Homologous DNA pairing domain peptides of RecA protein: intrinsic propensity to form beta-structures and filaments.

The 20 amino acid residue peptides derived from RecA loop L2 have been shown to be the pairing domain of RecA. The peptides bind to ss- and dsDNA, unstack ssDNA, and pair the ssDNA to its homologous target in a duplex DNA. As shown by circular dichroism, upon binding to DNA the disordered peptides adopt a beta-structure conformation. Here we show that the conformational change of the peptide from random coil to beta-structure is important in binding ss- and dsDNA. The beta-structure in the DNA pairing peptides can be induced by many environmental conditions such as high pH, high concentration, and non-micellar sodium dodecyl sulfate (6 mM). This behavior indicates an intrinsic property of these peptides to form a beta-structure. A beta-structure model for the loop L2 of RecA protein when bound to DNA is thus proposed. The fact that aromatic residues at the central position 203 strongly modulate the peptide binding to DNA and subsequent biochemical activities can be accounted for by the direct effect of the aromatic amino acids on the peptide conformational change. The DNA-pairing domain of RecA visualized by electron microscopy self-assembles into a filamentous structure like RecA. The relevance of such a peptide filamentous structure to the structure of RecA when bound to DNA is discussed.

Pial and arachnoid welding for restoration of normal cord anatomy after excision of intramedullary spinal cord tumors.

A significant postoperative problem in patients undergoing excision of intramedullary tumors is painful dysesthesiae, attributed to various causes, including edema, arachnoid scarring and cord tethering. The authors describe a technique of welding the pia and arachnoid after the excision of intramedullary spinal cord tumors used in seven cases. Using a fine bipolar forcep and a low current, the pial edges of the myelotomy were brought together and welded under saline irrigation. A similar method was used for closing the arachnoid while the dura was closed with a running 5-0 vicryl suture. Closing the pia and arachnoid restores normal cord anatomy after tumor excision and may reduce the incidence of postoperative painful dysesthesiae.

Crystal structure of yeast peroxisomal multifunctional enzyme: structural basis for substrate specificity of (3R)-hydroxyacyl-CoA dehydrogenase units.

(3R)-hydroxyacyl-CoA dehydrogenase is part of multifunctional enzyme type 2 (MFE-2) of peroxisomal fatty acid beta-oxidation. The MFE-2 protein from yeasts contains in the same polypeptide chain two dehydrogenases (A and B), which possess difference in substrate specificity. The crystal structure of Candida tropicalis (3R)-hydroxyacyl-CoA dehydrogenase AB heterodimer, consisting of dehydrogenase A and B, determined at the resolution of 2.2A, shows overall similarity with the prototypic counterpart from rat, but also important differences that explain the substrate specificity differences observed. Docking studies suggest that dehydrogenase A binds the hydrophobic fatty acyl chain of a medium-chain-length ((3R)-OH-C10) substrate as bent into the binding pocket, whereas the short-chain substrates are dislocated by two mechanisms: (i) a short-chain-length 3-hydroxyacyl group ((3R)-OH-C4) does not reach the hydrophobic contacts needed for anchoring the substrate into the active site; and (ii) Leu44 in the loop above the NAD(+) cofactor attracts short-chain-length substrates away from the active site. Dehydrogenase B, which can use a (3R)-OH-C4 substrate, has a more shallow binding pocket and the substrate is correctly placed for catalysis. Based on the current structure, and together with the structure of the 2-enoyl-CoA hydratase 2 unit of yeast MFE-2 it becomes obvious that in yeast and mammalian MFE-2s, despite basically identical functional domains, the assembly of these domains into a mature, dimeric multifunctional enzyme is very different.

Microscopic origin of exchange bias in core/shell nanoparticles

We report the results of Monte Carlo simulations with the aim to clarify the microscopic origin of exchange bias in the magnetization hysteresis loops of a model of individual core/shell nanoparticles. Increase of the exchange coupling across the core/shell interface leads to an enhancement of exchange bias and to an increasing asymmetry between the two branches of the loops which is due to different reversal mechanisms. A detailed study of the magnetic order of the interfacial spins shows compelling evidence that the existence of a net magnetization due to uncompensated spins at the shell interface is responsible for both phenomena and allows to quantify the loop shifts directly in terms of microscopic parameters with striking agreement with the macroscopic observed values.

Pouchography, CT, and MRI features of ileal J pouch-anal anastomosis

OBJECTIVE: Our objective is to describe pouchography, CT, and MRI features of the J-shaped pouch, both normal and with pouch-related complications. CONCLUSION: Pouchography is performed before closure of the loop ileostomy to assess the integrity of the ileal pouch and anastomosis. CT and MRI can be performed when postoperative complications, such as small-bowel obstruction, pouchitis, leakage, abscess, intramural hematoma, desmoid tumor, or recurrent Crohn's disease, are suspected.

Examination of Existing Highway Maintenance Garage Locations in Tama and Blairstown Study Area, 1983

An optimum allocation model has been utilized to examine the existing allocation of highway segments to maintenance garages in the Tama and Blairstown study area. The model has also been used to evaluate the financial impact of closing the highway maintenance garages at Tama and Blairstown and building a new garage at the junction of U.S. 30 and Iowa 21. The examination of the study area shows that only 13 of 91 highway segments were reallocated under optimum procedures at an annual operational savings of approximately $13,200. The study concludes there would be an annual operational savings of approximately $48,200 if the garages at Tama and Blairstown were closed and a new garage was built at the junction of U.S. 30 and Iowa 21.

Low environmental impact bleaching sequences for attaining high brightness level with eucalyptus SPP pulp

The alternatives used for minimizing the usage of chlorine dioxide in bleaching sequences included a hot acid hydrolysis (Ahot) stage, the use of hot chlorine dioxide (Dhot) and ozone stages at medium consistency and high consistency (Zmc and Zhc), in addition to stages with atmospheric hydrogen peroxide (P) and pressurized hydrogen peroxide (PO). The results were interpreted based on the cost of the chemical products, bleaching process yields and on minimizing the environmental impact of the bleaching process. In spite of some process restrictions, high ISO brightness levels were kept around 90 % brightness. Additionally, the inclusion of stages like acid hydrolysis, pressurized peroxide and ozone in the bleaching sequences provided an increase in operating flexibility, aimed at reducing environmental impact (ECF Light). The Dhot(EOP)D(PO) sequence presented lower operating cost for ISO brightness above 92 %. However, this kind of sequence was not allowed for closing the wastewater circuit, even partially. For ISO brightness level around 91%, the AhotZhcDP sequence presented a lower operating cost than the others

Viral- and myelin-specific cellular immune response in patients treated with natalizumab: a cross-sectional and a longitudinal prospective study

Introduction: Natalizumab, a monoclonal antibody binding to the alpha4 integrins, is efficient in preventing relapses and progression of disability in multiple sclerosis (MS) patients. However, a total of seven MS patients treated with natalizumab suffered from progressive multifocal leukoencephalopathy (PML), on a total of 53?000 patients (data of March 6, 2009) treated with this drug. PML is a disease affecting immunosuppressed people, which is caused by the polyomavirus JC (JCV). This virus produces a lytic infection of the oligodendrocytes. Yet, natalizumab cannot be considered as a classical immunosuppressant, such as suggested by the fact that no increased incidence of other opportunistic infections was reported with this drug. It has been postulated that, by closing the blood-brain, natalizumab might prevent JCV-specific CD8_ T cells to reach the CNS and perform immune surveillance. Alternatively, it has been suggested that this drug acts by releasing JCV from the bone marrow, one of its site of latency. In this study, we address the question whether there is an increased activity of JCV in the blood of natalizumab-treated MS patients. Material and Methods: In this prospective longitudinal study, we are following a cohort of 24 MS patients receiving monthly injections of natalizumab. Blood and urine are drawn every one to three months, up to 12 months. As a control group, we follow 16 MS patients treated with IFN-beta. For this control group, there are two time-points: before and 1094 months after treatment onset. We are analysing the viral (JCV-, EBV- and CMV-) as well as the myelin- (MOG-, MOBP-) specific cellular immune responses using proliferation and ELISPOT (IFNgamma) assays. For JCV, we study the response against VP1, the major capsid protein. For JCV VP1, MOG and MOBP, we use 15-mer peptides overlapping by 10 amino acids, thus eliciting CD4_ as well as CD8_ T cell response. These peptides encompasse the whole sequence of the proteins. For EBV and CMV, we use pools of immunodominant 8- to 10-mer peptides eliciting CD8_ T cells. At the same time-points, using RTPCR, we determine the presence of JCV DNA coding for the VP1 protein in the PBMC, plasma, and urine. Results: At the time of writing this abstract, 16 patients have reached the 9-month (T9), and 11 the T12 time-point. We expect that by the ISNV meeting in June 2009, 18 and 14 patients will be at T9 and T12, respectively. Virological and immunological results will be presented. 9th International Symposium on NeuroVirology 2_6 June 2009 39 J Neurovirol Downloaded from informahealthcare.com by Cantonale et Universitaire on 06/25/10 For personal use only. Conclusions: This ongoing longitudinal prospective study should tell us whether there is an enhanced JCV activity in the peripheral blood of patients on natalizumab. This work is supported by the FNS (PP00B-106716), the Swiss MS Society and a research grant from Biogen Dompe.

A minimal i-motif stabilized by minor groove G:T:G:T tetrads

The repetitive DNA sequences found at telomeres and centromeres play a crucial role in the structure and function of eukaryotic chromosomes. This role may be related to the tendency observed in many repetitive DNAs to adopt non-canonical structures. Although there is an increasing recognition of the importance of DNA quadruplexes in chromosome biology, the co-existence of different quadruplex-forming elements in the same DNA structure is still a matter of debate. Here we report the structural study of the oligonucleotide d(TCGTTTCGT) and its cyclic analog d. Both sequences form dimeric quadruplex structures consisting of a minimal i-motif capped, at both ends, by a slipped minor groove-aligned G:T:G:T tetrad. These mini i-motifs, which do not exhibit the characteristic CD spectra of other i-motif structures, can be observed at neutral pH, although they are more stable under acidic conditions. This finding is particularly relevant since these oligonucleotide sequences do not contain contiguous cytosines. Importantly, these structures resemble the loop moiety adopted by an 11-nucleotide fragment of the conserved centromeric protein B (CENP-B) box motif, which is the binding site for the CENP-B.

A minimal i-motif stabilized by minor groove G:T:G:T tetrads

The repetitive DNA sequences found at telomeres and centromeres play a crucial role in the structure and function of eukaryotic chromosomes. This role may be related to the tendency observed in many repetitive DNAs to adopt non-canonical structures. Although there is an increasing recognition of the importance of DNA quadruplexes in chromosome biology, the co-existence of different quadruplex-forming elements in the same DNA structure is still a matter of debate. Here we report the structural study of the oligonucleotide d(TCGTTTCGT) and its cyclic analog d. Both sequences form dimeric quadruplex structures consisting of a minimal i-motif capped, at both ends, by a slipped minor groove-aligned G:T:G:T tetrad. These mini i-motifs, which do not exhibit the characteristic CD spectra of other i-motif structures, can be observed at neutral pH, although they are more stable under acidic conditions. This finding is particularly relevant since these oligonucleotide sequences do not contain contiguous cytosines. Importantly, these structures resemble the loop moiety adopted by an 11-nucleotide fragment of the conserved centromeric protein B (CENP-B) box motif, which is the binding site for the CENP-B.

Génération d'une souris dépourvue du gène VIT32 de manière conditionnelle: étude du phénotype rénal chez les souris dépourvues de RGS2

Résumé Dans le rein, la vasopressine possède un rôle essentiel dans la régulation fine du transport d'eau et participe au contrôle de la réabsorption du sodium. Cette action est conduite par l'activation du récepteur à la vasopressine V2R situé dans l'anse de Henle, dans le tubule connecteur et dans le canal collecteur du néphron des rongeurs et conduit à la formation d'AMPc entraînant un mécanisme d'action caractérisé par deux phases distinctes. Le premier effet de la vasopressine est non génomique et a lieu rapidement après l'activation du récepteur, la deuxième phase est plus tardive et possède la caractéristique de moduler la transcription d'un réseau de gènes. Parmi ces gènes, plusieurs sont directement impliqués dans le transport d'eau et de sodium, comme l'Aqp2 et 3, ENaC et la Na,K-ATPase. L'identification des effets de la voie de signalisation de la vasopressine représente un point crucial pour la compréhension des mécanismes moléculaires de la réabsorption de l'eau et du sodium dans le néphron. L'analyse en série de l'expression de gènes (SAGE) réalisée en 2001 dans notre laboratoire a permis de caractériser le transcriptome dépendant de la vasopressine dans la lignée cellulaire mpkCCDc14,a dérivée du canal collecteur cortical (CCD) de souris. Deux des transcrits induits par la vasopressine (VIT) ont fait l'objet des études de ce travail de thèse. Le premier est VIT32 (Vasopressin induced transcript 32) qui code pour une protéine ne possédant aucune homologie avec des domaines protéiques dont la fonction est connue. Dans le système d'expression de l'ovocyte de Xenopus laevis, VIT32 induit la maturation des ovocytes et diminue le courant sensible à l'amiloride de manière dépendante de la voie des MAPK. Dans les mpkCCDc14, l'inhibition de la voie des MAPK diminue le courant sodique en diminuant l'activité de la Na,K-ATPase, mais sans modifier le courant d'ENaC. Ainsi la voie de signalisation des MAPK peut avoir des cibles différentes suivant le système dans lequel elle est étudiée. C'est pourquoi nous avons décidé de poursuivre l'étude de VIT32 dans un contexte physiologique en créant une souris dépourvue du gène codant pour VIT32 de manière conditionnelle (conditional knockout). La première partie de cette thèse a donc consisté à générer cette souris. Le deuxième transcrit induit par la vasopressine qui a été étudié dans cette thèse est RGS2 (Regulator of G protein Signaling 2). In vitro, il a été montré que RGS2 inhibe des voies de signalisation dépendantes de récepteurs couplés à des protéines Gq et Gs. Dans notre étude, nous avons montré que dans le néphron de rein de souris, RGS2 est colocalisé avec V2R. In vivo, la vasopressine sécrétée lors d'une restriction en eau imposée à des souris augmente l'expression de RGS2. De plus, l'accumulation d'AMPc engendrée par l'action de la vasopressine sur les canaux collecteurs est significativement plus grande chez les souris dépourvues de RGS2 (rgs2 -/-). Cette induction de la signalisation de la vasopressine est corrélée à une augmentation de la réabsorption d'eau chez les souris rgs2 -/-. Ainsi RGS2 serait impliqué dans le rétrocontrôle négatif de la voie de signalisation de la vasopressine. Abstract In the kidney, vasopressin plays a key role in the control of water balance and participates in salt reabsorption. These actions are induced by the activation of V2 vasopressin receptor (V2R) located in the loop of Henle, in the connecting tubule and in the collecting duct leading to an increase in intracellular cAMP levels. The V2R-mediated vasopressin action elicits a rapid, non-genomic effect, during which water and salt reabsorption is rapidly increased and a late or genomic effect characterised by the long-term regulation of water and salt reabsorption through the transcriptional activation of a gene network that includes Aqp2, Aqp3, ENaC and Na,K-ATPase. Serial analysis of gene expression (SAGE) performed in 2001 in our laboratory characterised the vasopressin induced transcripts (VIT) in the mpkCCDc14 cell line. Two of them are studied in this thesis. The first one is VIT32 (Vasopressin induced transcript 32) that encodes a protein that has no homology with any protein domain of known function. In the Xenopus laevis oocyte, VIT32 induces oocyte maturation and downregulates the ENaC amiloride sensitive current via the activation of the MAPK pathway. In mpkCCDc14 cell line, the MAPK pathway inhibition leads to a decrease of Na,K-ATPase activity without affecting ENaC current. Therefore, the MAPK pathway can act on different targets depending on the cellular context. Thus, we decided to investigate the function of VIT32 in its physiological environment by performing a conditional knockout mouse of VIT32. The first part of this thesis consisted in generating this mouse. The second studied vasopressin induced transcript is RGS2 (Regulator of G protein Signaling 2). In vitro, RGS2 has been shown to inhibit Gq and Gs protein-coupled receptor pathway. In our study we show that RGS2 is co-localized with V2R in the mouse nephron. In vivo, vasopressin secreted during water restriction up-regulates RGS2 expression. Moreover, vasopressin-dependant accumulation of CAMP is significantly increased in the cortical collecting duct of RGS2 knockout mice. This increase is correlated with an increase in water reabsorption. RGS2 could be involved in the negative feedback regulation of V2R signalling. Résumé tout public Le corps humain est composé d'environ 60% d'eau répartie à l'intérieur et à l'extérieur des cellules de notre organisme. Les cellules, unités fondamentales du vivant, puisent l'oxygène et les nutriments indispensables à leur fonctionnement dans le liquide extracellulaire. La composition du milieu doit être constante, car les variations peuvent perturber considérablement et parfois fatalement la fonction des cellules. Ainsi les organismes pluricellulaires ont développé des mécanismes permettant de contrôler la constance du milieu extracellulaire afin de maintenir l'état d'équilibre nommé homéostasie. Le rein joue un rôle majeur dans cette homéostasie grâce à sa capacité de réabsorber l'eau et les solutés en fonction des besoins de l'organisme. Cette fonction du rein est régulée par différentes hormones comme la vasopressine, qui permet de contrôler la réabsorption fine de l'eau et des solutés. Dans leurs membranes, les cellules possèdent des récepteurs leur permettant de répondre aux signaux extracellulaires comme le sont entre autres les hormones. Ainsi les cellules sensibles à la vasopressine possèdent un récepteur nommé V2R qui permet d'intégrer les signaux de la vasopressine en déclenchant tout une cascade d'événements conduisant à une modification de l'expression de certaines protéines impliquées directement ou non dans la réabsorption de l'eau et des solutés. Une étude précédente élaborée au sein de notre laboratoire a permis de répertorier les protéines dont l'expression est augmentée par de la vasopressine. Deux de ces protéines ont fait l'objet des études de cette thèse. La première protéine induite par la vasopressine est VIT32 (Vasopressin induced transcript 32). Cette protéine est entre autres impliquée dans la réabsorption du sodium, mais la fonction précise de VIT32 dans ce transport n'a pas pu être déterminée. Une des approches possibles pour l'étude de la fonction d'une protéine est de supprimer son expression chez la souris et d'étudier les conséquences de son absence. Ces souris sont appelées des souris knockout, puisque la protéine en question ne peut plus agir. La première partie de cette thèse a donc consisté à générer une souris dépourvue du gène de VIT32. La deuxième protéine étudiée est RGS2 (Regulator of G protein Signaling 2). Cette protéine inhibe certaines voies de signalisation activées par différentes hormones. Dans cette partie du travail de thèse, nous avons pu mettre en évidence que RGS2 agit comme un inhibiteur de la voie de signalisation de la vasopressine. En modifiant cette signalisation, RGS2 serait donc un médiateur du contrôle de la réabsorption d'eau dans les cellules du rein sensibles à la vasopressine.

Undercoverage and Nonresponse in a List-sampled Telephone Election Survey

For landline telephone surveys in particular, undercoverage has been a growing problem. However, research regarding the relative contributions of socio-demographic bias and other composition effects is scarce. We propose to address this issue by analyzing an election survey which used a sample from a register-based sampling frame containing basic socio-demographic information and to which telephone numbers were subsequently matched. With respect to socio-demographic representation of the final sample, we find that difficult to match groups are also difficult to contact, while those who cooperate tend to have different characteristics. We find bias due to undercoverage to be of greater magnitude than noncontact bias, while noncooperation falls between the two. As for substantive variables, both additional efforts to match missing telephone numbers and the construction of better weights are successful in closing the gap between survey estimates of voting behavior and true values from the election results.

Kustannusrakenteen simulointi ja optimointi

Primääripakatun tuotteen liiketoiminnallisen arvoketjun kustannusrakenteen tunnistaminen tuo merkittävää lisäarvoa pakkausliiketoiminnan suunnittelua koskevaan päätöksentekoon. Tämän konstruktiivisen tutkimuksen tavoitteena on rakentaa pakkaustuotannon liiketoiminnallisen arvoketjun simulointimalli, jonka avulla voidaan analysoida pakkaustuotannon arvoketjun kustannusrakennetta lähtien pakkausraaka-aineen valmistuksesta ja päättyen kaupan vähittäismyyntiin. Käytettävä tutkimusaineisto koostuu jonoteoriaan ja tuotannonsuunnitteluun liittyvästä kirjallisuudesta, tieteellisistä artikkeleista sekä asiantuntijalausunnoista. Tutkimuksen yhteydessä rakennetun simulointimallin avulla määritettiin erään primääripakatun tuotteen konvertointivaiheen optimaalinen valmistuseräkoko ja liiketoiminnallisen arvoketjun kustannusrakenne. Arvoketjuanalyysissä primääripakatun tuotteen kustannustekijöiksi määritettiin pakkausmateriaali, pakkausvalmistus, pakattava tuote, pakkauksen täyttö ja suljenta sekä pakatun tuotteen jakelulogistiikka ja vähittäismyynti. Arvoketjuanalyysin johtopäätöksenä voidaan todeta, että primääripakatulle esimerkkituotteelle kohdistuvista kustannuksista noin 97 % on brand ownerin ja vähittäismyynnin aiheuttamia ja noin 3 % varsinaisesta tuotteen pakkaamisesta aiheutuvia.

Tool-supported invariant-based programming

The development of correct programs is a core problem in computer science. Although formal verification methods for establishing correctness with mathematical rigor are available, programmers often find these difficult to put into practice. One hurdle is deriving the loop invariants and proving that the code maintains them. So called correct-by-construction methods aim to alleviate this issue by integrating verification into the programming workflow. Invariant-based programming is a practical correct-by-construction method in which the programmer first establishes the invariant structure, and then incrementally extends the program in steps of adding code and proving after each addition that the code is consistent with the invariants. In this way, the program is kept internally consistent throughout its development, and the construction of the correctness arguments (proofs) becomes an integral part of the programming workflow. A characteristic of the approach is that programs are described as invariant diagrams, a graphical notation similar to the state charts familiar to programmers. Invariant-based programming is a new method that has not been evaluated in large scale studies yet. The most important prerequisite for feasibility on a larger scale is a high degree of automation. The goal of the Socos project has been to build tools to assist the construction and verification of programs using the method. This thesis describes the implementation and evaluation of a prototype tool in the context of the Socos project. The tool supports the drawing of the diagrams, automatic derivation and discharging of verification conditions, and interactive proofs. It is used to develop programs that are correct by construction. The tool consists of a diagrammatic environment connected to a verification condition generator and an existing state-of-the-art theorem prover. Its core is a semantics for translating diagrams into verification conditions, which are sent to the underlying theorem prover. We describe a concrete method for 1) deriving sufficient conditions for total correctness of an invariant diagram; 2) sending the conditions to the theorem prover for simplification; and 3) reporting the results of the simplification to the programmer in a way that is consistent with the invariantbased programming workflow and that allows errors in the program specification to be efficiently detected. The tool uses an efficient automatic proof strategy to prove as many conditions as possible automatically and lets the remaining conditions be proved interactively. The tool is based on the verification system PVS and i uses the SMT (Satisfiability Modulo Theories) solver Yices as a catch-all decision procedure. Conditions that were not discharged automatically may be proved interactively using the PVS proof assistant. The programming workflow is very similar to the process by which a mathematical theory is developed inside a computer supported theorem prover environment such as PVS. The programmer reduces a large verification problem with the aid of the tool into a set of smaller problems (lemmas), and he can substantially improve the degree of proof automation by developing specialized background theories and proof strategies to support the specification and verification of a specific class of programs. We demonstrate this workflow by describing in detail the construction of a verified sorting algorithm. Tool-supported verification often has little to no presence in computer science (CS) curricula. Furthermore, program verification is frequently introduced as an advanced and purely theoretical topic that is not connected to the workflow taught in the early and practically oriented programming courses. Our hypothesis is that verification could be introduced early in the CS education, and that verification tools could be used in the classroom to support the teaching of formal methods. A prototype of Socos has been used in a course at Åbo Akademi University targeted at first and second year undergraduate students. We evaluate the use of Socos in the course as part of a case study carried out in 2007.