tendon is reinserted at the patella 10-15 mm more distally and fixed with Mitek anchors. Full weight bearing in extension is possible immediately after surgery. An active vastus medialis training is started after 6 weeks.Of the patients, 27 were evaluated clinically and radiologically in 2004 (a mean of 5 years postoperatively). A total of 83% of the patients estimated the result to be good or excellent, 10% were satisfied and 7% were discontent. The mean Lysholm-Knee-Score was 83.1 points. Two patients suffered a patella redislocation (7%). A statistically significant improvement of the congruence angle was noted in the radiographs, even in medium-term controls. In 89% of the cases no or only little retropatellar arthrosis was observed. These 5 year results are comparable to those of other techniques for distal or proximal realignments. The rate of redislocation was below average. Compared to the rate of retropatellar arthrosis in long-term results of rigid distal realignment, our patients demonstrated a relative low rate after 5 years. We attribute this to the minimal interference in physiological joint mechanics and to the restored anatomy. In terms of future long-term results, our findings are promising. The idea of a proximal dynamic stabilization and the causal operative approach at the origin of pathology using vmo-plasty was confirmed in recent anatomic and biomechanic studies. Over or under correction of soft tissues could be adapted. More rigid techniques of distal realignment do not allow an adaptation to this extent and can lead to prearthrotic hyperpression in the medial femoropatellar and femorotibial joints.

An in vivo study of a growth-factor enhanced, cell free, two-layered collagen-tricalcium phosphate in deep osteochondral defects

Focal osteochondral defects are still a challenging problem in joint surgery. We have developed a two-layered implant consisting of a basal porous beta-tricalcium phosphate (TCP) for bone reconstruction and a superficial fibrous collagen type I/III layer for cartilage regeneration. Fifty-four osteochondral defects in the trochlear groove of 27 Göttinger Minipigs were created and either left untreated, treated with the implant alone, or the implant augmented with an additional growth factor mixture, which was assumed to stimulate cell and tissue differentiation. Follow-up was 6, 12 and 52 weeks with n=6 for each group. The repair tissue was evaluated for its gross appearance and biomechanical properties. Histological sections were semi-quantitatively scored for their histomorphological structure. Treatment with the two-layered implant improved defect filling and subchondral bone repair at 6 and 12 weeks follow-up. The TCP was replaced by cancellous bone at 52 weeks. Cartilage repair tissue mainly consisted of fibrocartilage and showed a moderate cell density up to the joint surface. Growth factor treatment improved the mechanical and histomorphological properties of the cartilage repair tissue at 12, but not at 52 weeks postoperatively. In conclusion, the two-layered collagen-TCP implant augmented with chondroinductive growth factors seems a promising new option for the treatment of deep osteochondral defects in joint surgery.