REPSA: A method for determining the sequence specificity of DNA binding ligands

We developed a novel combinatorial method termed restriction endonuclease protection selection and amplification (REPSA) to identify consensus binding sites of DNA-binding ligands. REPSA uses a unique enzymatic selection based on the inhibition of cleavage by a type IIS restriction endonuclease, an enzyme that cleaves DNA at a site distal from its recognition sequence. Sequences bound by a ligand are protected from cleavage while unprotected sequences are cleaved. This enzymatic selection occurs in solution under mild conditions and is dependant only on the DNA-binding ability of the ligand. Thus, REPSA is useful for a broad range of ligands including all classes of DNA-binding ligands, weakly binding ligands, mixed populations of ligands, and unknown ligands. Here I describe REPSA and the application of this method to select the consensus DNA-binding sequences of three representative DNA-binding ligands; a nucleic acid (triplex-forming single-stranded DNA), a protein (the TATA-binding protein), and a small molecule (Distamycin A). These studies generated new information regarding the specificity of these ligands in addition to establishing their DNA-binding sequences. ^

Identification of antigen-encoding genes of Enterococcus faecalis during human infections and characterization of a gene cluster for the biosynthesis of an antigenic polysaccharide

Genomic libraries of two Enterococcus faecalis strains, OG1RF and TX52 (an isolate from an endocarditis patient), were constructed in Escherichia coli and were screened with serum from a rabbit immunized with surface proteins of an E. faecalis endocarditis isolate and sera from four patients with enterococcal endocarditis. Thirty-eight immunopositive cosmid clones reacted with at least two of the patient sera and contained distinct inserts based on their DNA restriction patterns. These were chosen for further subcloning in a pBluescript SK ($-$) vector. Each sublibrary was screened with one of the five sera. Analysis of sequences from the immunopositive subclones revealed similarities to a range of proteins, including bacterial virulence factors, transporters, two-component regulators, metabolic enzymes, and membrane or cell surface proteins. Fourteen subclones did not show significant similarity to any sequence in the databases and may contain novel genes. Thirteen of the immunopositive cosmid clones did not yield immunopositive subclones and one such cosmid clone, TX5159, produced an antigenic polysaccharide in Escherichia coli. The insert of TX5159 was found to contain a multicistronic gene cluster containing genes similar to those involved in the biosynthesis and export of polysaccharides from both Gram-positive and Gram-negative organisms. Insertions in several genes within the cluster abolished the immunoreactivity of TX5159. RT-PCR of genes within the cluster with total RNA from OG1RF showed that these genes are transcribed. The polysaccharide was detected in two recently reported E. faecalis mucoid strains using specific antibody, but not in the other strains tested. This is the first report on a gene cluster of E. faecalis involved in the biosynthesis of an antigenic polysaccharide. ^

A FUNCTIONAL VARIANT OF HLA-DR1 DELINEATED BY T-LYMPHOCYTE CLONE REACTIVITY, PROTEIN CONFORMATION, AND GENOMIC RESTRICTION SITES

This research characterized a serologically indistinguishable form of HLA-DR1 that: (1) cannot stimulate some DR1-restricted or specific T-lymphocyte clones; (2) displays an unusual electrophoretic pattern on two dimensional gels; and (3) is marked by a polymorphic restriction site of the alpha gene. Inefficient stimulation of some DR1-restricted clones was a property of DR1$\sp{+}$ cells that shared HLA-B14 on the same haplotype and/or were carriers of 21-hydroxylase (21-OH) deficiency. Nonclassical 21-OH deficiency frequently demonstrates genetic linkage with HLA-B14;DR1 haplotypes and associates with duplications of C4B and one 21-OH gene. Cells having both stimulatory (DR1$\sb{\rm n}$) and nonstimulatory (DR1$\sb{\rm x}$) parental haplotypes did not mediate proliferation of these clones. However, heterozygous DR1$\sb{\rm x}$, 2 and DR1$\sb{\rm x}$, 7 cells were efficient stimulators of DR2 and DR7 specific clones, respectively, suggesting that a trans acting factor may modify DR1 alleles or products to yield a dominant DR1$\sb{\rm x}$ phenotype. Incompetent stimulator populations did not secrete an intercellular soluble or contact dependent suppressor factor nor did they express interleukin-2 receptors competing for T-cell growth factors. Two dimensional gel analysis of anti-DR immunoprecipitates revealed, in addition to normal DR$\alpha$ and DR$\beta$ chains, a 50kD species from DR1$\sb{\rm x}$ but not from the majority of DR1$\sb{\rm n}$ or non-DR1 cells. The 50kD structure was stable under reducing conditions in SDS and urea, had antigenic homology with DR, and dissociated after boiling into 34kD and 28kD peptide chains apparently identical with DR$\alpha$ and DR$\beta$ as shown by limited digest peptide maps. N-linked glycosylation and sialation of DRgp50 appeared to be unchanged from normal DR$\alpha$ and DR$\beta$. Bg1II digestion and $DR\alpha$ probing of DR1$\sb{\rm x}$ genomic DNA revealed a 4.5kb fragment while DR1$\sb{\rm n}$ DNA yielded 3.8 and 0.76kb fragments; all restriction sites mapped to the 3$\sp\prime$ untranslated region of $DR\alpha$. Collectively, these data suggest that DRgp50 represents a novel combinatorial association between constitutive chains of DR that may interfere with or compete for normal T cell receptor recognition of DR1 as both an alloantigen and restricting element. Furthermore, extensive chromosomal abnormalities previously mapped to the class III region of B14;DR1 haplotypes may extend into the adjacent class II region with consequent intrusion on immune function. ^

DNA hypomethylation and oxidative stress-mediated increase in genomic instability in equine sarcoid-derived fibroblasts

It is widely accepted that equine sarcoid disease, the most common skin associated neoplasm in equids, is induced by bovine papillomavirus (BPV-1). Although BPV-1 DNA has been found in almost all examined sarcoids so far, its detailed impact on the horse's host cell metabolism is largely unknown. We used equine fibroblast cell lines originating from sarcoid biopsies to study BPV-1-associated changes on DNA methylation status and oxidative stress parameters. Sarcoid-derived fibroblasts manifested increased proliferation in vitro, transcriptional rDNA activity (NORs expression) and DNA hypomethylation compared to control cells. Cells isolated from equine sarcoids suffered from oxidative stress: the expression of antioxidant enzymes was decreased and the superoxide production was increased. Moreover, increased ploidy, oxidative DNA damage and micronuclei formation was monitored in sarcoid cells. We postulate that both altered DNA methylation status and redox milieu may affect genomic stability in BPV-1-infected cells and in turn contribute to sarcoid pathology.

The Topoisomerase I Inhibitor Irinotecan and the Tyrosyl-DNA Phosphodiesterase 1 Inhibitor Furamidine Synergistically Suppress Murine Lupus Nephritis

OBJECTIVE The treatment of lupus nephritis is still an unmet medical need requiring new therapeutic approaches. Our group found recently that irinotecan, an inhibitor of topoisomerase I (topo I), reversed proteinuria and prolonged survival in mice with advanced lupus nephritis. While irinotecan is known to stabilize the complex of topo I and DNA, the enzyme tyrosyl-DNA phosphodiesterase 1 (TDP-1) functions in an opposing manner by releasing topo I from DNA. Therefore, we undertook this study to test whether the TDP-1 inhibitor furamidine has an additional effect on lupus nephritis when used in combination with irinotecan. METHODS NZB/NZW mice were treated with low-dose irinotecan and furamidine either alone or in combination beginning at age 26 weeks. DNA relaxation was visualized using gel electrophoresis. Binding of anti-double-stranded DNA (anti-dsDNA) antibodies to DNA modified by topo I, TDP-1, and the topo I inhibitor camptothecin was determined by enzyme-linked immunosorbent assay. RESULTS Compared to treatment with either agent alone, simultaneous treatment with low-dose irinotecan and furamidine significantly improved survival of NZB/NZW mice. Similar to what has been previously shown for irinotecan alone, the combination treatment did not change the levels of anti-dsDNA antibodies. In vitro, recombinant TDP-1 increased topo I-mediated DNA relaxation, resulting in enhanced binding of anti-dsDNA antibodies. In combination with topo I and camptothecin, TDP-1 reversed the inhibitory effects of camptothecin on DNA relaxation and anti-dsDNA binding. CONCLUSION Affecting DNA relaxation by the enzymes topo I and TDP-1 and their inhibitors may be a promising approach for the development of new targeted therapies for systemic lupus erythematosus.

GENETIC ORGANIZATION OF THE STRUCTURAL GENES FOR NITRATE REDUCTASE (TN5)

Nitrate reductase in Escherichia coli is a membrane-bound anaerobic enzyme that is repressed by oxygen and induced by nitrate. The genetic organization of the structural genes for the two larger subunits of nitrate reductase ((alpha) and (beta)) was determined by immunoprecipitation analysis of the formation of these proteins in nitrate reductase-deficient mutants resulting from transposon Tn5 mutagenesis. The results suggested that the genes encoding the (alpha) and (beta) subunits (narG and H) were arranged in an operon with transcription in the direction promoter(--->)(alpha)(--->)(beta). Segments of the chromosome containing the Tn5 inserts from several of the mutants were cloned into plasmid pBR322 and the positions of the transposons determined by restriction mapping. The Tn5 insertion sites were localized on two contiguous EcoRI fragments spanning about 6.6 kilobases of DNA. The narI gene (proposed to encode the (gamma) subunit) was positioned immediately downstream from the (beta)-gene (narH) by Southern analysis of Tn10 insertions into the narI locus. A Tn10 insertion into the narK locus, proposed to encode a nitrate-sensitive repressor of other anaerobic enzymes, was located about 1.5 kilobases upstream from the narGHI operon promoter. The narL locus, proposed to encode a nitrate-sensitive positive regulator of the narGHI operon and known to be genetically linked to the other nar genes, was demonstrated to lie outside a 19.3-kilobase region of the chromosome which encompasses the other nar genes. The physical limit of the narGHI promoter was defined by studying the effect of Tn5 insertions into a hybrid plasmid containing the functional operon. The points of origin of the coding regions for the (alpha) and (beta) genes were deduced by alignment of the chromosomal map of Tn5 insertion sites with the sizes of (alpha) and (beta) subunit fragments produced by plasmids carrying these Tn5 inserts in the nar operon. The coding region for the (alpha) subunit (143,000 daltons) begins about 250 nucleotides downstream from the deduced limit of the promoter region and includes about 4.0 kilobases of DNA; the region encoding (beta) (60,000 daltons) lies immediately downstream from the (alpha)-gene and is approximately 1.6 kilobases in length. The adjacent region encoding the (gamma) subunit (19,000 daltons) is approximately 0.5 kilobase in length. ^

DNA incisions stimulate genetic instability of triplet repeat sequences related to human hereditary neurological diseases

The molecular mechanisms responsible for the expansion and deletion of trinucleotide repeat sequences (TRS) are the focus of our studies. Several hereditary neurological diseases including Huntington's disease, myotonic dystrophy, and fragile X syndrome are associated with the instability of TRS. Using the well defined and controllable model system of Escherichia coli, the influences of three types of DNA incisions on genetic instability of CTG•CAG repeats were studied: DNA double-strand breaks (DSB), single-strand nicks, and single-strand gaps. The DNA incisions were generated in pUC19 derivatives by in vitro cleavage with restriction endonucleases. The cleaved DNA was then transformed into E. coli parental and mutant strains. Double-strand breaks induced deletions throughout the TRS region in an orientation dependent manner relative to the origin of replication. The extent of instability was enhanced by the repeat length and sequence (CTG•CAG vs. CGG•CCG). Mutations in recA and recBC increased deletions, mutations in recF stabilized the TRS, whereas mutations in ruvA had no effect. DSB were repaired by intramolecular recombination, versus an intermolecular gene conversion or crossover mechanism. 30 nt gaps formed a distinct 30 nt deletion product, whereas single strand nicks and gaps of 15 nts did not induce expansions or deletions. Formation of this deletion product required the CTG•CAG repeats to be present in the single-stranded region and was stimulated by E. coli DNA ligase, but was not dependent upon the RecFOR pathway. Models are presented to explain the DSB induced instabilities and formation of the 30 nucleotide deletion product. In addition to the in vitro creation of DSBs, several attempts to generate this incision in vivo with the use of EcoR I restriction modification systems were conducted. ^

Searching for the ideal DNA recognition code of covalent ligands

The combitiatorial approach restriction endonuclease protection selection and amplification REPSA was successfully used to determine ideal DNA interactions sites of covalent ligands. Unlike most other combinatorial methods, REPSA is based on inhibition of enzymatic cleavage by specific ligand-DNA complexes, which enables identification of binding sites of various ligands. However, the inherent nature of this technique posses a problem during selection of binding sites of covalent ligands. By modifying the technique according to the nature of the ligand, we demonstrate the flexibility of REPSA in identifying the preferred binding sites for monocovalent ligands, topoisomerase I and tallimustine, and the bicovalent ligand topoisomerase II. From among the preferred binding sites, we identified the consensus binding sequence of camptothecin induced topoisomerase I cleavage as ‘aGWT/Gc’, and tallimustine consensus sequences as ‘GTTCTA’ and ‘TTTTTTC’. We have shown for the first time that preferential binding of tallimustine occurs at sequences not previously reported. Furthermore, our data indicate that tallimustine is a novel DNA minor groove, guanine-specific alkylating agent. ^ Additionally, we have demonstrated in vivo that sequence-specific covalent DNA-binding small molecules have the ability to regulate transcription by inhibiting RNA polymerase II. Tallimustine, binding to its preferred sequences located in the 5′ untranslated region were an effective impediment for transcribing polymerase II. The ability of covalent binding small molecules to target predetermined DNA sequences located downstream of the promoter suggests a general approach for regulation of gene expression. ^

Bases moleculares de la resistencia a insecticidas en la mosca mediterránea de la fruta Ceratitis Capitata (Wiedemann)

La mosca mediterránea de la fruta Ceratitis capitata (Wiedemann, 1824) está considerada una de las plagas clave para la fruticultura. El malatión es un insecticida organofosforado que fue empleado mayoritariamente en España para el control de C. capitata hasta 2009, año en el que dejó de utilizarse por no estar incluido en el anexo I de la Directiva Europea 91/414/ECC. El incremento del uso del malatión, debido a las graves pérdidas económicas causadas por C. capitata, provocó la aparición de poblaciones de campo resistentes. El estudio de una población resistente a malatión, recogida en Castelló en 2004, permitió la identificación de dos mecanismos de resistencia: una mutación puntual (G328A) en la acetilcolinesterasa (AChE) y un mecanismo de resistencia metabólica, probablemente mediado por carboxilesterasas. Teniendo en cuenta estos antecedentes, nos propusimos estudiar los mecanismos implicados en la resistencia a malatión en C. capitata. Además, durante el desarrollo de esta Tesis, el malatión fue sustituido por otros insecticidas como el espinosad y la lambda-cialotrina para el control de la plaga. En este nuevo contexto, es extremadamente importante analizar la susceptibilidad de poblaciones de campo frente a espinosad y estudiar la posible existencia de resistencia cruzada a estos insecticidas, así como sentar las bases para el estudio de futuros mecanismos de resistencia. En primer lugar, analizamos mediante bioensayos con dosis discriminante la susceptibilidad a malatión y espinosad en doce poblaciones de C. capitata de Andalucía, Aragón, Cataluña, Comunidad Valenciana e Islas Baleares; y nuestros resultados sugirieron la presencia de individuos resistentes a malatión en la mayoría de las poblaciones analizadas. En el caso del espinosad, observamos que la susceptibilidad a este insecticida de origen biológico fue elevada en la mayoría de las poblaciones, sin embargo, la población recogida en Xàbia (Alicante) mostró un nivel de susceptibilidad unas dos veces menor al resto de poblaciones. Mediante la selección en laboratorio, obtuvimos dos líneas resistentes a malatión, W-4Km y W-10Km, con unos niveles de resistencia con respeto a la línea susceptible C de 178 y 400 veces, respectivamente. Además, se seleccionó por primera vez en C. capitata una línea altamente resistente a espinosad (Xàbia-W-100s), que actualmente es unas 500 veces más resistente que la línea de laboratorio C. Con el objetivo de escoger la estrategia más adecuada para el manejo de la plaga, estudiamos la susceptibilidad a diferentes tipos de insecticidas en la línea resistente a malatión W- 4Km. En esta línea detectamos resistencia cruzada moderada a los organofosforados fentión, diazinón, fosmet, triclorfón y metil-clorpirifos (de 7 a 16 veces) y frente al carbamato carbaril, al piretroide lambda-cialotrina y al quimioesterilizante lufenurón (de 4 a 6 veces). Por otra parte, la resistencia cruzada frente a espinosad fue baja (1,5 veces). Es importante destacar que los niveles de resistencia estimados frente a todos los insecticidas fueron de uno o dos órdenes de magnitud inferiores al observado en la línea W-4Km frente a malatión (178 veces), hecho que podría deberse, al menos, a dos posibles hipótesis: que la mutación AChE G328A confiera mayor insensibilidad al malaoxón (forma activa del malatión) que a otros insecticidas que tienen como diana la AChE y/o, en segundo lugar, que el mecanismo de resistencia mediado por carboxilesterasas hidrolice el malatión de manera más eficiente que los otros insecticidas analizados. En el estudio de nuevos mecanismos de resistencia en C. capitata, por un lado, analizamos la diversidad de enzimas citocromo P450, asociadas con resistencia metabólica en otras especies, y por otro lado, desarrollamos un sistema para la detección de nuevas mutaciones puntuales que pudiesen aparecer en los genes que codifican la AChE (Ccace2) y la aliesterasa (Ccae7). Mediante el empleo de cebadores degenerados obtuvimos 37 genes CYP, que codifican enzimas P450, pertenecientes a cinco familias. Posteriormente, en un estudio de inducción con fenobarbital, observamos que la expresión de cuatro de los seis genes analizados era susceptible de ser inducida. Por otro lado, se puso a punto un sistema que permite amplificar y secuenciar, a partir de DNA genómico, los exones de los genes Ccace2 y Ccae7 en los que se han encontrado mutaciones relacionadas con resistencia a insecticidas en otras especies. Los resultados obtenidos facilitarán el estudio de nuevos mecanismos de resistencia mediados por estas enzimas en C. capitata. Se diseñó un método PCR-RFLP para identificar los individuos portadores de la mutación AChE G328A (alelo de resistencia Ccace2R) sin la necesidad de realizar bioensayos y que, además, permite detectar resistencia cuando ésta se encuentra a baja frecuencia. Según el análisis realizado, el alelo Ccace2R se observó en 25 de las 27 localidades españolas muestreadas en el territorio español, incluyendo las Islas Baleares y Canarias. Sin embargo, este alelo no se detectó en poblaciones procedentes de once países y de cinco continentes. El análisis de la presencia del alelo Ccace2R en las líneas resistentes a malatión durante el proceso de selección en el laboratorio mostró una rápida disminución de los homocigotos, tanto para el alelo susceptible como para el alelo de resistencia, en favor de los individuos heterocigotos. Así, después de 52 generaciones de selección, se observó que la totalidad de los individuos analizados de la línea W-10Km presentaban un genotipo heterocigoto para la mutación AChE G328A. Este desequilibrio contradice la segregación mendeliana esperada para un gen con dos alelos pero podría ser explicado por la existencia de una duplicación del gen Ccace2. La demostración de la presencia de esta duplicación se realizó mediante: i) el cruzamiento de individuos heterocigotos de la línea W-10Km con homocigotos susceptibles de la línea C, que dio lugar a una descendencia en la que el 100% de los individuos eran heterocigotos; ii) la evaluación del número de copias del gen Ccace2 por PCR cuantitativa en tiempo real (qPCR), que resultó dos veces mayor en individuos de la línea W-10Km en comparación con los de la línea C; iii) el análisis del nivel de expresión de Ccace2, que fue el doble en la línea W-10Km con respecto a la línea C, y iv) el estudio de la actividad AChE, que resultó mayor en los individuos de la línea W-10Km. Según los resultados obtenidos, una duplicación del gen Ccace2 provoca la coexistencia en un mismo cromosoma del alelo silvestre y del alelo mutado y, además, las dos copias del gen Ccace2, al estar ligadas, producen una heterocigosis permanente (Ccace2RS). De esta manera se explica que el hecho de que 100% de los individuos de la línea W-10Km mostrasen un perfil de restricción correspondiente a un individuo heterocigoto ya que, en realidad, eran homocigotos estructurales para la duplicación (genotipo CCace2RS/RS). Se ha detectado un coste biológico asociado a la duplicación que consiste en un incremento en la mortalidad acumulada de los adultos a partir del séptimo día después de la emergencia. La descripción de la duplicación Ccace2RS supone la identificación de un nuevo mecanismo de resistencia a malatión en C. capitata. Finalmente, mediante el diseño de un método de doble PCR-RFLP se determinó la presencia de la duplicación Ccace2RS en la mayoría de las poblaciones españolas. La proporción de individuos portadores de la duplicación osciló entre el 5% y el 35%, observándose los mayores valores de frecuencia en las poblaciones de C. capitata recogidas en la cuenca mediterránea. Podemos por lo tanto concluir que la resistencia a malatión asociada a la mutación AChE G328A y a la duplicación Ccace2RS está ampliamente establecida en las poblaciones españolas de C. capitata. Nuestros resultados desaconsejan la utilización del malatión (si fuera de nuevo autorizado) o de otros organofosforados para el control de esta plaga. Además, una de las líneas resistentes a malatión mostró resistencia cruzada frente a insecticidas con diferentes modos de acción y que se utilizan actualmente para el control de C. capitata, tales como lambda-cialotrina y lufenurón. La alta susceptibilidad a espinosad observada en las poblaciones españolas, así como la reducida resistencia cruzada estimada para este insecticida, sugieren que su utilización es adecuada para el control de la plaga. Sin embargo, la utilización de un sólo insecticida puede entrañar riesgos por favorecer la selección de resistencia, de hecho, mediante selección en laboratorio se obtuvo una población altamente resistente a espinosad. Por tanto, es recomendable implementar programas de control integrado y de manejo de la resistencia en C. capitata utilizando distintos sistemas de control e insecticidas con diferentes mecanismos de acción que permitan su sostenibilidad en el tiempo. Los sistemas de detección de alelos de resistencia desarrollados en este trabajo permitirán la detección precoz de resistencia en campo, facilitando la decisión sobre el sistema de control más adecuado. Además, los conocimientos generados podrán contribuir al desarrollo de nuevos sistemas de detección para otros mecanismos de resistencia. Abstract. The Mediterranean fruit fly, Ceratitis capitata (Wiedemann, 1824), is considered one of the most harmful pests in fruit crops. Until 2009, when malathion use was banned due to its not inclusion in the Annex I of Directive 91/414/EEC, the application of this organophosphate (OP) insecticide in Spain increased gradually due to the large economic losses caused by C. capitata. The increase in the frequency of treatments resulted in the development of resistant field populations. The study of a malathion-resistant population, collected in 2004 in Castelló (Comunidad Valenciana), allowed the identification of two resistance mechanisms: a single point mutation (G328A) in the target acetylcholinesterase (AChE), as well as a metabolic resistance mechanism, most likely carboxylesterase-mediated. Taking all the preceding into account, we studied the malathion resistance mechanisms in C. capitata. During the development of this PhD Thesis malathion use was banned by the European Union, being replaced by other insecticides, such as spinosad and lambda-cyhalotrin. Within this new working frame, the need to analyse the possible existence of cross-resistance to these insecticides and the susceptibility to spinosad in field populations was raised. This would define the baseline for future studies on resistance mechanisms. Firstly, through discriminant dose bioassays, we analysed malathion and spinosad susceptibility in twelve C. capitata populations from Andalucia, Aragon, Cataluña, C. Valenciana and the Baleares Islands. Our results suggest the presence of malathion-resistant individuals in most of the populations analysed. Regarding spinosad, we noticed a high susceptibility to this biologically derived insecticide in most of the populations, but in the one collected in Xabia (Alicante), which had a susceptibility level two times lower than the rest of populations. Through laboratory selection, we obtained two malathion-resistant strains, W-4Km and W-10Km, with resistance levels 178- and 400-fold, respectively, compared to the control susceptible C strain. Besides, a strain highly-resistant to spinosad (Xabia-W-100s), 500-times more resistant than control C strain, was selected. In order to decide the most appropriate management strategy for the pest, we studied the susceptibility to different insecticides in the malathion-resistant W-4Km strain. We detected a moderated cross-resistance to the OPs fenthion, diazinon, phosmet, trichlorphon and methylchlorpyrifos (7- to 16-fold), and to the carbamate carbaryl, the pyretroid lambda-cyhalotrin and the chemosterilizer lufenuron (4- to 6-fold). On the other hand, cross-resistance to spinosad was low (1.5-fold). It is important to note that resistance levels to all insecticides were one or two orders of magnitude less than that observed against malathion in W-4Km strain (178-fold), a fact that might be due to, at least, two possible causes: mutation AChE G328A may provide a higher insensitivity to malaoxon (the active form of malathion) than to other insecticides having AChE as target, and/or, secondly, the carboxylesterase-mediated resistance mechanism hydrolyzes malathion more efficiently than all other analysed insecticides. To investigate new resistance mechanisms in C. capitata we analysed the diversity of the cytochrome P450 enzymes, which have been associated to metabolic resistance in insects, and we developed a new method to detect single point mutations in acetylcholinesterase (Ccace2) and aliesterase (Ccae7) genes that could appear. Using degenerate primers we obtained 37 CYP genes, coding P450 enzymes, included in five families. Afterwards, in a phenobarbital-induction study, we observed that the expression of 4 out of the 6 analysed genes could be induced. On the other hand, a system was set up to amplify and to sequence from genomic DNA the exons of genes Ccace2 and Ccae7 where mutations related to insecticide resistance have been found in other species. The results obtained could facilitate the study of new resistance mechanisms in C. capitata mediated by these enzymes. A PCR-RFLP method was designed to detect the presence of the mutation AChE G328A (resistance allele Ccace2R), with no need to perform bioassays and allowing detecting resistance at low frequency. According to the analysis, the resistance allele was found in 25 out of 27 sampled locations in Spain, including the Balearic and the Canary Islands. However, this allele was not detected in other populations collected in 11 countries from 5 continents. The follow-up of the presence of the allele Ccace2R in the malathion-resistant strains during the selection process in the laboratory showed a quick decrease in homozygous individuals, for both the susceptible and the resistant alleles, favouring heterozygous. Thus, after 52 generations of selection, all the individuals analysed from W-10Km strain showed a heterozygous genotype for mutation AChE G328A, contradicting mendelian segregation as expected for a gene with two alleles. Afterwards, we were able to demonstrate that this was caused by the presence of a duplication of the gene coding acetylcholinesterase by: i) crossing heterozygous individuals from W-10Km strain with susceptible homozygous from C strain, originating a F1 population in which 100% of individuals were heterozygous; ii) evaluating the number of copies of gen Ccace2 by quantitative PCR in real time (qPCR), that happened to be twice higher in individuals from W-10Km VII strain when compared with C strain; iii) analysing the level of expression of Ccace2, twice in W- 10Km strain when compared to C strain; iv) studying the acetylcholinesterase activity, that was higher in individuals from W-10Km strain. According to these results, duplication of gen Ccace2 originates the coexistence of the susceptible and the resistant allele in the same chromosome. The two linked copies of the gene Ccace2 provoke the existence of permanent heterozygosis (Ccace2RS). This explains why the 100% of individuals from W-10Km strain showed an heterozygous restriction pattern since, in fact, they were structural homozygotes for the duplication (genotype Ccace2RS/RS). A biological cost has been detected associated to this duplication, consisting in a rise in accumulated adult mortality from the seventh day after emergence. The Ccace2RS duplication described in this study represents a new resistance mechanism to malathion in C. capitata. Finally, by the design of a double PCR-RFLP method, the presence of Ccace2RS duplication was confirmed in most of the Spanish populations. We observed that the proportion of individuals carrying the duplication oscillated between 5 and 35%, the frequency being higher in those C. capitata populations collected in the area of the Mediterranean basin. Therefore, we can conclude that malathion resistance associated to mutation AChE G328A and to Ccace2RS duplication are widely distributed in Spanish populations of C. capitata. Our results advice against the use of malathion (if it came to be newly authorized for use) or other OPs for the control of this pest. Besides, one of the malathion-resistant strains showed cross-resistance against insecticides with diverse action modes that are currently used for pest control, such as lambdacyhalotrin and lufenuron. High susceptibility to spinosad in the Spanish populations, as well as the reduced cross-resistance estimated for this insecticide suggests its adequacy for Medfly control. However, the use of a single insecticide is a risky strategy since it favours the selection of resistance. In fact, a population highly resistant to spinosad was obtained through laboratory selection. Therefore, it is advisable to implement integrated pest management (IPM) and resistance management programs for C. capitata control. Using insecticides with different modes of action and diverse control systems would contribute to the sustainability of the pest control. The resistance allele detection systems developed through this work will allow the early detection of resistance in the field, making possible the selection of the most appropriate method for pest control. Besides, the generated knowledge may also contribute to the development of new detection systems for other resistance mechanisms.

Probabilistic reasoning with an enzyme-driven DNA device

We present a biomolecular probabilistic model driven by the action of a DNA toolbox made of a set of DNA templates and enzymes that is able to perform Bayesian inference. The model will take single-stranded DNA as input data, representing the presence or absence of a specific molecular signal (the evidence). The program logic uses different DNA templates and their relative concentration ratios to encode the prior probability of a disease and the conditional probability of a signal given the disease. When the input and program molecules interact, an enzyme-driven cascade of reactions (DNA polymerase extension, nicking and degradation) is triggered, producing a different pair of single-stranded DNA species. Once the system reaches equilibrium, the ratio between the output species will represent the application of Bayes? law: the conditional probability of the disease given the signal. In other words, a qualitative diagnosis plus a quantitative degree of belief in that diagno- sis. Thanks to the inherent amplification capability of this DNA toolbox, the resulting system will be able to to scale up (with longer cascades and thus more input signals) a Bayesian biosensor that we designed previously.

A human homolog of the Saccharomyces cerevisiae REV3 gene, which encodes the catalytic subunit of DNA polymerase ζ

To get a better understanding of mutagenic mechanisms in humans, we have cloned and sequenced the human homolog of the Saccharomyces cerevisiae REV3 gene. The yeast gene encodes the catalytic subunit of DNA polymerase ζ, a nonessential enzyme that is thought to carry out translesion replication and is responsible for virtually all DNA damage-induced mutagenesis and the majority of spontaneous mutagenesis. The human gene encodes an expected protein of 3,130 residues, about twice the size of the yeast protein (1,504 aa). The two proteins are 29% identical in an amino-terminal region of ≈340 residues, 39% identical in a carboxyl-terminal region of ≈850 residues, and 29% identical in a 55-residue region in the middle of the two genes. The sequence of the expected protein strongly predicts that it is the catalytic subunit of a DNA polymerase of the pol ζ type; the carboxyl-terminal domain possesses, in the right order, the six motifs characteristic of eukaryotic DNA polymerases, most closely resembles yeast pol ζ among all polymerases in the GenBank database, and is different from the human α, δ, and ɛ enzymes. Human cells expressing high levels of an hsREV3 antisense RNA fragment grow normally, but show little or no UV-induced mutagenesis and are slightly more sensitive to killing by UV. The human gene therefore appears to carry out a function similar to that of its yeast counterpart.

Transgenic DNA integrated into the oat genome is frequently interspersed by host DNA

Integration of transgenic DNA into the plant genome was investigated in 13 transgenic oat (Avena sativa L.) lines produced using microprojectile bombardment with one or two cotransformed plasmids. In all transformation events, the transgenic DNA integrated into the plant genome consisted of intact transgene copies that were accompanied by multiple, rearranged, and/or truncated transgene fragments. All fragments of transgenic DNA cosegregated, indicating that they were integrated at single gene loci. Analysis of the structure of the transgenic loci indicated that the transgenic DNA was interspersed by the host genomic DNA. The number of insertions of transgenic DNA within the transgene loci varied from 2 to 12 among the 13 lines. Restriction endonucleases that do not cleave the introduced plasmids produced restriction fragments ranging from 3.6 to about 60 kb in length hybridizing to a probe comprising the introduced plasmids. Although the size of the interspersing host DNA within the transgene locus is unknown, the sizes of the transgene-hybridizing restriction fragments indicated that the entire transgene locus must be at least from 35–280 kb. The observation that all transgenic lines analyzed exhibited genomic interspersion of multiple clustered transgenes suggests a predominating integration mechanism. We propose that transgene integration at multiple clustered DNA replication forks could account for the observed interspersion of transgenic DNA with host genomic DNA within transgenic loci.

Translocation and specific cleavage of bacteriophage T7 DNA in vivo by EcoKI

Infection of Escherichia coli containing the type I restriction enzyme EcoKI by bacteriophage T7 0.3 mutants leads to restriction during the late stages of genome entry and during DNA replication. Patterns of cleavage in vivo suggest that some cutting occurs near the midpoint of two recognition sites, consistent with the idea that EcoKI translocates DNA bidirectionally through itself and cuts when two enzyme molecules collide. Rapid ejection of a 0.3+ T7 genome from a bacteriophage λ particle results in degradation of the infecting DNA by EcoKI, showing that the normal T7 DNA translocation process delays restriction. A unique recognition site inserted at the genomic left end allows EcoKI to function as a molecular motor and to translocate the remaining 39 kilobases of T7 DNA into the cell.

Philopatry of male marine turtles inferred from mitochondrial DNA markers

Recent studies of mitochondrial DNA (mtDNA) variation among marine turtle populations are consistent with the hypothesis that females return to beaches in their natal region to nest as adults. In contrast, less is known about breeding migrations of male marine turtles and whether they too are philopatric to natal regions. Studies of geographic structuring of restriction fragment and microsatellite polymorphisms at anonymous nuclear loci in green turtle (Chelonia mydas) populations indicate that nuclear gene flow is higher than estimates from mtDNA analyses. Regional populations from the northern and southern Great Barrier Reef were distinct for mtDNA but indistinguishable at nuclear loci, whereas the Gulf of Carpentaria (northern Australia) population was distinct for both types of marker. To assess whether this result was due to reduced philopatry of males across the Great Barrier Reef, we determined the mtDNA haplotypes of breeding males at courtship areas for comparison with breeding females from the same three locations. We used a PCR-restriction fragment length polymorphism approach to determine control region haplotypes and designed mismatch primers for the identification of specific haplotypes. The mtDNA haplotype frequencies were not significantly different between males and females at any of the three areas and estimates of Fst among the regions were similar for males and females (Fst = 0.78 and 0.73, respectively). We conclude that breeding males, like females, are philopatric to courtship areas within their natal region. Nuclear gene flow between populations is most likely occurring through matings during migrations of both males and females through nonnatal courtship areas.

Phylogeny of mRNA capping enzymes

The m7GpppN cap structure of eukaryotic mRNA is formed cotranscriptionally by the sequential action of three enzymes: RNA triphosphatase, RNA guanylyltransferase, and RNA (guanine-7)-methyltransferase. A multifunctional polypeptide containing all three active sites is encoded by vaccinia virus. In contrast, fungi and Chlorella virus encode monofunctional guanylyltransferase polypeptides that lack triphosphatase and methyltransferase activities. Transguanylylation is a two-stage reaction involving a covalent enzyme-GMP intermediate. The active site is composed of six protein motifs that are conserved in order and spacing among yeast and DNA virus capping enzymes. We performed a structure–function analysis of the six motifs by targeted mutagenesis of Ceg1, the Saccharomyces cerevisiae guanylyltransferase. Essential acidic, basic, and aromatic functional groups were identified. The structural basis for covalent catalysis was illuminated by comparing the mutational results with the crystal structure of the Chlorella virus capping enzyme. The results also allowed us to identify the capping enzyme of Caenorhabditis elegans. The 573-amino acid nematode protein consists of a C-terminal guanylyltransferase domain, which is homologous to Ceg1 and is strictly conserved with respect to all 16 amino acids that are essential for Ceg1 function, and an N-terminal phosphatase domain that bears no resemblance to the vaccinia triphosphatase domain but, instead, has strong similarity to the superfamily of protein phosphatases that act via a covalent phosphocysteine intermediate.