Origins of the Xylella fastidiosa Prophage-Like Regions and Their Impact in Genome Differentiation

Xylella fastidiosa is a Gram negative plant pathogen causing many economically important diseases, and analyses of completely sequenced X. fastidiosa genome strains allowed the identification of many prophage-like elements and possibly phage remnants, accounting for up to 15% of the genome composition. To better evaluate the recent evolution of the X. fastidiosa chromosome backbone among distinct pathovars, the number and location of prophage-like regions on two finished genomes (9a5c and Temecula1), and in two candidate molecules (Ann1 and Dixon) were assessed. Based on comparative best bidirectional hit analyses, the majority (51%) of the predicted genes in the X. fastidiosa prophage-like regions are related to structural phage genes belonging to the Siphoviridae family. Electron micrograph reveals the existence of putative viral particles with similar morphology to lambda phages in the bacterial cell in planta. Moreover, analysis of microarray data indicates that 9a5c strain cultivated under stress conditions presents enhanced expression of phage anti-repressor genes, suggesting switches from lysogenic to lytic cycle of phages under stress-induced situations. Furthermore, virulence-associated proteins and toxins are found within these prophage-like elements, thus suggesting an important role in host adaptation. Finally, clustering analyses of phage integrase genes based on multiple alignment patterns reveal they group in five lineages, all possessing a tyrosine recombinase catalytic domain, and phylogenetically close to other integrases found in phages that are genetic mosaics and able to perform generalized and specialized transduction. Integration sites and tRNA association is also evidenced. In summary, we present comparative and experimental evidence supporting the association and contribution of phage activity on the differentiation of Xylella genomes.

Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli

Background: Leifsonia xyli is a xylem-inhabiting bacterial species comprised of two subspecies: L. xyli subsp. xyli (Lxx) and L. xyli subsp. cynodontis (Lxc). Lxx is the causal agent of ratoon stunting disease in sugarcane commercial fields and Lxc colonizes the xylem of several grasses causing either mild or no symptoms of disease. The completely sequenced genome of Lxx provided insights into its biology and pathogenicity. Since IS elements are largely reported as an important source of bacterial genome diversification and nothing is known about their role in chromosome architecture of L. xyli, a comparative analysis of Lxc and Lxx elements was performed. Results: Sample sequencing of Lxc genome and comparative analysis with Lxx complete DNA sequence revealed a variable number of IS transposable elements acting upon genomic diversity. A detailed characterization of Lxc IS elements and a comparative review with IS elements of Lxx are presented. Each genome showed a unique set of elements although related to same IS families when considering features such as similarity among transposases, inverted and direct repeats, and element size. Most of the Lxc and Lxx IS families assigned were reported to maintain transposition at low levels using translation regulatory mechanisms, consistent with our in silico analysis. Some of the IS elements were found associated with rearrangements and specific regions of each genome. Differences were also found in the effect of IS elements upon insertion, although none of the elements were preferentially associated with gene disruption. A survey of transposases among genomes of Actinobacteria showed no correlation between phylogenetic relatedness and distribution of IS families. By using Southern hybridization, we suggested that diversification of Lxc isolates is also mediated by insertion sequences in probably recent events. Conclusion: Collectively our data indicate that transposable elements are involved in genome diversification of Lxc and Lxx. The IS elements were probably acquired after the divergence of the two subspecies and are associated with genome organization and gene contents. In addition to enhancing understanding of IS element dynamics in general, these data will contribute to our ongoing comparative analyses aimed at understanding the biological differences of the Lxc and Lxx.

Risk Score to Predict the Outcome of Patients with Cerebral Vein and Dural Sinus Thrombosis

Background: Around 15% of patients die or become dependent after cerebral vein and dural sinus thrombosis (CVT). Method: We used the International Study on Cerebral Vein and Dural Sinus Thrombosis (ISCVT) sample (624 patients, with a median follow-up time of 478 days) to develop a Cox proportional hazards regression model to predict outcome, dichotomised by a modified Rankin Scale score > 2. From the model hazard ratios, a risk score was derived and a cut-off point selected. The model and the score were tested in 2 validation samples: (1) the prospective Cerebral Venous Thrombosis Portuguese Collaborative Study Group (VENO-PORT) sample with 91 patients; (2) a sample of 169 consecutive CVT patients admitted to 5 ISCVT centres after the end of the ISCVT recruitment period. Sensitivity, specificity, c statistics and overall efficiency to predict outcome at 6 months were calculated. Results: The model (hazard ratios: malignancy 4.53; coma 4.19; thrombosis of the deep venous system 3.03; mental status disturbance 2.18; male gender 1.60; intracranial haemorrhage 1.42) had overall efficiencies of 85.1, 84.4 and 90.0%, in the derivation sample and validation samples 1 and 2, respectively. Using the risk score (range from 0 to 9) with a cut-off of 6 3 points, overall efficiency was 85.4, 84.4 and 90.1% in the derivation sample and validation samples 1 and 2, respectively. Sensitivity and specificity in the combined samples were 96.1 and 13.6%, respectively. Conclusions: The CVT risk score has a good estimated overall rate of correct classifications in both validation samples, but its specificity is low. It can be used to avoid unnecessary or dangerous interventions in low-risk patients, and may help to identify high-risk CVT patients. Copyright (C) 2009 S. Karger AG, Basel

Mosaic maternal ancestry in the Great Lakes region of East Africa

The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.

T-cell response to my mycobacterial antigens in lepromatous and tuberculoid leprosy

We showed that a large fraction of lepromatous patients do harbor helper-type circulating T-cells that can be activated in vitro by Mycobacterium leprae. M. leprae and PPD triggered T-cell lines could be then obtained from both tuberculoid and lepromatous patients. The proliferative response of these helper T-cells is predominantly directed against epitopes shared by several species of mycobacteria, in lepromatous patients as well as in tuberculoid patients, but species specific T-cells are also present. When presented in the context of M. leprae, these cross reactive epitopes usually fail to stimulate the T-cell lines of lepromatous patients, because of the contamination of the lines by supressor T-cells actavable by M. leprae. In one lepromatous patient, PPD and M. leprae reactive T-cell lines and clones (of the CD4 phenotype), exhibited a strong cytotoxic activity to autologous target cells coated with antigen: the relevance of this phenomenon to the pathophysiology of lepromatous leprosy remains however unknown.

Ordonnance de Sa Majesté qui ordonne que, le jour de l'entrée de l'infante d'Espagne, toutes les rues & places y nommées, qui se trouveront sur son passage, soient ornées & les maisons illuminées , &c. Du vingt-trois fevrier mil sept cens vingt-deux

[Acte royal. 1722-02-23. Paris]

Recherches sur la vie et les oeuvres d'une précieuse / par M. Théry,...

Comprend : [Poèmes de Marie-Anne de La Vigne]

Descripción del desarrollo gonadal de Mesodesma Donacium (bivalvia: Mesodesmatidae), durante el periodo 2006 - 2014, en el litoral de Tacna

Mesodesma donacium (Lamarck, 1818), ha disminuido su abundancia durante los últimos 30 años, debido a los eventos El Niño más recientes y a la sostenida extracción sin medidas de control, lo que generado repercusiones sobre los grupos de pescadores que se dedicaban únicamente a la extracción de este recurso. Para lograr una recuperación y administración sostenible de este recurso, se requiere actualizar conocimientos biológicos básicos en temas reproductivos como el desarrollo gonadal y su variación estacional, talla de primera madurez, periodos de desove y proporción sexual. Esta información no ha sido publicada en el Perú luego de los eventos El Niño de 1982 – 83 y 1997 – 98, por lo que la investigación a realizar está destinada a aportar y fortalecer el conocimiento sobre estos aspectos. El objetivo de este trabajo fue describir el desarrollo gonadal de M. donacium que se distribuye desde Cerro Cortado por el norte (18º10´3´´S, 70º40´5´´W) hasta Santa Rosa por el sur (18º20´56´´S, 70º22´47´´W), Tacna, durante el periodo 2006 – 2014. El estudio se basó en el análisis histológico de 2503 muestras de gónadas, colectadas durante 32 meses. Se determinó la proporción sexual para los meses de estudio y se describió la ovogénesis y espermatogénesis, confirmando a la especie como dioica con reproducción de tipo parcial. Además, se realizó la descripción de una escala de madurez gonadal por procesamiento histológico y teniendo como base esta escala, se estableció una escala de madurez gonadal por frotis. Se halló la frecuencia de estadios de madurez gonadal y el índice de actividad reproductiva por estación, utilizando la información obtenida luego del análisis histológico. Se encontró que la proporción sexual fue 1:1 en los meses de mayor actividad reproductiva, sin embargo, existió una predominancia significativa de machos en otoño del 2010, 2012 y verano del 2012, 2014, estaciones en las que existió un elevado porcentaje de organismos indiferenciados y en estadio V (recuperación/ post expulsión). En la nueva escala de madurez, realizada por procesamiento histológico, se consideraron seis estadios: virginal (0), reposo (I), en maduración (II), maduro (III), desovante/ expulsante (IV) y recuperación/ post expulsante (V), en hembras y machos. Se definieron tres estadios en la escala de madurez realizada por frotis: virginales, inactivos y activos. Las frecuencias relativas de estadios de madurez muestran un predominio del estadio V, a partir del año 2008, en verano y otoño. Además, las frecuencias de los estadios III y IV aumentaron de forma creciente, de verano a primavera. Los valores mensuales del índice de actividad reproductiva variaron según el año de estudio, observándose los mayores valores en primavera. Se halló la talla de primera madurez, siendo 34.4 mm para machos y 34.9 mm para hembras de longitud valvar.

Madurez gonadal de algunos peces de importancia comercial: escalas macroscópicas validadas microscópicamente

Describen las escalas de madurez gonadal macroscópicas, validadas mediante análisis microscópicos, de diez especies de peces: Engraulis ringens anchoveta peruana, Merluccius gayi peruanus merluza, Sarda chiliensis chiliensis bonito, Scomber japonicus peruanus caballa, Anchoa nasus anchoveta blanca, Paralabrax humeralis cabrilla, Paralichthys adspersus lenguado, Cynoscion analis cachema, Hippoglossina macrops lenguado de ojo grande y Vinciguerria lucetia. Todas las escalas tienen seis estadios de madurez para hembras y machos: 0 (virginal), I (reposo), II (en maduración), III (maduro), IV (desovante/expulsante), V (recuperación/post expulsante). Se describen características y criterios claros para diferenciación entre estadios de madurez por especie y se discute la importancia de la validación y sus múltiples aplicaciones

Escala de madurez gonadal de anchoveta peruana Engraulis ringens (Jenyns, 1842

En este trabajo, se describe la escala de madurez gonadal macroscópica, validada microscópicamente, de anchoveta peruana Engraulis ringens. Se analizó 1970 gónadas (1251 ovarios, 719 testículos), procedentes del seguimiento de la pesquería pelágica del 2006, 2008, 2009 y 2012 y de cruceros de Evaluación Hidroacústica de Recursos Pelágicos del 2006, 2009 y 2012. La escala establece seis estadios de madurez para hembras y machos: 0 (virginal), I (reposo), II (en maduración), III (maduro), IV (desovante/expulsante), V (recuperación/post expulsante).

Escala de madurez gonadal de bonito Sarda chiliensis chiliensis (Cuvier, 1832)

El objetivo fue elaborar la escala de madurez gonadal macroscópica de Sarda chiliensis chiliensis con una validación basada en análisis histológicos. Se analizaron 591 muestras de gónadas provenientes del plan de seguimiento de la pesquería pelágica en el año 2014. A cada gónada se asignó un estadio de madurez macroscópico luego de la observación del desarrollo ovocitario y espermatogénico en los cortes histológicos. Se describieron seis estadios de maduración que van desde 0 (virginal) hasta el estadio 5 (recuperación en hembras, post expulsante en machos). Se compara la descripción de esta escala con trabajos anteriormente realizados, se discuten los criterios de catalogación y se dan recomendaciones para el seguimiento de la pesquería.

Escala de madurez gonadal de caballa Scomber japonicus peruanus (Jordan y Hubbs, 1925)

En el presente trabajo se realizó la validación de la escala de madurez gonadal macroscópica de la caballa Scomber japonicus peruanus. Se analizaron 464 muestras de gónadas provenientes del plan de seguimiento de la pesquería pelágica del 2006, 2008, 2009 y 2014. Sobre la base del desarrollo ovocitario, se asignó a cada individuo el estadio de madurez gonadal macroscópico. Se describieron seis estadios de maduración que va desde el estadio 0 (virginal) hasta el estadio 5 (recuperación en hembras, post expulsante en machos). Se compara la presente escala con trabajos anteriormente realizados, se discute acerca de los beneficios de su uso y recomendaciones futuras como parte del seguimiento de la pesquería.

Escala de madurez gonadal de anchoveta blanca Anchoa nasus (Kner y Steindachner, 1867)

Se presenta la escala de madurez gonadal de anchoveta blanca Anchoa nasus. El proceso de maduración y desove se ha clasificado en seis estadios tanto para hembras como para machos. Se examinaron cortes histológicos de 442 individuos de anchoveta blanca colectados a bordo del BIC J. Olaya, durante las operaciones de verano del 2008 y 2009 y del invierno primavera del 2012 y 2013. Se describe las características visuales externas y las microscópicas que definen cada uno de los estadios.