Single-Nucleotide Polymorphism and Copy Number Variation of the Multidrug Resistance-1 Locus of Plasmodium vivax: Local and Global Patterns

Emerging resistance to chloroquine (CQ) poses a major challenge for Plasmodium vivax malaria control, and nucleotide substitutions and copy number variation in the P. vivax multidrug resistance 1 (pvmdr-1) locus, which encodes a digestive vacuole membrane transporter, may modulate this phenotype. We describe patterns of genetic variation in pvmdr-1 alleles from Acre and Amazonas in northwestern Brazil, and compare then with those reported in other malaria-endemic regions. The pvmdr-1 mutation Y976F, which is associated with CQ resistance in Southeast Asia and Oceania, remains rare in northwestern Brazil (1.8%) and its prevalence mirrors that of CO resistance worldwide. Gene amplification of pvmdr-1, which is associated with mefloquine resistance but increased susceptibility to CO, remains relatively rare in northwestern Brazil (0.9%) and globally (< 4%), but became common (> 10%) in Tak Province, Thailand, possibly because of drug-mediated selection. The global database we have assembled provides a baseline for further studies of genetic variation in pvmdr-1 and drug resistance in P. vivax malaria.

Genetic relatedness of Plasmodium falciparum isolates and the origin of allelic diversity at the merozoite surface protein-1 (MSP-1) locus in Brazil and Vietnam

Abstract Background Despite the extensive polymorphism at the merozoite surface protein-1 (MSP-1) locus of Plasmodium falciparum, that encodes a major repetitive malaria vaccine candidate antigen, identical and nearly identical alleles frequently occur in sympatric parasites. Here we used microsatellite haplotyping to estimate the genetic distance between isolates carrying identical and nearly identical MSP-1 alleles. Methods We analyzed 28 isolates from hypoendemic areas in north-western Brazil, collected between 1985 and 1998, and 23 isolates obtained in mesoendemic southern Vietnam in 1996. MSP-1 alleles were characterized by combining PCR typing with allele-specific primers and partial DNA sequencing. The following single-copy microsatellite markers were typed : Poly��, TA42 (only for Brazilian samples), TA81, TA1, TA87, TA109 (only for Brazilian samples), 2490, ARAII, PfG377, PfPK2, and TA60. Results The low pair-wise average genetic distance between microsatellite haplotypes of isolates sharing identical MSP-1 alleles indicates that epidemic propagation of discrete parasite clones originated most identical MSP-1 alleles in parasite populations from Brazil and Vietnam. At least one epidemic clone propagating in Brazil remained relatively unchanged over more than one decade. Moreover, we found no evidence that rearrangements of MSP-1 repeats, putatively created by mitotic recombination events, generated new alleles within clonal lineages of parasites in either country. Conclusion Identical MSP-1 alleles originated from co-ancestry in both populations, whereas nearly identical MSP-1 alleles have probably appeared independently in unrelated parasite lineages.

A multi-locus approach to barcoding in the Anopheles strodei subgroup (Diptera: Culicidae)

Abstract Background The ability to successfully identify and incriminate pathogen vectors is fundamental to effective pathogen control and management. This task is confounded by the existence of cryptic species complexes. Molecular markers can offer a highly effective means of species identification in such complexes and are routinely employed in the study of medical entomology. Here we evaluate a multi-locus system for the identification of potential malaria vectors in the Anopheles strodei subgroup. Methods Larvae, pupae and adult mosquitoes (n���=���61) from the An. strodei subgroup were collected from 21 localities in nine Brazilian states and sequenced for the COI, ITS2 and white gene. A Bayesian phylogenetic approach was used to describe the relationships in the Strodei Subgroup and the utility of COI and ITS2 barcodes was assessed using the neighbor joining tree and ���best close match��� approaches. Results Bayesian phylogenetic analysis of the COI, ITS2 and white gene found support for seven clades in the An. strodei subgroup. The COI and ITS2 barcodes were individually unsuccessful at resolving and identifying some species in the Subgroup. The COI barcode failed to resolve An. albertoi and An. strodei but successfully identified approximately 92% of all species queries, while the ITS2 barcode failed to resolve An. arthuri and successfully identified approximately 60% of all species queries. A multi-locus COI-ITS2 barcode, however, resolved all species in a neighbor joining tree and successfully identified all species queries using the ���best close match��� approach. Conclusions Our study corroborates the existence of An. albertoi, An. CP Form and An. strodei in the An. strodei subgroup and identifies four species under An. arthuri informally named A-D herein. The use of a multi-locus barcode is proposed for species identification, which has potentially important utility for vector incrimination. Individuals previously found naturally infected with Plasmodium vivax in the southern Amazon basin and reported as An. strodei are likely to have been from An. arthuri C identified in this study.

Genomic analysis of ERVWE2 locus in patients with multiple sclerosis: absence of genetic association but potential role of human endogenous retrovirus type W elements in molecular mimicry with myelin antigen

Human endogenous retroviruses (HERVs) arise from ancient infections of the host germline cells by exogenous retroviruses, constituting 8% of the human genome. Elevated level of envelope transcripts from HERVs-W has been detected in CSF, plasma and brain tissues from patients with Multiple Sclerosis (MS), most of them from Xq22.3, 15q21.3, and 6q21 chromosomes. However, since the locus Xq22.3 (ERVWE2) lack the 5' LTR promoter and the putative protein should be truncated due to a stop codon, we investigated the ERVWE2 genomic loci from 84 individuals, including MS patients with active HERV-W expression detected in PBMC. In addition, an automated search for promoter sequences in 20 kb nearby region of ERVWE2 reference sequence was performed. Several putative binding sites for cellular cofactors and enhancers were found, suggesting that transcription may occur via alternative promoters. However, ERVWE2 DNA sequencing of MS and healthy individuals revealed that all of them harbor a stop codon at site 39, undermining the expression of a full-length protein. Finally, since plaque formation in central nervous system (CNS) of MS patients is attributed to immunological mechanisms triggered by autoimmune attack against myelin, we also investigated the level of similarity between envelope protein and myelin oligodendrocyte glycoprotein (MOG). Comparison of the MOG to the envelope identified five retroviral regions similar to the Ig-like domain of MOG. Interestingly, one of them includes T and B cell epitopes, capable to induce T effector functions and circulating Abs in rats. In sum, although no DNA substitutions that would link ERVWE2 to the MS pathogeny was found, the similarity between the envelope protein to MOG extends the idea that ERVEW2 may be involved on the immunopathogenesis of MS, maybe facilitating the MOG recognizing by the immune system. Although awaiting experimental evidences, the data presented here may expand the scope of the endogenous retroviruses involvement on MS pathogenesis

Local cohomology with supports in the non-free locus

[EN] The groups of local cohomology with supports in the non-free locus of a module are used in order to obtain three classifications and one characterization of four classes of modules

"Quietis et deliciarum locus" restauro e rifunzionalizzazione della dimora padronale di "Villa Cappello-Mora"

VILLA ���CAPELLO - MORA���: PROGETTO DI RESTAURO E RIFUNZIONALIZZAZIONE Il restauro �� da intendere come un intervento diretto sull���opera, e anche come sua eventuale modifica, condotta sempre sotto un rigoroso controllo tecnico-scientifico e storico-critico, se parliamo di conservazione, intendiamo l���operare in un intento di salvaguardia e di prevenzione, da attuare proprio per evitare che si debba poi intervenire con il restauro, che comprende un evento traumatico per il manufatto. Un seconda parola chiave in questo discorso �� la ���materia��� il restauro interviene sulla materia di un monumento e questa costituisce il tramite dei valori culturali antichi, la sua conservazione e il suo restauro garantisce la trasmissione anche dei significati estetici, storici simbolici del costruito. Ma certamente influisce il tempo sulle cose per cui il progetto di restauro non pu�� astenersi dall���intervenire, in una logica di minimo intervento, di reversibilit��, di facile lettura. Il concetto di nuovo in un opera antica, concetto che a parere personale, pare centrare in pieno il problema. Il nuovo infatti ���deve avere carattere di autonomia e di chiara leggibilit��: come l���<<aggiunta>> di Boito deve essere inequivocabilmente opera nuova, come prodotto figurativo e materiale autonomo, chiara ed inequivocabile espressione <<della nostra cultura e del nostro tempo>>���. Ne deriva riassumendo che oggi l���obbiettivo deve essere quello di conservare da un lato senza non sotrarre altra materia alla fabbrica e di valorizzare, ossia aggiungere, nuove ���presenze��� di cultura contemporanea. Per questo si parler�� di progetto di restauro e rifunzionalizzazione. La fabbrica ha subito nel corso dell���ultimo decennio una serie di ���rovinose��� manomissioni, che a differenza di quelle operate in tempi pi�� antichi (coincidenti con esigenze funzionali corrispondenti alla logica dell���adattare) appaiano ben pi�� gravi, e contribuiscono a peggiorare la lettura del fabbricato. Il Veneto e soprattutto la zona intorno a Bassano del Grappa presenta una infinit�� di dimore padronali casini di caccia, resti di antiche residenze (colombare, oratori, ecc.) risalenti al periodo di maggior fioritura della residenza di ���Villa��� della Serenissima. Nel caso specifico di studio , quindi della rifunzionalizzazione dell���edificio, la domanda sorge spontanea; Come ristabilire un senso a questi spazi? E nell���ipotesi di poter realmente intervenire che cosa farne di questi oggetti?. E ultimo ma non ultimo in che modo poter ristabilire un ���dialogo��� con l���edificio in una lettura corretta del suo significato non solo per quel che riguarda la materia ma anche per ci�� che ci trasmette nel ���viverlo���, nell���usufruirne nel fatto stesso di poterlo vedere, passandoci davanti. t��. Lidea si forma prima ancora da un esigenza del territorio, il comune di Cassola dove ha sede la Villa,pur avendo un discreto numero di abitanti e collocandosi in posizione nevralgica in quanto molto vicino al centro diBasssano (ne �� quasi la promulgazione), non possiede uno spazio espositivo /rappresentativo, un edificio a carattere pubblico, sede di ���eventi��� culturali locali e non. Villa Capello ���Mora, potrebbe rispondere bene a questo tipo di utilizzo. Si �� deciso di pensare ad un luogo a carattere espositivo che possa funzionare durante tutto l���anno e nei periodi etsivi includa anche il giardino esterno. Il progetto muove da due principi il principio di ���reversibilit����� e quello del ���minimo intervento��� sottolinenando volutamente che siano gli ogetti esposti e lo spazio dei locali a fare da protagonisti, Punti chiave nell���interpretazione degli spazi sono stati i percorsi, la ���narrazione��� degli oggetti esposti avviene per momenti e viene rimarcata nell���allestimento tramite i materiali i colori e le superfici espositive, perch�� nel momento in cui visito una mostra o un museo, �� come se stessi vivendo la narrazione di un qualcosa, oggetto semplice od opera complessa che sia inteso nell���ambito museale-espositivo esso assume una capacit�� di trasmissione maggiore rispetto a qundo lo stesso ogetto si trova in un contesto differente, la luce e la sua disposizione nello spazio, fanno s�� che il racconto sia narrato, bene o male, ancora pi�� importante �� lo sfondo su cui si staglia l���opera, che pu�� essere chiuso, come una serie di scatole dentro la scatola (edificio) oppure aperto, con singole e indipendenti pannellature dove l���edificio riveste il carattere proprio di sfondo. Scelta la seconda delle due ipotesi, si �� voluto rimarcare nella composizione degli interni i momenti della narrazione, cos�� ad esempio accedendo dall���ingresso secondario (lato nord-ovest) al quale si �� dato l���ingresso alla mostra, -superata la prima Hall- si viene, catapultati in uno spazio porticato in origine aperto e che prevediamo chiuso da una vetrata continua, portata a debita distanza dal colonnato. Questo spazio diventa la prima pagina del testo, una prima pagina bianca, uno spazio libero, di esposizione e non di relax e di presentazione dell���evento, uno spazio distributivo non votato solo a questo scopo, ma passibile di trasformazione. A rimarcare il percorso una pavimentazione in cemento lisciato, che invita l���accesso alle due sale espositive a sinista e a destra dell���edificio. Nell���ala a sinistra (rispetto al nord) si apre la stanza con camino seicentesco forse un tempo ad uso cucina? Sala che ospita dei pannelli a sospesi a muro e delle teche espositive appese a soffitto. L���ala di destra, diametralmente opposta, l���unica che al piano terra mantiene la pavimentazione originale, stabiliva il vero atrio d���entrata, nel XVII sec. riconoscibile da quattro colonne tuscaniche centrali a reggere un solaio ligneo, in questa stanza il percorso segnato a terra torna nella disposizione dei pannelli espositivi che si dispongono in un a formare un vero corridoio, tra uno e l���atro di questi pannelli degli spazi sufficienti a intravedere le colonne centrali, i due lati dello stretto percorso non sono paralleli e aprono in senso opposto a due restanti spazi dell���intero salone, La sala suddivisa cos�� in queste tre parti - una di percorrenza due di esposizione - , risulta modificata nella lettura che ne annulla l���originale funzione. Questa nuova ���forma���, non vuole essere permanente infatti i pannelli non sono fissi. la narrazione avviene cos�� per momenti, per parti, , che non devono necessariamente far comprendere il ���tutto���, ma suggerirlo. Cos�� come per il percorso che non �� obbligato ma suggerito. A terminare il piano altre due sale di minore dimensione e di modesto carattere, nelle quali sono presenti pannellature a parete come nella prima sala. L���allestimento prosegue al piano primo a cui si accede tramite due rampe, trattate nel progetto difformemente, in base al loro stato e al loro significato, la rampa pi�� recente (XIX sec) rompe lo spazio al piano nobile stravolgendo l���ingresso a questo salone, che originariamente avveniva salendo dalla scala principale e oltrepassando un disimpegno. La scala ottocentesca introduce direttamente all���ambiente che ora risulta liberato dalle superfetazioni dello scorso secolo, mostrandosi come era stato previsto in origine. Questa rottura dello spazio viene marcata nel progetto da un volume che ���imprigiona��� la rampa e segna l���inizio della sala espositiva, la sala delle architetture. Al centro della sala in un gioco di pieni e vuoti i pannelli, espositivi, distaccati di poco gli uni dagli altri questa volta non a incorniciare delle colonne ma a richiamo delle pitture murali che raffiguranti una loggia alludono ad una lettura per ���parti��� e scandiscono lo spazio in una ���processione��� di eventi. A seguito del ���gioco��� sono presenti in senso ortogonale ai pannelli sopradescritti ulteriori pannellature appese ad una struttura metallica indipendente dalle capriate lignee. Tale struttura assume ad una duplice funzione, funge sia da irrigidimento della struttura (edificio) che da supporto alla pannellatura, ad essa infatti �� collegata una fune, che entrer�� in tensione, quando il pannello verr�� ad appendersi. Infine questa fune passante da due puleggie permetter�� al pannello di traslare da un lato all���altro dell���edificio, bloccandosi nella posizione desiderata tramite freno interno, azionato manualmente.

A dictionary of modular threefolds

The thesis deals with the modularity conjecture for three-dimensional Calabi-Yau varieties. This is a generalization of the work of A. Wiles and others on modularity of elliptic curves. Modularity connects the number of points on varieties with coefficients of certain modular forms. In chapter 1 we collect the basics on arithmetic on Calabi-Yau manifolds, including general modularity results and strategies for modularity proofs. In chapters 2, 3, 4 and 5 we investigate examples of modular Calabi-Yau threefolds, including all examples occurring in the literature and many new ones. Double octics, i.e. Double coverings of projective 3-space branched along an octic surface, are studied in detail. In chapter 6 we deal with examples connected with the same modular forms. According to the Tate conjecture there should be correspondences between them. Many correspondences are constructed explicitly. We finish by formulating conjectures on the occurring newforms, especially their levels. In the appendices we compile tables of coefficients of weight 2 and weight 4 newforms and many examples of double octics.

Algebraische Zyklen auf abelschen Varietäten der Dimension 4 mit Polarisierung von Typ (1,2,2,2)

Diese Arbeit besch"aftigt sich mit algebraischen Zyklen auf komplexen abelschen Variet"aten der Dimension 4. Ziel der Arbeit ist ein nicht-triviales Element in $Griff^{3,2}(A^4)$ zu konstruieren. Hier bezeichnet $A^4$ die emph{generische} abelsche Variet"at der Dimension 4 mit Polarisierung von Typ $(1,2,2,2)$. Die ersten drei Kapitel sind eine Wiederholung von elementaren Definitionen und Begriffen und daher eine Festlegung der Notation. In diesen erinnern wir an elementare Eigenschaften der von Saito definierten Filtrierungen $F_S$ und $Z$ auf den Chowgruppen (vgl. cite{Sa0} und cite{Sa}). Wir wiederholen auch eine Beziehung zwischen der $F_S$-Filtrierung und der Zerlegung von Beauville der Chowgruppen (vgl. cite{Be2} und cite{DeMu}), welche aus cite{Mu} stammt. Die wichtigsten Begriffe in diesem Teil sind die emph{h"ohere Griffiths' Gruppen} und die emph{infinitesimalen Invarianten h"oherer Ordnung}. Dann besch"aftigen wir uns mit emph{verallgemeinerten Prym-Variet"aten} bez"uglich $(2:1)$ "Uberlagerungen von Kurven. Wir geben ihre Konstruktion und wichtige geometrische Eigenschaften und berechnen den Typ ihrer Polarisierung. Kapitel ref{p-moduli} enth"alt ein Resultat aus cite{BCV} "uber die Dominanz der Abbildung $p(3,2):mathcal R(3,2)longrightarrow mathcal A_4(1,2,2,2)$. Dieses Resultat ist von Relevanz f"ur uns, weil es besagt, dass die generische abelsche Variet"at der Dimension 4 mit Polarisierung von Typ $(1,2,2,2)$ eine verallgemeinerte Prym-Variet"at bez"uglich eine $(2:1)$ "Uberlagerung einer Kurve vom Geschlecht $7$ "uber eine Kurve vom Geschlecht $3$ ist. Der zweite Teil der Dissertation ist die eigentliche Arbeit und ist auf folgende Weise strukturiert: Kapitel ref{Deg} enth"alt die Konstruktion der Degeneration von $A^4$. Das bedeutet, dass wir in diesem Kapitel eine Familie $Xlongrightarrow S$ von verallgemeinerten Prym-Variet"aten konstruieren, sodass die klassifizierende Abbildung $Slongrightarrow mathcal A_4(1,2,2,2)$ dominant ist. Desweiteren wird ein relativer Zykel $Y/S$ auf $X/S$ konstruiert zusammen mit einer Untervariet"at $Tsubset S$, sodass wir eine explizite Beschreibung der Einbettung $Yvert _Thookrightarrow Xvert _T$ angeben k"onnen. Das letzte und wichtigste Kapitel enth"ahlt Folgendes: Wir beweisen dass, die emph{ infinitesimale Invariante zweiter Ordnung} $delta _2(alpha)$ von $alpha$ nicht trivial ist. Hier bezeichnet $alpha$ die Komponente von $Y$ in $Ch^3_{(2)}(X/S)$ unter der Beauville-Zerlegung. Damit und mit Hilfe der Ergebnissen aus Kapitel ref{Cohm} k"onnen wir zeigen, dass [ 0neq [alpha ] in Griff ^{3,2}(X/S) . ] Wir k"onnen diese Aussage verfeinern und zeigen (vgl. Theorem ref{a4}) begin{theorem}label{maintheorem} F"ur $sin S$ generisch gilt [ 0neq [alpha _s ]in Griff ^{3,2}(A^4) , ] wobei $A^4$ die generische abelsche Variet"at der Dimension $4$ mit Polarisierung vom Typ $(1,2,2,2)$ ist. end{theorem}

Transcriptional dynamics of the human DMD locus

The human DMD locus encodes dystrophin protein. Absence or reduced levels of dystrophin (DMD or BMD phenotype, respectively) lead to progressive muscle wasting. Little is known about the complex coordination of dystrophin expression and its transcriptional regulation is a field of intense interest. In this work we found that DMD locus harbours multiple long non coding RNAs which orchestrate and control transcription of muscle dystrophin mRNA isoforms. These lncRNAs are tissue-specific and highly expressed during myogenesis, suggesting a possible role in tissue-specific expression of DMD gene isoforms. Their forced ectopic expression in human muscle and neuronal cells leads to a specific and negative regulation of endogenous dystrophin full lenght isoforms. An intriguing aspect regarding the transcription of the DMD locus is the gene size (2.4Mb). The mechanism that ensures the complete synthesis of the primary transcript and the coordinated splicing of 79 exons is still completely unknown. By ChIP-on-chip analyses, we discovered novel regions never been involved before in the transcription regulation of the DMD locus. Specifically, we observed enrichments for Pol II, P-Ser2, P-Ser5, Ac-H3 and 2Me-H3K4 in an intronic region of 3Kb (approximately 21Kb) downstream of the end of DMD exon 52 and in a region of 4Kb spanning the DMD exon 62. Interestingly, this latter region and the TSS of Dp71 are strongly marked by 3Me-H3K36, an histone modification associated with the regulation of splicing process. Furthermore, we also observed strong presence of open chromatin marks (Ac-H3 and 2Me-H3K4) around intron 34 and the exon 45 without presence of RNA pol II. We speculate that these two regions may exert an enhancer-like function on Dp427m promoter, although further investigations are necessary. Finally, we investigated the nuclear-cytoplasmic compartmentalization of the muscular dystrophin mRNA and, specifically, we verified whether the exon skipping therapy could influence its cellular distribution.

Heterozygous deletion of the PU.1 locus in human AML

The transcription factor PU.1 is essential for myeloid development. Targeted disruption of an upstream regulatory element (URE) decreases PU.1 expression by 80% and leads to acute myeloid leukemia (AML) in mice. Here, we sequenced the URE sequences of PU.1 in 120 AML patients. Four polymorphisms (single nucleotide polymorphisms [SNPs]) in the URE were observed, with homozygosity in all SNPs in 37 patients. Among them, we compared samples at diagnosis and remission, and one patient with cytogenetically normal acute myeloid leukemia M2 was identified with heterozygosity in 3 of the SNPs in the URE at remission. Loss of heterozygosity was further found in this patient at 2 polymorphic sites in the 5' promoter region and in 2 intronic sites flanking exon 4, thus suggesting loss of heterozygosity covering at least 40 kb of the PU.1 locus. Consistently, PU.1 expression in this patient was markedly reduced. Our study suggests that heterozygous deletion of the PU.1 locus can be associated with human AML.

Mapping of a new locus for congenital anomalies of the kidney and urinary tract on chromosome 8q24

Congenital anomalies of the kidney and urinary tract (CAKUT) account for the majority of end-stage renal disease in children (50%). Previous studies have mapped autosomal dominant loci for CAKUT. We here report a genome-wide search for linkage in a large pedigree of Somalian descent containing eight affected individuals with a non-syndromic form of CAKUT.

Novel association to the proprotein convertase PCSK7 gene locus revealed by analysing soluble transferrin receptor (sTfR) levels

The level of body iron storage and the erythropoietic need for iron are indicated by the serum levels of ferritin and soluble transferrin receptor (sTfR), respectively. A meta-analysis of five genome-wide association studies on sTfR and ferritin revealed novel association to the PCSK7 and TMPRSS6 loci for sTfR and the HFE locus for both parameters. The PCSK7 association was the most significant (rs236918, P = 1.1 �� 10E-27) suggesting that proprotein convertase 7, the gene product of PCSK7, may be involved in sTfR generation and/or iron homeostasis. Conditioning the sTfR analyses on transferrin saturation abolished the HFE signal and substantially diminished the TMPRSS6 signal while the PCSK7 association was unaffected, suggesting that the former may be mediated by transferrin saturation whereas the PCSK7-associated effect on sTfR generation appears to be more direct.

A locus on chromosome 5 is associated with dilated cardiomyopathy in Doberman Pinschers

Dilated cardiomyopathy (DCM) is a heterogeneous group of heart diseases with a strong genetic background. Currently, many human DCM cases exist where no causative mutation can be identified. DCM also occurs with high prevalence in several large dog breeds. In the Doberman Pinscher a specific DCM form characterized by arrhythmias and/or echocardiographic changes has been intensively studied by veterinary cardiologists. We performed a genome-wide association study in Doberman Pinschers. Using 71 cases and 70 controls collected in Germany we identified a genome-wide significant association to DCM on chromosome 5. We validated the association in an independent cohort collected in the United Kingdom. There is no known DCM candidate gene under the association signal. Therefore, DCM in Doberman Pinschers offers the chance of identifying a novel DCM gene that might also be relevant for human health.