A second generation radiation hybrid map to aid the assembly of the bovine genome sequence

BACKGROUND: Several approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from technical deficiencies or lack of statistical support to distinguish between alternative orders of loci. The accuracy of the genome maps could be improved, in principle, if information from different sources was combined to produce integrated maps. The publicly available bovine genomic sequence assembly with 6x coverage (Btau_2.0) is based on whole genome shotgun sequence data and limited mapping data however, it is recognised that this assembly is a draft that contains errors. Correcting the sequence assembly requires extensive additional mapping information to improve the reliability of the ordering of sequence scaffolds on chromosomes. The radiation hybrid (RH) map described here has been contributed to the international sequencing project to aid this process. RESULTS: An RH map for the 30 bovine chromosomes is presented. The map was built using the Roslin 3000-rad RH panel (BovGen RH map) and contains 3966 markers including 2473 new loci in addition to 262 amplified fragment-length polymorphisms (AFLP) and 1231 markers previously published with the first generation RH map. Sequences of the mapped loci were aligned with published bovine genome maps to identify inconsistencies. In addition to differences in the order of loci, several cases were observed where the chromosomal assignment of loci differed between maps. All the chromosome maps were aligned with the current 6x bovine assembly (Btau_2.0) and 2898 loci were unambiguously located in the bovine sequence. The order of loci on the RH map for BTA 5, 7, 16, 22, 25 and 29 differed substantially from the assembled bovine sequence. From the 2898 loci unambiguously identified in the bovine sequence assembly, 131 mapped to different chromosomes in the BovGen RH map. CONCLUSION: Alignment of the BovGen RH map with other published RH and genetic maps showed higher consistency in marker order and chromosome assignment than with the current 6x sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.

Academic cooperation to foster research and advocacy competences in the occupied Palestinian territory (West Bank)

Palestinians living in the West Bank, a territory occupied by the State of Israel according to International Law, face deprived access to land and a limited ability to move freely which pertains to the presence of Israeli settlements and other infrastructure (closures, restricted or forbidden roads, etc.). This confinement has significant impacts on their economic and social livelihoods, and it is even worsening with the on-going construction of a 709 km long Barrier which mainly runs inside the West Bank. With regard to this situation, there is a clear need to strengthen the capacity of civil society and its representatives to apply sound research processes as a basis for improved advocacy for Palestinian human rights. Monitoring processes and tools are needed to assess the impacts of the Palestinians’ confinement, particularly in relation to the Barrier’s construction. Reliable data has also to be collected, managed, and above all, shared. These challenges have been addressed within the Academic Cooperation Palestine Project (ACPP) that brings together academic partners from the occupied Palestinian territory (oPt) West Bank (WB), and Switzerland as well as other international academic institutions and Palestinian governmental and non-governmental agencies. ACPP started in early 2011 and is designed as a large cooperation networking platform involving researchers, students, public servants and experts from the oPt WB. A large set of actions have already been developed during the first year of the project, including courses, training, and research actions. First relevant results and impacts of the different actions are presented in this paper. Taken as a whole, the project produces valuable results for all partners: useful advocacy material for the Palestinian partners, and a unique “real-scale laboratory” where investigations are jointly conducted to develop novel confinement and change indicators.

Eocene to Early Miocene palaeoclimate of Saxony, Germany (Table 4)

In the present study, proxy data concerning changes in atmospheric CO2 and climatic conditions from the Late Eocene to the Early Miocene were acquired by applying palaeobotanical methods. Fossil floras from 10 well-documented locations in Saxony, Germany, were investigated with respect to (1) stomatal density/index of fossil leaves from three different taxa (Eotrigonobalanus furcinervis, Laurophyllum pseudoprinceps and Laurophyllum acutimontanum), (2) the coexistence approach (CA) based on nearest living relatives (NLR) and (3) leaf margin analysis (LMA). Whereas the results of approach (1) indicate changes in atmospheric CO2 concentration, approaches (2) and (3) provide climate data. The results of the analysis of stomatal parameters indicate that the atmospheric CO2 concentration was higher during the Late Eocene than during the Early Oligocene and increased towards the Late Oligocene. A lower atmospheric pCO2 level after the Late Eocene is also suggested by an increase in marine palaeoproductivity at this time. From the Late Oligocene onwards, no changes in atmospheric CO2 concentration can be detected with the present data. For the considered sites, the results of the coexistence approach and of the leaf margin analysis document a significant cooling event from the Late Eocene to the Early Oligocene. The pCO2 decrease from the Late Eocene to the Early Oligocene indicated by the stomatal data raised in this study was thus coupled to a temperature decrease which is reflected by the present datasets. From the Early Oligocene onwards, however, no further fundamental climate change can be inferred for the considered locations. The pCO2 increase from the Early Oligocene to the Late Oligocene, which is indicated by the present data, is thus not accompanied by a climate change at the considered sites. A warming event during the Late Oligocene is, however, recorded by marine climate archives. According to the present data, no change in pCO2 occurred during the cooling event at the Oligocene/Miocene boundary, which is also indicated by marine data. The quality and validity of stomatal parameters as sensors for atmospheric CO2 concentration are discussed.

La inserción social del indígena en las urbes y campañas del territorio bonaerense y su relación con la justicia criminal hispanocriolla durante el período independiente temprano (1810-1835)

La sociedad bonaerense del período independiente temprano, no sólo se caracterizó por estar fuertementejerarquizada desde el punto de vista socioeconómico, sinoademás por ser legalmente desigual y altamente punitiva. Los hechos asentados en los expedientes judiciales correspondientes a causas criminales y correccionales presentadas ante el Juzgado del Crimen, muestran claramente -entre otros aspectos- las características de la justicia criminal hispanocriolla: cómo operaba y se administraba la ley vigente, frente a la cual, los sectores bajos de la pirámide social y en particular, los individuos de casta (indios, negros, morenos, etc.), resultaban ser los más desprotegidos y vulnerables. Por lo tanto, en el presente proyecto, nos interesa abordar la inserción social del indígena en las urbes y campañas, y su integración en el mercado laboral de la época, y a partir de este marco y desde esa sociedad que lo incluía, se pretende indagar alindígena frente al delito y dentro de la dinámica del campo judicial, articulando las dimensiones social, económica y jurídica. De esta manera, combinando las fuentes judiciales de 1810 a 1835 con otros documentos del período, se intenta dar cuenta no sólo de los aspectos sociales y económicos de la vida personal y cotidiana del indígena sino además de las particularidades del proceso de juzgamiento y penalización de sus acciones durante el incipiente período independentista.

Le Goff : Balance crítico de un legado

Los primeros trabajos de Jacques Le Goff, sobre mercaderes, banqueros e intelectuales de la Edad Media, presentan cualidades que anuncian su desarrollo posterior: débil teoría económica y mayor desarrollo sobre historia de las ideas. A partir de 1964, con la publicación de La civilización del occidente medieval, se produce un cambio. Ese cambio se inscribe en una nueva orientación general de la escuela de Annales: el estudio de las mentalidades. Le Goff pretende realizar un análisis de la mentalidad del hombre medieval. Su estudio se basa principalmente en textos eruditos eclesiásticos. Se demuestra en este artículo que ese tipo de fuentes permiten acceder a la mentalidad de la parte sacerdotal de la clase de poder. De manera secundaria, Le Goff estudió fuentes literarias que permiten acercarse a la mentalidad de los caballeros. Para el análisis de los campesinos y de distintos sectores subalternos se necesitarían otro tipo de fuentes que nunca fueron utilizadas por Le Goff. Este análisis mantiene algunas semejanzas con el materialismo histórico, pero también tiene profundas diferencias con la doctrina de Marx. En base a esto se determina el alcance del legado de Le Goff

Le Goff : Balance crítico de un legado

Los primeros trabajos de Jacques Le Goff, sobre mercaderes, banqueros e intelectuales de la Edad Media, presentan cualidades que anuncian su desarrollo posterior: débil teoría económica y mayor desarrollo sobre historia de las ideas. A partir de 1964, con la publicación de La civilización del occidente medieval, se produce un cambio. Ese cambio se inscribe en una nueva orientación general de la escuela de Annales: el estudio de las mentalidades. Le Goff pretende realizar un análisis de la mentalidad del hombre medieval. Su estudio se basa principalmente en textos eruditos eclesiásticos. Se demuestra en este artículo que ese tipo de fuentes permiten acceder a la mentalidad de la parte sacerdotal de la clase de poder. De manera secundaria, Le Goff estudió fuentes literarias que permiten acercarse a la mentalidad de los caballeros. Para el análisis de los campesinos y de distintos sectores subalternos se necesitarían otro tipo de fuentes que nunca fueron utilizadas por Le Goff. Este análisis mantiene algunas semejanzas con el materialismo histórico, pero también tiene profundas diferencias con la doctrina de Marx. En base a esto se determina el alcance del legado de Le Goff

La inserción social del indígena en las urbes y campañas del territorio bonaerense y su relación con la justicia criminal hispanocriolla durante el período independiente temprano (1810-1835)

La sociedad bonaerense del período independiente temprano, no sólo se caracterizó por estar fuertementejerarquizada desde el punto de vista socioeconómico, sinoademás por ser legalmente desigual y altamente punitiva. Los hechos asentados en los expedientes judiciales correspondientes a causas criminales y correccionales presentadas ante el Juzgado del Crimen, muestran claramente -entre otros aspectos- las características de la justicia criminal hispanocriolla: cómo operaba y se administraba la ley vigente, frente a la cual, los sectores bajos de la pirámide social y en particular, los individuos de casta (indios, negros, morenos, etc.), resultaban ser los más desprotegidos y vulnerables. Por lo tanto, en el presente proyecto, nos interesa abordar la inserción social del indígena en las urbes y campañas, y su integración en el mercado laboral de la época, y a partir de este marco y desde esa sociedad que lo incluía, se pretende indagar alindígena frente al delito y dentro de la dinámica del campo judicial, articulando las dimensiones social, económica y jurídica. De esta manera, combinando las fuentes judiciales de 1810 a 1835 con otros documentos del período, se intenta dar cuenta no sólo de los aspectos sociales y económicos de la vida personal y cotidiana del indígena sino además de las particularidades del proceso de juzgamiento y penalización de sus acciones durante el incipiente período independentista.

La inserción social del indígena en las urbes y campañas del territorio bonaerense y su relación con la justicia criminal hispanocriolla durante el período independiente temprano (1810-1835)

La sociedad bonaerense del período independiente temprano, no sólo se caracterizó por estar fuertementejerarquizada desde el punto de vista socioeconómico, sinoademás por ser legalmente desigual y altamente punitiva. Los hechos asentados en los expedientes judiciales correspondientes a causas criminales y correccionales presentadas ante el Juzgado del Crimen, muestran claramente -entre otros aspectos- las características de la justicia criminal hispanocriolla: cómo operaba y se administraba la ley vigente, frente a la cual, los sectores bajos de la pirámide social y en particular, los individuos de casta (indios, negros, morenos, etc.), resultaban ser los más desprotegidos y vulnerables. Por lo tanto, en el presente proyecto, nos interesa abordar la inserción social del indígena en las urbes y campañas, y su integración en el mercado laboral de la época, y a partir de este marco y desde esa sociedad que lo incluía, se pretende indagar alindígena frente al delito y dentro de la dinámica del campo judicial, articulando las dimensiones social, económica y jurídica. De esta manera, combinando las fuentes judiciales de 1810 a 1835 con otros documentos del período, se intenta dar cuenta no sólo de los aspectos sociales y económicos de la vida personal y cotidiana del indígena sino además de las particularidades del proceso de juzgamiento y penalización de sus acciones durante el incipiente período independentista.

Le Goff : Balance crítico de un legado

Los primeros trabajos de Jacques Le Goff, sobre mercaderes, banqueros e intelectuales de la Edad Media, presentan cualidades que anuncian su desarrollo posterior: débil teoría económica y mayor desarrollo sobre historia de las ideas. A partir de 1964, con la publicación de La civilización del occidente medieval, se produce un cambio. Ese cambio se inscribe en una nueva orientación general de la escuela de Annales: el estudio de las mentalidades. Le Goff pretende realizar un análisis de la mentalidad del hombre medieval. Su estudio se basa principalmente en textos eruditos eclesiásticos. Se demuestra en este artículo que ese tipo de fuentes permiten acceder a la mentalidad de la parte sacerdotal de la clase de poder. De manera secundaria, Le Goff estudió fuentes literarias que permiten acercarse a la mentalidad de los caballeros. Para el análisis de los campesinos y de distintos sectores subalternos se necesitarían otro tipo de fuentes que nunca fueron utilizadas por Le Goff. Este análisis mantiene algunas semejanzas con el materialismo histórico, pero también tiene profundas diferencias con la doctrina de Marx. En base a esto se determina el alcance del legado de Le Goff

Eocene to Quaternary benthic foraminifers from the Izu-Bonin Arc

The benthic foraminifer fauna at Sumisu Rift Sites 790 and 791 indicates that a deep open-ocean (>2300 m) or a basin with open-ocean access existed between 1.1 and 0.7 Ma at the time of the initiation of rifting. The appearance of a low- to medium-oxygen fauna (1600-2300 m) between 0.7 and 0.5 Ma suggests that the open-ocean access may have been terminated at this time because of the development of volcanoes and rift flank uplifts around the basin. The occurrence of low-oxygen faunas at 0.03 Ma suggests a secondary closing of the basin. The lower bathyal benthic faunas from lower Pliocene sediments of rift margin Site 788 suggest about 0.6-1.6 km of total basement uplift. This uplift may have led to the formation of the major hiatus between 2.3 and <0.3 Ma. The faunal changes of benthic foraminifers at Sites 792 and 793 in the forearc basin document a shallowing water depth from below the carbonate compensation depth (CCD) (about 3.5 km) in the late early Oligocene to the present depths of 1800 and 2975 m, respectively. These data suggest about 1 km of total basement uplift in the inner part of the forearc basin (Site 792) and about 0.6 km total basement subsidence in the central part of the forearc basin (Site 793) since about 31 Ma. The former uplift led to a thinner sediment accumulation (800 m) and the latter subsidence to a thicker sediment accumulation (1400 m) at these sites. Faunal changes of benthic foraminifers observed in Sites 782 and 786 sequences drilled at the outer-arc high document a deepening water depth from 1.3 to 2.1 km in late Eocene to the present depth of about 3 km. These data suggest about 1.1-1.9 and 1.3-2.1 km of total basement subsidence at Sites 786 and 782, respectively. These results indicate total basement uplift in the inner part of the Bonin arc-trench system since late Oligocene and total basement subsidence in the outer part of the system since late Eocene. The last occurrence (LO) of Stilostomella spp. and Pleurostomella spp. and the first occurrence (F0) of Bulimina aculeata d'Orbigny occurred consistently at 0.7 Ma at all three arc proximal sites (790,791, and 792). This fact is taken to suggest a change of water mass, from one originating from the central part of the ocean to that originating from ocean-margin areas at that time.

Late Miocene to Early Pliocene radiolarians from ODP Hole 178-1095B

Early Pliocene to middle late Miocene hemipelagic and distal turbidite sediments from Hole 1095B, near the Antarctic Peninsula, yield moderately abundant, moderately well preserved radiolarian faunas and other biosiliceous material (diatoms, silicoflagellates, and sponge spicules). Preservation characteristics, however, vary strongly even between closely related samples, and there are many intervals of poor preservation. In the 140- to 460-meters below seafloor interval studied, it was possible to identify the following standard Southern Ocean radiolarian zones: Upsilon, Tau, Amphymenium challengerae, Acrosphaera? labrata, Siphonosphaera vesuvius, and upper Acrosphaera australis (total age range ~4-10 Ma). Some normally common radiolarian groups, such as actinommids, are unusually rare in the studied material, and the relative ranges of several individual species, such as Acrosphaera labrata vs. A. australis, appear to be somewhat anomalous. These observations imply that the ranges of taxa in this section may be somewhat diachronous, due to either local ecologic factors and/or the highly variable preservation of the faunas. Thus, the ages of events reported are probably only approximate, although they are still useful for constraining the age of sediments in this section.

Paleogene and early Neogene stable isotope record of foraminifera from ODP Leg 119 samples

Oxygen and carbon isotopic records of monogeneric and monospecific benthic and planktonic foraminifer samples from Sites 744 and 738 drilled on the southern end of the Kerguelen Plateau during ODP Leg 119 reveal the evolution of polar Indian Ocean water masses from the early Paleocene to the middle Miocene. Results from Site 738 are from sediments of early Paleocene to late Eocene age and those from Site 744 are late Eocene to middle Miocene. They suggest that intermediate waters at this location did not originate in the high latitudes during the early Eocene. Surface and near-surface waters cooled gradually after the maximum warming at 56 Ma, when surface waters were about 18°C. Intermediate waters cooled after 52 Ma. The highest temperatures (lowest d18O values) of the Cenozoic occurred from 56 to 52 Ma. The records of equatorial Pacific Site 577 and Weddell Sea Site 690 resemble that of the polar Indian Ocean in this interval. The well-documented d13C excursions toward positive values in the late Paleocene and negative values in the early Eocene are represented by foraminifers increases of 1.5 per mil and following decreases of about 3 per mil. Most of the cooling in the Paleogene occurred in the middle and late Eocene. A 2°C decrease of surface water at about 38.4 Ma heralded the beginning of extensive glacial conditions in Antarctica in the early Oligocene. At Site 744, the global d18O shift just above the Eocene/Oligocene boundary is 1.15 per mil, and occurred gradually in sediments dated at 36.5-35.9 Ma. Ice-rafted debris was deposited beginning at 36.1 Ma for about the next 2 m.y. This simultaneous occurrence of the global d18O shift with ice-rafted debris is evidence for early Oligocene glaciation in East Antarctica. Moreover, early and late Oligocene Cibicidoides d18O values between 2 and 2.2 per mil indicate intermediate water cooling and a small ice-volume effect. Production of cold dense bottom water in Antarctica was intensified with continental cooling and glaciation in the early Oligocene. Comparison of Oligocene and early Miocene isotopic data from high-latitude and low-latitude deepsea sites indicates that there were probably at least two sources of bottom waters at this time.

A nucleolar protein related to ribosomal protein L7 is required for an early step in large ribosomal subunit biogenesis

The Saccharomyces cerevisiae Rlp7 protein has extensive identity and similarity to the large ribosomal subunit L7 proteins and shares an RNA-binding domain with them. Rlp7p is not a ribosomal protein; however, it is encoded by an essential gene and therefore must perform a function essential for cell growth. In this report, we show that Rlp7p is a nucleolar protein that plays a critical role in processing of precursors to the large ribosomal subunit RNAs. Pulse–chase labeling experiments with Rlp7p-depleted cells reveal that neither 5.8SS, 5.8SL, nor 25S is produced, indicating that both the major and minor processing pathways are affected. Analysis of processing intermediates by primer extension indicates that Rlp7p-depleted cells accumulate the 27SA3 precursor RNA, which is normally the major substrate (85%) used to produce the 5.8S and 25S rRNAs, and the ratio of 27SBL to 27SBS precursors changes from approximately 1:8 to 8:1 (depleted cells). Because 27SA3 is the direct precursor to 27SBS, we conclude that Rlp7p is specifically required for the 5′ to 3′ exonucleolytic trimming of the 27SA3 into the 27SBS precursor. As it is essential for processing in both the major and minor pathways, we propose that Rlp7p may act as a specificity factor that binds precursor rRNAs and tethers the enzymes that carry out the early 5′ to 3′ exonucleolytic reactions that generate the mature rRNAs. Rlp7p may also be required for the endonucleolytic cleavage in internal transcribed spacer 2 that separates the 5.8S rRNA from the 25S rRNA.

Differential Control of Xanthophylls and Light-Induced Stress Proteins, as Opposed to Light-Harvesting Chlorophyll a/b Proteins, during Photosynthetic Acclimation of Barley Leaves to Light Irradiance

Barley (Hordeum vulgare L.) plants were grown at different photon flux densities ranging from 100 to 1800 μmol m−2 s−1 in air and/or in atmospheres with reduced levels of O2 and CO2. Low O2 and CO2 partial pressures allowed plants to grow under high photosystem II (PSII) excitation pressure, estimated in vivo by chlorophyll fluorescence measurements, at moderate photon flux densities. The xanthophyll-cycle pigments, the early light-inducible proteins, and their mRNA accumulated with increasing PSII excitation pressure irrespective of the way high excitation pressure was obtained (high-light irradiance or decreased CO2 and O2 availability). These findings indicate that the reduction state of electron transport chain components could be involved in light sensing for the regulation of nuclear-encoded chloroplast gene expression. In contrast, no correlation was found between the reduction state of PSII and various indicators of the PSII light-harvesting system, such as the chlorophyll a-to-b ratio, the abundance of the major pigment-protein complex of PSII (LHCII), the mRNA level of LHCII, the light-saturation curve of O2 evolution, and the induced chlorophyll-fluorescence rise. We conclude that the chlorophyll antenna size of PSII is not governed by the redox state of PSII in higher plants and, consequently, regulation of early light-inducible protein synthesis is different from that of LHCII.

The XMM deep survey in the CDF-S. VI. Obscured AGN selected as infrared power-law galaxies

Context. Accretion onto supermassive black holes is believed to occur mostly in obscured active galactic nuclei (AGN). Such objects are proving rather elusive in surveys of distant galaxies, including those at X-ray energies. Aims. Our main goal is to determine whether the revised IRAC criteria of Donley et al. (2012, ApJ, 748, 142; objects with an infrared (IR) power-law spectral shape), are effective at selecting X-ray type-2 AGN (i.e., absorbed N_H > 10^22 cm^-2). Methods. We present the results from the X-ray spectral analysis of 147 AGN selected by cross-correlating the highest spectral quality ultra-deep XMM-Newton and the Spitzer/IRAC catalogues in the Chandra Deep Field South. Consequently it is biased towards sources with high S/N X-ray spectra. In order to measure the amount of intrinsic absorption in these sources, we adopt a simple X-ray spectral model that includes a power-law modified by intrinsic absorption at the redshift of each source and a possible soft X-ray component. Results. We find 21/147 sources to be heavily absorbed but the uncertainties in their obscuring column densities do not allow us to confirm their Compton-Thick nature without resorting to additional criteria. Although IR power-law galaxies are less numerous in our sample than IR non-power-law galaxies (60 versus 87 respectively), we find that the fraction of absorbed (N_H^intr > 10^22 cm^-2) AGN is significantly higher (at about 3 sigma level) for IR-power-law sources (similar to 2/3) than for those sources that do not meet this IR selection criteria (~1/2). This behaviour is particularly notable at low luminosities, but it appears to be present, although with a marginal significance, at all luminosities. Conclusions. We therefore conclude that the IR power-law method is efficient in finding X-ray-absorbed sources. We would then expect that the long-sought dominant population of absorbed AGN is abundant among IR power-law spectral shape sources not detected in X-rays.