Disease-causing mutations improving the branch site and polypyrimidine tract: pseudoexon activation of LINE-2 and antisense Alu lacking the poly(T)-tail.

Cryptic exons or pseudoexons are typically activated by point mutations that create GT or AG dinucleotides of new 5' or 3' splice sites in introns, often in repetitive elements. Here we describe two cases of tetrahydrobiopterin deficiency caused by mutations improving the branch point sequence and polypyrimidine tracts of repeat-containing pseudoexons in the PTS gene. In the first case, we demonstrate a novel pathway of antisense Alu exonization, resulting from an intronic deletion that removed the poly(T)-tail of antisense AluSq. The deletion brought a favorable branch point sequence within proximity of the pseudoexon 3' splice site and removed an upstream AG dinucleotide required for the 3' splice site repression on normal alleles. New Alu exons can thus arise in the absence of poly(T)-tails that facilitated inclusion of most transposed elements in mRNAs by serving as polypyrimidine tracts, highlighting extraordinary flexibility of Alu repeats in shaping intron-exon structure. In the other case, a PTS pseudoexon was activated by an A>T substitution 9 nt upstream of its 3' splice site in a LINE-2 sequence, providing the first example of a disease-causing exonization of the most ancient interspersed repeat. These observations expand the spectrum of mutational mechanisms that introduce repetitive sequences in mature transcripts and illustrate the importance of intronic mutations in alternative splicing and phenotypic variability of hereditary disorders.

Systemic effects of epidural Methylprednisolone injection on glucose tolerance in diabetic patients.

ABSTRACT: BACKGROUND: Several studies have shown that in diabetic patients, the glycemic profile was disturbed after intra-articular injection of corticosteroids. Little is known about the impact of epidural injection in such patients. The goal of this study was double, at first comparing the glycaemic profile in diabetic patients after a unique injection of 80 mg of acetate methylprednisolone either intra-articular or epidural and secondly to compare the amount of systemic diffusion of the drug after both procedures. METHODS: Seventeen patients were included. Glycemic changes were compared in 9 diabetic patients following intra-articular (4 patients) and epidural injections (5 patients). Epidural injections were performed using the sacral route under fluoroscopic control in patients with lumbar spinal stenosis. Diabetes control had to stable for more than 10 days and the renal function to be preserved. Blood glucose was monitored using a validated continuous measuring device (GMS, Medtronic) the day before and for two days following the injection. Results were expressed in the form of daily glycemic profiles and as by mean, peak and minimal values +/ SD. The urinary excretion of methylprednisolone after the 2 routes of injection was analyzed in 8 patients (4 in each group). Urine samples were cropped one hour before the injections, then 4 times during the first day and 3 times a week for 2 weeks. The measurements included the free and conjugated fraction RESULTS: The glycaemic profile remains unchanged with no significant changes in the group of the 5 diabetic patients receiving epidural injections. On the other end, the average peak and mean values were enhanced up to 3 mmol/l above baseline two days after the infiltration in the groups of the 4 diabetic patients infiltrated intra-articular. The mean urinary excretion of the steroid was about ten times higher in the intra-articular versus epidural group: 7000 ng/ml versus 700 ng/ml. Looking at each individual there were marked differences especially after intra-articular injections. CONCLUSION: This is the first study to show that a single epidural steroid injection of 80 mg depot methylprednisolone had no effect on the glycemic control in diabetic patients. The absence of glycemic control changes correlated well with the very low urinary excretion of the drug after epidural injection. Trial registration NCT01420497.

Clinical experience with Adalimumab in a multicenter Swiss cohort of patients with Crohn's disease

Background. Des études précédentes ont démontré l'efficacité et la tolérance de l'adalimumab chez les patients avec maladie de Crohn modérée ou sévère. Les patients qu'on rencontre dans la pratique quotidienne peuvent être différents des patients rigoureusement sélectionnés dans les études contrôlées.But. Dans ce travail, nous résumons notre expérience avec l'adalimumab durant une période de 3 ans.Méthodes. Nous avons analysé rétrospectivement les dossiers de 55 patients atteints d'une maladie de Crohn modérée ou sévère et traités par adalimumab dans les hôpitaux universitaires de Bâle, Zurich, Genève et Lausanne, ainsi que dans un cabinet médical à Olten. Les informations collectées étaient les suivantes : données démographiques, localisation, phénotype et durée de la maladie, traitements chirurgicaux précédents, traitements précédents par anti-TNF alpha ou immunosuppresseur, le traitement concomitant et l'activité de la maladie à la « baseline » et durant le traitement. La sévérité de la maladie à l'inclusion a été établie en utilisant le score Harvey- Bradshaw Index (HBI). Durant le traitement, la rémission a été définie avec un HBI<4 et la réponse comme une réduction de l'HBI de plus de 3 points. L'analyse de régression logistique univariée a été utilisée pour déterminer si les variables étudiées étaient associées à la réponse ou à la rémission durant le traitement.Résultats. L'âge moyen des patients a été de 37.5 ± 11.4 ans et la durée moyenne de maladie à été de 12.7 ans. 29 des 55 patients étaient des fumeurs. Le traitement d'induction a été effectué chez 31 patients avec l'adalimumab en sous-cutané 160 mg à la semaine 0 et 80 mg à la semaine 2 et chez 24 patients avec 80 mg à la semaine 0 et 40 mg à la semaine 2. Le traitement d'entretien a été de 40 mg en sous-cutané toutes les 2 semaines. 13 patients (23.6%) ont nécessité l'augmentation de la dose d'adalimumab pour maintenir la rémission ou la réponse.Le taux de rémission et de réponse à la semaine 4-6 était de 52.7%, respectivement 83.6%. La rémission a été maintenue aux semaines 12, 24 et 52 chez 89.6%, 72.4%, respectivement 44.7% des patients. Le taux de rémission et de réponse n'a pas été influencé par le tabagisme, la location ou la durée de la maladie, la dose totale donnée durant le premier mois de traitement, la dose d'adalimumab par kilogramme-corps ou par le traitement précédent par infliximab. La rémission à la semaine 4-6 a été significativement plus élevée chez les patients intolérants à l'infliximab comparativement à ceux qui avaient perdu la réponse à l'infliximab (78.9% vs 42.1%, p=0.02). Le traitement par adalimumab a été bien toléré. Les effets secondaires les plus signalés ont été : la douleur au site d'injection (10.9%), l'asthénie (9%) et des infections (7.2%).Conclusions. L'adalimumab a démontré une bonne efficacité et tolérance dans la pratique quotidienne chez les patients avec une maladie de Crohn modérée ou sévère.

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Preferential binding of the methyl-CpG binding domain protein 2 at methylated transcriptional start site regions.

Methyl-CpG Binding Domain (MBD) proteins are thought to be key molecules in the interpretation of DNA methylation signals leading to gene silencing through recruitment of chromatin remodeling complexes. In cancer, the MBD-family member, MBD2, may be primarily involved in the repression of genes exhibiting methylated CpG at their 5' end. Here we ask whether MBD2 randomly associates methylated sequences, producing chance effects on transcription, or exhibits a more specific recognition of some methylated regions. Using chromatin and DNA immunoprecipitation, we analyzed MBD2 and RNA polymerase II deposition and DNA methylation in HeLa cells on arrays representing 25,500 promoter regions. This first whole-genome mapping revealed the preferential localization of MBD2 near transcription start sites (TSSs), within the region analyzed, 7.5 kb upstream through 2.45 kb downstream of 5' transcription start sites. Probe by probe analysis correlated MBD2 deposition and DNA methylation. Motif analysis did not reveal specific sequence motifs; however, CCG and CGC sequences seem to be overrepresented. Nonrandom association (multiple correspondence analysis, p < 0.0001) between silent genes, DNA methylation and MBD2 binding was observed. The association between MBD2 binding and transcriptional repression weakened as the distance between binding site and TSS increased, suggesting that MBD2 represses transcriptional initiation. This hypothesis may represent a functional explanation for the preferential binding of MBD2 at methyl-CpG in TSS regions.

Hydrocarbon biomarkers in the Topla-Mezica zinc-lead deposits, northern Karavanke/Drau Range, Slovenia: Paleoenvironment at the site of ore formation

The Mississippi Valley-type zinc and lead deposits at Topla (250,150 metric tons (t) of ore grading 1.0 wt % Zn and 3.3 wt % Pb) and Mezica (19 million metric tons (Mt) of ore grading 5.3 wt % Pb and 2.7 wt % Zn) occur within the Middle to Upper Triassic platform carbonate rocks of the northern Karavanke/Drau Range geotectonic units of the Eastern Alps, Slovenia. The ore and host rocks of these deposits have been investigated by a combination of inorganic and organic geochemical methods to determine major, trace, and rare earth element (REE) concentrations, hydrocarbon distribution, and stable isotope ratios of carbonates, kerogen, extractable organic matter, and individual hydrocarbons. These data combined with sedimentological evidence provide insight into the paleoenvironmental conditions at the site of ore formation. The carbonate isotope composition, the REE patterns, and the distribution of hydrocarbon biomarkers (normal alkanes and steranes) suggest a marine depositional environment. At Topla, a relatively high concentration of redox sensitive trace elements (V, Mo, U) in the host dolostones and REE patterns parallel to that of the North American shale composite suggest that sediments were deposited in a reducing environment. Anoxic conditions enhanced the preservation of organic matter and resulted in relatively higher total organic carbon contents (up to 0.4 wt %). The isotopic composition of the kerogen (delta C-13(kerogon) = -29.4 to -25.0 parts per thousand, delta N-15(kerogen) = -.13.6 to 6.8 parts per thousand) suggests that marine algae and/or bacteria were the main source of organic carbon with a very minor contribution from detrital continental plants and a varying degree of alteration. Extractable organic matter from Topla ore is generally depleted in C-13 compared to the associated kerogen, which is consistent with an indigenous source of the bitumens. The mineralization correlates with delta N-15(kerogen) values around 0 per mil, C-13 depleted kerogen, C-13 enriched n-heptadecane, and relatively high concentrations of bacteria] hydrocarbon biomarkers, indicating a high cyanobacterial biomass at the site of ore formation. Abundant dissimilatory sulfate-reducing bacteria, feeding on the cyanobacterial remains, led to accumulation of biogenic H2S in the pore water of the sediments. This biogenic H2S was mainly incorporated into sedimentary organic matter and diagenetic pyrite. Higher bacterial activity at the ore site also is indicated by specific concentration ratios of hydrocarbons, which are roughly correlated with total Pb plus Zn contents. This correlation is consistent with mixing of hydrothermal metal-rich, fluids and local bacteriogenic sulfide sulfur. The new geochemical data provide supporting evidence that Topla is a low-temperature Mississippi Valley-type deposit formed in an anoxic supratidal saline to hypersaline environment. A laminated cyanobacterial mat, with abundant sulfate-reducing bacteria was the main site of sulfate reduction.

Drug uptake in a rodent sarcoma model after intravenous injection or isolated lung perfusion of free/liposomal doxorubicin.

The distribution of free and liposomal doxorubicin (Liporubicin) administered by intravenous injection (IV) or isolated lung perfusion (ILP) was compared in normal and tumor tissues of sarcoma bearing rodent lungs. A single sarcomatous tumor was generated in the left lung of 35 Fischer rats, followed 10 days later by left-sided ILP (n=20) or IV drug administration (n=12), using 100 microg and 400 microg free or liposomal doxorubicin, respectively. The tumor and lung tissue drug concentration was measured by HPLC. Free doxorubicin administered by ILP resulted in a three-fold (100 microg) and 10-fold (400 microg) increase of the drug concentration in the tumor and normal lung tissue compared to IV administration. In contrast, ILP with Liporubicin resulted in a similar drug uptake in the tumor and lung tissue compared to IV injection. For both drug formulations and dosages, ILP resulted in a higher tumor to lung tissue drug ratio but also in a higher spatial heterogeneity of drug distribution within the lung compared to IV administration. ILP resulted in a higher tumor to lung tissue drug ratio and in a more heterogeneous drug distribution within the lung compared to IV drug administration.

Protective effect of intravitreal administration of tresperimus, an immunosuppressive drug, on experimental autoimmune uveoretinitis.

PURPOSE: To test the efficiency of locally administrated tresperimus in experimental autoimmune uveoretinitis (EAU). METHODS: EAU was induced in Lewis rats by S-antigen (S-Ag) immunization. Three intravitreal injections of tresperimus (prevention or prevention/treatment protocols) were performed at different time points after immunization. The pharmacokinetics of tresperimus was evaluated in the ocular tissues and plasma. The in vitro effect of tresperimus was evaluated on macrophages. EAU was graded clinically and histologically. Blood ocular barrier permeability was evaluated by protein concentration in ocular fluids. Immune response to S-Ag was examined by delayed type hypersensitivity, the expression of inflammatory cytokines in lymph nodes, ocular fluids and serum by multiplex ELISA, and in ocular cells by RT-PCR. RESULTS: In vitro, tresperimus significantly reduced the production of inflammatory cytokines by lipopolysaccharide-stimulated macrophages. In vivo, in the treatment protocol, efficient tresperimus levels were measured in the eye but not in the plasma up to 8 days after the last injection. Tresperimus efficiently reduced inflammation, retinal damage, and blood ocular barrier permeability breakdown. It inhibited nitric oxide synthase-2 and nuclear factor κBp65 expression in ocular macrophages. IL-2 and IL-17 were decreased in ocular media, while IL-18 was increased. By contrast, IL-2 and IL-17 levels were not modified in inguinal lymph nodes draining the immunization site. Moreover, cytokine levels in serum and delayed type hypersensitivity to S-Ag were not different in control and treated rats. In the prevention/treatment protocol, ocular immunosuppressive effects were also observed. CONCLUSIONS: Locally administered tresperimus appears to be a potential immunosuppressive agent in the management of intraocular inflammation.

Combined Ex-PRESS LR-50/IOL implantation in modified deep sclerectomy plus pharmacoemulsification for glaucoma associated with cataract

RAPPORT DE SYNTHESEBUTLe but de cette étude est de suivre prospectivement les résultats d'une sclérectomie profonde (SP) modifiée en utilisant le tube Ex-PRJESS LR-50, associée à une phacoémulsification avec implantation d'une lentille intraoculaire (LIO), dans la chirurgie combinée du glaucome et de la cataracte.METHODENous avons inclus dans l'étude 24 yeux de 24 patients présentant un glaucome médicalement non contrôlé et une cataracte justifiant son ablation.Une phacoémulsification avec implantation d'une LIO est effectuée. Puis le tube Ex-PRESS LR-50 est inséré au niveau du canal de Schlemm, dans la chambre antérieure, sous un volet scléral. Une SP postérieure partielle est ensuite pratiquée afin de créer une bulle de filtration intrasclérale.Le taux de succès complet a été défini par une pression intraoculaire (PIO) <18 mmHg sans traitement et le taux de succès relatif par une PIO <18 mmHg avec ou sans traitement. En cas de fibrose ou de kyste de la bulle de filtration, une injection sous-conjonctivale d'une solution de Mitomycin C à 0.02% est réalisée, avec ou sans needling.RESULTATSLe suivi moyen était de 40.1±10.8 [moyenne±DS] mois. En préopératoire, la PIO se situait à 18.1 ±5.3 mmHg; la meilleure acuité visuelle corrigée (MAVC) était mesurée à 0.6±0.3 (échelle de Snellen) et le nombre de médicaments hypotenseurs oculaires était de 2.3±1.1. La PIO a diminué de 25.4% à 24 mois et de 27.0% à 48 mois. A 24 mois, 19 patients (86.3%) avaient une MAVC supérieure ou égal à 0.5, et à 48 mois la MAVC était mesurée à 0.7±0.3. Lors de la dernière visite, le nombre moyen de médicaments se situait à 0.6±0.8 (p<0.05). Des injections sous conjonctivales d'une solution de Mitomycin C à 0.02% ont été nécessaires dans 5 yeux. Aucune érosion conjonctivale n'a été constatée. Deux complications majeures ont été observées. Une endophtalmie, deux jours après l'intervention chirurgicale avec phtisis secondaire du globe oculaire. Une obstruction du tube Ex-PRESS LR-50 par de la fibrine, ayant justifié son ablation avec SP classique en un autre site.CONCLUSIONLe tube Ex-PRESS LR-50 inséré dans la chambre antérieure avec une SP modifiée réduit efficacement la PIO dans la chirurgie combinée du glaucome et prévient l'érosion conjonctivale, une complication importante lorsque l'implant n'est pas couvert par un volet scléral.

Functional analysis of the post-transcriptional regulator RsmA reveals a novel RNA-binding site.

The RsmA family of RNA-binding proteins are global post-transcriptional regulators that mediate extensive changes in gene expression in bacteria. They bind to, and affect the translation rate of target mRNAs, a function that is further modulated by one or more, small, untranslated competitive regulatory RNAs. To gain new insights into the nature of this protein/RNA interaction, we used X-ray crystallography to solve the structure of the Yersinia enterocolitica RsmA homologue. RsmA consists of a dimeric beta barrel from which two alpha helices are projected. From structure-based alignments of the RsmA protein family from diverse bacteria, we identified key amino acid residues likely to be involved in RNA-binding. Site-specific mutagenesis revealed that arginine at position 44, located at the N terminus of the alpha helix is essential for biological activity in vivo and RNA-binding in vitro. Mutation of this site affects swarming motility, exoenzyme and secondary metabolite production in the human pathogen Pseudomonas aeruginosa, carbon metabolism in Escherichia coli, and hydrogen cyanide production in the plant beneficial strain Pseudomonas fluorescens CHA0. R44A mutants are also unable to interact with the small untranslated RNA, RsmZ. Thus, although possessing a motif similar to the KH domain of some eukaryotic RNA-binding proteins, RsmA differs substantially and incorporates a novel class of RNA-binding site.

Protein-binding site at the immunoglobulin mu membrane polyadenylylation signal: possible role in transcription termination.

mRNAs specifying immunoglobulin mu and delta heavy chains are encoded by a single large, complex transcription unit (mu + delta gene). The transcriptional activity of delta gene segments in terminally differentiated, IgM-secreting B lymphocytes is 10-20 times lower than in earlier B-lineage cells expressing delta mRNA. We find that transcription of the mu + delta gene in IgM-secreting murine myeloma cells terminates within a region of 500-1000 nucleotides immediately following the mu membrane (mu m) polyadenylylation site. Transcription decreases only minimally through this region in murine cell lines representative of earlier stages in B-cell development. A DNA fragment containing the mu m polyadenylylation signal gives protein-DNA complexes with different mobilities in gel retardation assays with nuclear extracts from myeloma cells than with nuclear extracts from earlier B-lineage cells. However, using a recently developed "footprinting" procedure in which protein-DNA complexes resolved in gel retardation assays are subjected to nucleolytic cleavage while still in the polyacrylamide gel, we find that the DNA sequences protected by factors from the two cell types are indistinguishable. The factor-binding site on the DNA is located 5' of the mu m polyadenylylation signal AATAAA and includes the 15-nucleotide-long A + T-rich palindrome CTGTAAACAAATGTC. This type of palindromic binding site exhibits orientation-dependent activity consistent with the reported properties of polymerase II termination signals. This binding site is followed by two sets of directly repeated DNA sequences with different helical conformation as revealed by their reactivity with the chemical nuclease 1,10-phenanthroline-copper. The close proximity of these features to the signals for mu m mRNA processing may reflect a linkage of the processes of developmentally regulated mu m polyadenylylation and transcription termination.

Evaluation of the anti-arenaviral activity of the subtilisin kexin isozyme-1/site-1 protease inhibitor PF-429242.

The cellular protease subtilisin kexin isozyme-1 (SKI-1)/site-1 protease (S1P) is implicated in the proteolytic processing of the viral envelope glycoprotein precursor (GPC) of arenaviruses, a step strictly required for production of infectious progeny. The small molecule SKI-1/S1P inhibitor PF-429242 was shown to have anti-viral activity against Old World arenaviruses. Here we extended these studies and show that PF-429242 also inhibits GPC processing and productive infection of New World arenaviruses, making PF-429242 a broadly active anti-arenaviral drug. In combination therapy, PF-429242 potentiated the anti-viral activity of ribavirin, indicating a synergism between the two drugs. A hallmark of arenaviruses is their ability to establish persistent infection in vitro and in vivo. Notably, PF-429242 was able to efficiently and rapidly clear persistent infection by arenaviruses. Interruption of drug treatment did not result in re-emergence of infection, indicating that PF-429242 treatment leads to virus extinction.

Evaluation of tumor vascularisation in two rat sarcoma models for studying isolated lung perfusion : Injection route determines the origin of tumour vessels

Résumé Introduction: La perfusion isolée cytostatique du poumon est une technique attractive qui permet l'administration des doses élevées d'un agent cytostatique tout en épargnant dans la mesure du possible la circulation systémique. Cependant, la perfusion de l'artère pulmonaire risque d'épargner le territoire pulmonaire vascularisé par l'intermédiaire des artères bronchiques, ce qui pourrait diminuer l'efficacité de ce traitement au cas où la lésion ciblée est vascularisée par les artères bronchiques. Ce travail est destiné au développement d'un modèle tumoral au niveau des poumons de rongeur (rat) porteur d'un sarcome pulmonaire afin de déterminer si la voie d'injection des cellules tumorales (intraveineuse, versus intratumorale) influencera la vascularisation des tumeurs (provenant du système artères pulmonaires ou artères bronchiques). Méthod: Des tumeurs de sarcomes pulmonaires ont été générées par injection d'une suspension cellulaire de sarcome, soit par injection intraveineuse, soit directement dans le parenchyme pulmonaire par thoracotomie. Ensuite, une perfusion isolée du poumon porteur de la tumeur à l'aide de l'encre a été effectuée, soit par l'artère pulmonaire, soit par le système des artères bronchiques. La distribution de l'encre dans les vaisseaux tumoraux ainsi que dans les vaisseaux non tumoraux du poumon adjacent a été investiguée à l'aide d'une analyse histologique des poumons perfusés. Résultat: L'administration intraveineuse et intratumorale de la suspension de cellules tumorales résulte en des tumeurs similaires sur le plan histologique. Néanmoins, l'injection intra-parenchymateuse démontre des tumeurs plus homogènes et avec un développement plus prédictible, était associée à une survie plus longue qu'après injection intraveineuse. Les analyses histologiques après perfusion isolée à l'aide de l'encre démontre que les tumeurs résultant de l'injection intraveineuse ont développé une vascularisation se basant sur le système d'artères pulmonaires tandis que les tumeurs émergeant après injection intraparenchymateuse ont développé une vascularisation provenant du système des artères bronchiques. Conclusion: Ce travail démontre pour la première fois l'importance du mode de génération de tumeurs pulmonaires en ce qui concerne leur future vascularisation, ce qui pourrait avoir un impact sur leur traitement par perfusion isolée du poumon. Abstract Isolated cytostatic lung perfusion (ILP) is an attractive technique allowing delivery of a high-dose of cytostatic agents to the lungs while limiting systemic toxicity. In developing a rat model of ILP, we have analysed the effect of the route of tumour cell injection on the source of tumour vessels. Pulmonary sarcomas were estab¬lished by injecting a sarcoma cell suspension either by the intravenous (i.v.) route or directly into the lung paren¬chyma. Ink perfusion through either pulmonary artery (PA) or bronchial arteries (BA) was performed and the characteristics of the tumour deposits defined. i.v. and direct injection methods induced pulmonary sarcoma nodules, with similar histological features. The intraparenchymal injection of tumour cells resulted in more reli¬able and reproducible tumour growth and was associat¬ed with a longer survival of the animals. i.v. injected tumours developed a PA-derived vascular tree whereas directly injected tumours developed a BA-derived vasculature.