Identification of cancer/testis-antigen genes by massively parallel signature sequencing.

Massively parallel signature sequencing (MPSS) generates millions of short sequence tags corresponding to transcripts from a single RNA preparation. Most MPSS tags can be unambiguously assigned to genes, thereby generating a comprehensive expression profile of the tissue of origin. From the comparison of MPSS data from 32 normal human tissues, we identified 1,056 genes that are predominantly expressed in the testis. Further evaluation by using MPSS tags from cancer cell lines and EST data from a wide variety of tumors identified 202 of these genes as candidates for encoding cancer/testis (CT) antigens. Of these genes, the expression in normal tissues was assessed by RT-PCR in a subset of 166 intron-containing genes, and those with confirmed testis-predominant expression were further evaluated for their expression in 21 cancer cell lines. Thus, 20 CT or CT-like genes were identified, with several exhibiting expression in five or more of the cancer cell lines examined. One of these genes is a member of a CT gene family that we designated as CT45. The CT45 family comprises six highly similar (>98% cDNA identity) genes that are clustered in tandem within a 125-kb region on Xq26.3. CT45 was found to be frequently expressed in both cancer cell lines and lung cancer specimens. Thus, MPSS analysis has resulted in a significant extension of our knowledge of CT antigens, leading to the discovery of a distinctive X-linked CT-antigen gene family.

MLL2 mutation detection in 86 patients with Kabuki syndrome: a genotype-phenotype study.

Recently, pathogenic variants in the MLL2 gene were identified as the most common cause of Kabuki (Niikawa-Kuroki) syndrome (MIM#147920). To further elucidate the genotype-phenotype correlation, we studied a large cohort of 86 clinically defined patients with Kabuki syndrome (KS) for mutations in MLL2. All patients were assessed using a standardized phenotype list and all were scored using a newly developed clinical score list for KS (MLL2-Kabuki score 0-10). Sequencing of the full coding region and intron-exon boundaries of MLL2 identified a total of 45 likely pathogenic mutations (52%): 31 nonsense, 10 missense and four splice-site mutations, 34 of which were novel. In five additional patients, novel, i.e. non-dbSNP132 variants of clinically unknown relevance, were identified. Patients with likely pathogenic nonsense or missense MLL2 mutations were usually more severely affected (median 'MLL2-Kabuki score' of 6) as compared to the patients without MLL2 mutations (median 'MLL2-Kabuki score' of 5), a significant difference (p < 0.0014). Several typical facial features such as large dysplastic ears, arched eyebrows with sparse lateral third, blue sclerae, a flat nasal tip with a broad nasal root, and a thin upper and a full lower lip were observed more often in mutation positive patients.

Evolution and sedimentology of a channel fill in the sandy braided South Saskatchewan River and its comparison to the deposits of an adjacent compound bar

The depositional stratigraphy of within-channel deposits in sandy braided rivers is dominated by a variety of barforms (both singular `unit' bars and complex `compound' bars), as well as the infill of individual channels (herein termed `channel fills'). The deposits of bars and channel fills define the key components of facies models for braided rivers and their within-channel heterogeneity, knowledge of which is important for reservoir characterization. However, few studies have sought to address the question of whether the deposits of bars and channel fills can be readily differentiated from each other. This paper presents the first quantitative study to achieve this aim, using aerial images of an evolving modern sandy braided river and geophysical imaging of its subsurface deposits. Aerial photographs taken between 2000 and 2004 document the abandonment and fill of a 1 3 km long, 80 m wide anabranch channel in the sandy braided South Saskatchewan River, Canada. Upstream river regulation traps the majority of very fine sediment and there is little clay (<1%) in the bed sediments. Channel abandonment was initiated by a series of unit bars that stalled and progressively blocked the anabranch entrance, together with dune deposition and stacking at the anabranch entrance and exit. Complete channel abandonment and subsequent fill of up to 3 m of sediment took approximately two years. Thirteen kilometres of ground-penetrating radar surveys, coupled with 18 cores, were obtained over the channel fill and an adjacent 750 m long, 400 m wide, compound bar, enabling a quantitative analysis of the channel and bar deposits. Results show that, in terms of grain-size trends, facies proportions and scale of deposits, there are only subtle differences between the channel fill and bar deposits which, therefore, renders them indistinguishable. Thus, it may be inappropriate to assign different geometric and sedimentological attributes to channel fill and bar facies in object-based models of sandy braided river alluvial architecture.

Hablando de emociones fingidas: la relación entre la sintaxis de la complementación y la comprensión de la simulación emocional

Este trabajo se centra en investigar la relación entre el uso de la sintaxis de la complementación y la capacidad infantil para comprender la simulación emocional. Un total de 337 niñas y niños de cuatro a doce años realizaron cuatro tareas en las cuales los personajes fingían una emoción, para jugar o para engañar a un observador. Se preguntó a los participantes por la emoción externa e interna del protagonista, y también por las creen-cias del observador, solicitando la justificación de sus respuestas. Se analiza-ron tanto la capacidad para comprender las emociones fingidas como el uso de distintos tipos de oraciones completivas en las justificaciones de las res-puestas. Los resultados mostraron una contingencia significativa entre la comprensión de la simulación emocional y la utilización de oraciones com-pletivas con verbos cognitivos o comunicativos, aunque el uso de este tipo de oraciones no se mostró necesario ni suficiente para esta comprensión. Finalmente, se discute el alcance de la relación entre la comprensión de la simulación emocional y la utilización de oraciones completivas con verbos comunicativos o cognitivos

Quantification of the relation between surface morphodynamics and subsurface sedimentological product in sandy braided rivers

This study uses digital elevation models and ground-penetrating radar to quantify the relation between the surface morphodynamics and subsurface sedimentology in the sandy braided South Saskatchewan River, Canada. A unique aspect of the methodology is that both digital elevation model and ground-penetrating radar data were collected from the same locations in 2004, 2005, 2006 and 2007, thus enabling the surface morphodynamics to be tied explicitly to the associated evolving depositional product. The occurrence of a large flood in 2005 also allowed the influence of discharge to be assessed with respect to the processproduct relationship. The data demonstrate that the morphology of the study reach evolved even during modest discharges, but more extensive erosion was caused by the large flood. In addition, the study reach was dominated by compound bars before the flood, but switched to being dominated by unit bars during and after the flood. The extent to which the subsurface deposits (the product') were modified by the surface morphodynamics (the process') was quantified using the changes in radar-facies recorded in sequential ground-penetrating radar surveys. These surveys reveal that during the large flood there was an increase in the proportion of facies associated with bar margin accretion and larger dunes. In subsequent years, these facies became truncated and replaced with facies associated with smaller dune sets. This analysis shows that unit bars generally become truncated more laterally than vertically and, thus, they lose the high-angle bar margin deposits and smaller scale bar-top deposits. In general, the only fragments that remain of the unit bars are dune sets, thus making identification of the original unit barform problematic. This novel data set has implications for what may ultimately become preserved in the rock record.

Scales and causes of heterogeneity in bars in a large multi-channel river: Rio Parana, Argentina

To date, published studies of alluvial bar architecture in large rivers have been restricted mostly to case studies of individual bars and single locations. Relatively little is known about how the depositional processes and sedimentary architecture of kilometre-scale bars vary within a multi-kilometre reach or over several hundreds of kilometres downstream. This study presents Ground Penetrating Radar and core data from 11, kilometre-scale bars from the Rio Parana, Argentina. The investigated bars are located between 30km upstream and 540km downstream of the Rio Parana - Rio Paraguay confluence, where a significant volume of fine-grained suspended sediment is introduced into the network. Bar-scale cross-stratified sets, with lengths and widths up to 600m and thicknesses up to 12m, enable the distinction of large river deposits from stacked deposits of smaller rivers, but are only present in half the surface area of the bars. Up to 90% of bar-scale sets are found on top of finer-grained ripple-laminated bar-trough deposits. Bar-scale sets make up as much as 58% of the volume of the deposits in small, incipient mid-channel bars, but this proportion decreases significantly with increasing age and size of the bars. Contrary to what might be expected, a significant proportion of the sedimentary structures found in the Rio Parana is similar in scale to those found in much smaller rivers. In other words, large river deposits are not always characterized by big structures that allow a simple interpretation of river scale. However, the large scale of the depositional units in big rivers causes small-scale structures, such as ripple sets, to be grouped into thicker cosets, which indicate river scale even when no obvious large-scale sets are present. The results also show that the composition of bars differs between the studied reaches upstream and downstream of the confluence with the Rio Paraguay. Relative to other controls on downstream fining, the tributary input of fine-grained suspended material from the Rio Paraguay causes a marked change in the composition of the bar deposits. Compared to the upstream reaches, the sedimentary architecture of the downstream reaches in the top ca 5m of mid-channel bars shows: (i) an increase in the abundance and thickness (up to metre-scale) of laterally extensive (hundreds of metres) fine-grained layers; (ii) an increase in the percentage of deposits comprised of ripple sets (to >40% in the upper bar deposits); and (iii) an increase in bar-trough deposits and a corresponding decrease in bar-scale cross-strata (<10%). The thalweg deposits of the Rio Parana are composed of dune sets, even directly downstream from the Rio Paraguay where the upper channel deposits are dominantly fine-grained. Thus, the change in sedimentary facies due to a tributary point-source of fine-grained sediment is primarily expressed in the composition of the upper bar deposits.

Deposits of the sandy braided South Saskatchewan River: Implications for the use of modern analogs in reconstructing channel dimensions in reservoir characterization

Estimation of the dimensions of fluvial geobodies from core data is a notoriously difficult problem in reservoir modeling. To try and improve such estimates and, hence, reduce uncertainty in geomodels, data on dunes, unit bars, cross-bar channels, and compound bars and their associated deposits are presented herein from the sand-bed braided South Saskatchewan River, Canada. These data are used to test models that relate the scale of the formative bed forms to the dimensions of the preserved deposits and, therefore, provide an insight as to how such deposits may be preserved over geologic time. The preservation of bed-form geometry is quantified by comparing the Alluvial architecture above and below the maximum erosion depth of the modem channel deposits. This comparison shows that there is no significant difference in the mean set thickness of dune cross-strata above and below the basal erosion surface of the contemporary channel, thus suggesting that dimensional relationships between dune deposits and the formative bed-form dimensions are likely to be valid from both recent and older deposits. The data show that estimates of mean bankfull flow depth derived from dune, unit bar, and cross-bar channel deposits are all very similar. Thus, the use of all these metrics together can provide a useful check that all components and scales of the alluvial architecture have been identified correctly when building reservoir models. The data also highlight several practical issues with identifying and applying data relating to cross-strata. For example, the deposits of unit bars were found to be severely truncated in length and width, with only approximately 10% of the mean bar-form length remaining, and thus making identification in section difficult. For similar reasons, the deposits of compound bars were found to be especially difficult to recognize, and hence, estimates of channel depth based on this method may be problematic. Where only core data are available (i.e., no outcrop data exist), formative flow depths are suggested to be best reconstructed using cross-strata formed by dunes. However, theoretical relationships between the distribution of set thicknesses and formative dune height are found to result in slight overestimates of the latter and, hence, mean bankfull flow depths derived from these measurements. This article illustrates that the preservation of fluvial cross-strata and, thus, the paleohydraulic inferences that can be drawn from them, are a function of the ratio of the size and migration rate of bed forms and the time scale of aggradation and channel migration. These factors must thus be considered when deciding on appropriate length:thickness ratios for the purposes of object-based modeling in reservoir characterization.

Variación de peso y aporte energético del pasto en vacas de cría en condiciones de montaña: efecto de la época de parto

Se analizaron las variaciones de peso durante la estación de pastoreo de vacas multíparas de raza Parda Alpina con partos en otoño (n = 152) o primavera (n = 123) durante el período 1989-1996. Los animales pasta- ron en áreas boscosas (900-1.500 m, 0,2 vacas/ha) y en pastos supraforestales (1.500-2.200 m, 1,2 vacas/ha). Las vacas con parto en otoño presentaron mayores recuperaciones de peso en pastoreo que las de primavera (0,661 vs 0,071 kg/día, P < 0,001), diferencia observada tanto en los pastos forestales como en los supraforestales. Las variaciones de peso en pastoreo se relacionaron negativamente con las observadas en estabulación (r = –0,20, P < 0,05) y también con el peso a la salida al pasto (r = –0,32, P < 0,05). La contribución energética del pasto a los aportes recibidos anualmente de la dieta fue similar en ambas parideras (43,6 p. 100 y 42,2 p. 100 en otoño y primavera, respectivamente, NS), aunque la pauta de reparto de la energía hacia las funciones fisiológicas en los distintos períodos de manejo fue diferente.

Cereus peruvianus (Koubo) new cactus fruit for the world

Several different species of the columnar cacti of the genera Stenocereus and Pachycereus, were introduced into different semi-arid ecozones in Israel and most of these efforts were of disappointing outcomes, the only exception being the Cereus peruvianus (L.) Miller,which bore plenty of fruits, some of them of good taste. The original seeds of this plant were obtained from the late Mr. Amram (Ron) Kodish, who collected seeds from various private gardens in Southern California which bore fruits of reasonable qualities. The initial success of this species led us to initiate an intensive research study, and today it is already fruit-crop, marketed mainly in Israel under the name " Koubo" . This paper will describe our work of domestication of this new cactus fruit crop in Israel.

Género y cultura popular

En uno de los capítulos de Los Simpson, la pequeña Lisa compra, emocionada, la última versión de Stacy Malibú (el equivalente a nuestra Barbie). La novedad consiste en que después de 50 años de existencia, la muñeca habla. Pero para consternación de Lisa, el repertorio de frases es de lo más indignante: "Me encantaría que en la escuela enseñaran a ir de compras", "¡Vamos a hornear unas galletas para los chicos!" o "No me preguntes: sólo soy una chica (risita vacua)". Obviamente, la comprometida y concienciada Lisa no puede quedarse de brazos cruzados y pide a su madre que la lleve a la fábrica de Stacy Malibú para presentar sus quejas. La conversación entre ambas es enormemente reveladora: aunque Marge apoya a su hija e insiste en que siempre defienda sus ideas, considera que quizás está yendo más allá de lo razonable en su denuncia de que toda una generación de niñas se comportará como Stacy Malibú y la tomará como modelo y, finalmente, concluye en tono conciliador: "Yo tuve una Stacy Malibú de pequeña y no me ha pasado nada.¡Vamos a olvidarnos de estos problemas con un gran bol de helado de fresa!". La respuesta de Lisa no deja lugar a dudas; poniendo en funcionamiento a la muñeca y situándola frente a su madre, oímos a Stacy diciendo: "¡Vamos a olvidarnos de estos problemas con un gran bol de helado de fresa!". Huelgan los comentarios.

Género y cultura popular

En uno de los capítulos de Los Simpson, la pequeña Lisa compra, emocionada, la última versión de Stacy Malibú (el equivalente a nuestra Barbie). La novedad consiste en que después de 50 años de existencia, la muñeca habla. Pero para consternación de Lisa, el repertorio de frases es de lo más indignante: "Me encantaría que en la escuela enseñaran a ir de compras", "¡Vamos a hornear unas galletas para los chicos!" o "No me preguntes: sólo soy una chica (risita vacua)". Obviamente, la comprometida y concienciada Lisa no puede quedarse de brazos cruzados y pide a su madre que la lleve a la fábrica de Stacy Malibú para presentar sus quejas. La conversación entre ambas es enormemente reveladora: aunque Marge apoya a su hija e insiste en que siempre defienda sus ideas, considera que quizás está yendo más allá de lo razonable en su denuncia de que toda una generación de niñas se comportará como Stacy Malibú y la tomará como modelo y, finalmente, concluye en tono conciliador: "Yo tuve una Stacy Malibú de pequeña y no me ha pasado nada.¡Vamos a olvidarnos de estos problemas con un gran bol de helado de fresa!". La respuesta de Lisa no deja lugar a dudas; poniendo en funcionamiento a la muñeca y situándola frente a su madre, oímos a Stacy diciendo: "¡Vamos a olvidarnos de estos problemas con un gran bol de helado de fresa!". Huelgan los comentarios.

Development and evaluation of double locus sequence typing for molecular epidemiological investigations of Clostridium difficile.

Despite the development of novel typing methods based on whole genome sequencing, most laboratories still rely on classical molecular methods for outbreak investigation or surveillance. Reference methods for Clostridium difficile include ribotyping and pulsed-field gel electrophoresis, which are band-comparing methods often difficult to establish and which require reference strain collections. Here, we present the double locus sequence typing (DLST) scheme as a tool to analyse C. difficile isolates. Using a collection of clinical C. difficile isolates recovered during a 1-year period, we evaluated the performance of DLST and compared the results to multilocus sequence typing (MLST), a sequence-based method that has been used to study the structure of bacterial populations and highlight major clones. DLST had a higher discriminatory power compared to MLST (Simpson's index of diversity of 0.979 versus 0.965) and successfully identified all isolates of the study (100 % typeability). Previous studies showed that the discriminatory power of ribotyping was comparable to that of MLST; thus, DLST might be more discriminatory than ribotyping. DLST is easy to establish and provides several advantages, including absence of DNA extraction [polymerase chain reaction (PCR) is performed on colonies], no specific instrumentation, low cost and unambiguous definition of types. Moreover, the implementation of a DLST typing scheme on an Internet database, such as that previously done for Staphylococcus aureus and Pseudomonas aeruginosa ( http://www.dlst.org ), will allow users to easily obtain the DLST type by submitting directly sequencing files and will avoid problems associated with multiple databases.