Structural variety of arginine-rich RNA-binding peptides.

Arginine-rich domains are used by a variety of RNA-binding proteins to recognize specific RNA hairpins. It has been shown previously that a 17-aa arginine-rich peptide from the human immunodeficiency virus Rev protein binds specifically to its RNA site when the peptide is in an alpha-helical conformation. Here we show that related peptides from splicing factors, viral coat proteins, and bacteriophage antiterminators (the N proteins) also have propensities to form alpha-helices and that the N peptides require helical conformations to bind to their cognate RNAs. In contrast, introducing proline mutations into the arginine-rich domain of the human immunodeficiency virus Tat protein abolishes its potential to form an alpha-helix but does not affect RNA-binding affinity in vitro or in vivo. Based on results from several peptide-RNA model systems, we suggest that helical peptides may be used to recognize RNA structures having particularly wide major grooves, such as those found near loops or large bulges, and that nonhelical or extended peptides may be used to recognize less accessible grooves.

Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere.

In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

Proline-rich sequences that bind to Src homology 3 domains with individual specificities.

To study the binding specificity of Src homology 3 (SH3) domains, we have screened a mouse embryonic expression library for peptide fragments that interact with them. Several clones were identified that express fragments of proteins which, through proline-rich binding sites, exhibit differential binding specificity to various SH3 domains. Src-SH3-specific binding uses a sequence of 7 aa of the consensus RPLPXXP, in which the N-terminal arginine is very important. The SH3 domains of the Src-related kinases Fyn, Lyn, and Hck bind to this sequence with the same affinity as that of the Src SH3. In contrast, a quite different proline-rich sequence from the Btk protein kinase binds to the Fyn, Lyn, and Hck SH3 domains, but not to the Src SH3. Specific binding of the Abl SH3 requires a longer, more proline-rich sequence but no arginine. One clone that binds to both Src and Abl SH3 domains through a common site exhibits reversed binding orientation, in that an arginine indispensable for binding to all tested SH3 domains occurs at the C terminus. Another clone contains overlapping yet distinct Src and Abl SH3 binding sites. Binding to the SH3 domains is mediated by a common PXXP amino acid sequence motif present on all ligands, and specificity comes about from other interactions, often ones involving arginine. The rules governing in vivo usage of particular sites by particular SH3 domains are not clear, but one binding orientation may be more specific than another.

The Mice at play in the CALIFA survey. A case study of a gas-rich major merger between first passage and coalescence

We present optical integral field spectroscopy (IFS) observations of the Mice, a major merger between two massive (≳10^11 M_⊙) gas-rich spirals NGC 4676A and B, observed between first passage and final coalescence. The spectra provide stellar and gas kinematics, ionised gas properties, and stellar population diagnostics, over the full optical extent of both galaxies with ~1.6 kpc spatial resolution. The Mice galaxies provide a perfect case study that highlights the importance of IFS data for improving our understanding of local galaxies. The impact of first passage on the kinematics of the stars and gas has been significant, with strong bars most likely induced in both galaxies. The barred spiral NGC 4676B exhibits a strong twist in both its stellar and ionised gas disk. The edge-on disk galaxy NGC 4676A appears to be bulge free, with a strong bar causing its “boxy” light profile. On the other hand, the impact of the merger on the stellar populations has been minimal thus far. By combining the IFS data with archival multiwavelength observations we show that star formation induced by the recent close passage has not contributed significantly to the total star formation rate or stellar mass of the galaxies. Both galaxies show bicones of high ionisation gas extending along their minor axes. In NGC 4676A the high gas velocity dispersion and Seyfert-like line ratios at large scaleheight indicate a powerful outflow. Fast shocks (vs ~ 350 km s^-1) extend to ~6.6 kpc above the disk plane. The measured ram pressure (P/k = 4.8 × 10^6 K cm^-3) and mass outflow rate (~8−20 M_⊙ yr^-1) are similar to superwinds from local ultra-luminous infrared galaxies, although NGC 4676A only has a moderate infrared luminosity of 3 × 10^10 L_⊙. Energy beyond what is provided by the mechanical energy of the starburst appears to be required to drive the outflow. Finally, we compare the observations to mock kinematic and stellar population maps extracted from a hydrodynamical merger simulation. The models show little enhancement in star formation during and following first passage, in agreement with the observations. We highlight areas where IFS data could help further constrain the models.

Stratigraphic and geochemical study of the organic-rich black shales in the Tarcău Nappe of the Moldavidian Domain (Carpathian Chain, Romania)

An integrated stratigraphic analysis has been made of the Tarcău Nappe (Moldavidian Domain, Eastern Romanian Carpathians), coupled with a geochemical study of organic-rich beds. Two Main Sequence Boundaries (Early Oligocene and near to the Oligocene–Aquitanian boundary, respectively) divide the sedimentary record into three depositional sequences. The sedimentation occurred in the central area of a basin supplied by different and opposite sources. The high amount of siliciclastics at the beginning of the Miocene marks the activation of the “foredeep stage”. The successions studied are younger than previously thought and they more accurately date the deformation of the different Miocene phases affecting the Moldavidian Basin. The intervals with black shales identified are related to two main separate anoxic episodes with an age not older than Late Rupelian and not before Late Chattian. The most important organic-rich beds correspond to the Lower Menilites, Bituminous Marls and Lower Dysodilic Shales Members (Interval 2). These constitute a good potential source rock for petroleum, with homogeneous Type II oil-prone organic matter, highly lipidic and thermally immature. The deposition of black shales has been interpreted as occurring within a deep, periodically isolated and tectonically controlled basin.

Developing Semantic Rich Internet Applications with the Sm4RIA Extension for OIDE

This paper introduces the Sm4RIA Extension for OIDE, which implements the Sm4RIA approach in OIDE (OOH4RIA Integrated Development Environment). The application, based on the Eclipse framework, supports the design of the Sm4RIA models as well as the model-to-model and model-to-text transformation processes that facilitate the generation of Semantic Rich Internet Applications, i.e., RIA applications capable of sharing data as Linked data and consuming external data from other sources in the same manner. Moreover, the application implements mechanisms for the creation of RIA interfaces from ontologies and the automatic generation of administration interfaces for a previously design application.

Applying model-driven engineering to the development of Rich Internet Applications for Business Intelligence

Business Intelligence (BI) applications have been gradually ported to the Web in search of a global platform for the consumption and publication of data and services. On the Internet, apart from techniques for data/knowledge management, BI Web applications need interfaces with a high level of interoperability (similar to the traditional desktop interfaces) for the visualisation of data/knowledge. In some cases, this has been provided by Rich Internet Applications (RIA). The development of these BI RIAs is a process traditionally performed manually and, given the complexity of the final application, it is a process which might be prone to errors. The application of model-driven engineering techniques can reduce the cost of development and maintenance (in terms of time and resources) of these applications, as they demonstrated by other types of Web applications. In the light of these issues, the paper introduces the Sm4RIA-B methodology, i.e., a model-driven methodology for the development of RIA as BI Web applications. In order to overcome the limitations of RIA regarding knowledge management from the Web, this paper also presents a new RIA platform for BI, called RI@BI, which extends the functionalities of traditional RIAs by means of Semantic Web technologies and B2B techniques. Finally, we evaluate the whole approach on a case study—the development of a social network site for an enterprise project manager.

How much did China’s WTO accession increase economic growth in resource-rich countries? CEPS Working Document No. 384, 3 October 2013

This Working Document provides an estimate of China’s impact on the growth rate of resource-rich countries since its WTO accession in December 2001. The authors’ empirical approach follows the logic of the differences-in-differences estimator. In addition to temporal variation arising from the WTO accession, which they argue was exogenous to other countries’ growth trajectories, the authors exploit spatial variation arising from differences in natural resource wealth. In this way they can compare changes in economic growth in the pre- and post-accession periods between countries that benefited from the surge in demand for industrial commodities brought about by China’s WTO accession and countries that were less able to do so. They find that that roughly one-tenth of the average annual post-accession growth in resource-rich countries was due to China’s increased appetite for commodities. The authors use this finding to inform the debate about what will happen to economic growth in resource-rich countries as China rebalances and its demand for commodities weakens.

spotlight europe, August 2015: Sustainable Development Goals: Are the rich countries ready?

The Millennium Development Goals have led to tangible progress in many developing countries. Once adopted, the United Nations' new global Sustainable Development Goals will additionally require industrialized countries to implement such standards beginning in 2016. But the world's first comprehensive stocktaking shows that most industrialized nations are a long way from serving as role models for sustainable development.

Adaptation of yeasts to fructose rich environments: a role for horizontal gene transfer of a fructose transporter

Abstract of the poster presented 33rd Small Meeting on Yeast Transport and Energetics, 21-24 July 2015, Lisbon, Portugal.

Clay mineralogy of carbonate-rich sediments of ODP Leg 101 sites

The insoluble residues of samples from ODP Sites 626 and 627 can be subdivided into four groups: (1) illite, 7 A minerals, quartz and feldspar; (2) smectite and zeolite (clinoptilolite); (3) palygorskite and in places sepiolite; and (4) glauconite and pyrite. Whereas group 1 is clearly terrigenous and group 4 authigenic, group 2 is most probably authigenic, as indicated by its abundance in samples with small insoluble residues and its appearance in SEM photographs. Group 3 is authigenic in Albian peritidal dolomite and possibly terrigenous in middle Miocene slumps and debris flows. Smectite crystallinity increases with age. This increase, however, is less pronounced in the Bahamian carbonate-rich samples than in the carbonate-poor silts south of Guatemala (DSDP Leg 84, Sites 569 and 570, the only comparable investigation) as far as can be judged from such a small number of samples.

Sedimentation rates and geochemistry of three cores from eastern tropical Pacific

We have generated approx. 300 Kyr records of biogenic opal, calcite, and organic carbon (Corg) for three cores in the eastern and central equatorial Pacific Ocean and have compared the records to determine whether common periods of biogenic sedimentation have occurred throughout the region. We find that Corg has been deposited in common pulses throughout the area, while opal has a much more local pattern of variation. Calcite varies regionally, but the record is shaped by superimposed dissolution and productivity processes. The most intense Corg peak occurs at 18 ka and can have greater than 2 times the Holocene Corg content. Other major Corg peaks occur 150 ka and perhaps at 280 ka. We have compared the Corg record in one of the cores, V19-28, to a model deepwater oxygen record developed from d13C data in the nearby V19-30 to test whether the Corg record has been mostly shaped by degradation or by the rain of organic matter from the euphotic zone. We found no coherence between the two records, implying that the Corg record is primarily a measure of productivity. By comparing the opal, calcite, and Corg records in V19-28, a core which is at or above the lysocline, we found that both increased calcite and opal deposition matches high Corg accumulation. We also found, however, that the calcite and opal records were uncorrelated, so that episodes of high opal deposition do not necessarily accumulate calcite rapidly. We hypothesize that at least two different plankton communities have been dominant in the waters above this site, one rich in opal-secreting plankton and one more dominated by calcite producers. The opal-rich plankton community was dominant during the intervals 10-15 ka and 35-60 ka.

Organic geochemistry of ODP Hole 162-985A sediments

Dark, organic-rich sediments were recovered from the lower Miocene section (~16.6 Ma) in Hole 985A in the Norway Basin during Ocean Drilling Program Leg 162. Organic carbon and total sulfur contents of the dark sediments showed a maximum concentration of 5.6 and 26.1 wt%, respectively. Sulfur enrichment in the sediments indicates that these dark layers were formed under anoxic conditions in bottom water. Four dark and eight greenish gray sediment samples, ranging in age from early Miocene to Pleistocene, were analyzed for lipid-class compounds (aliphatic hydrocarbons, fatty alcohols, and sterols) using gas chromatography (GC) and GC/mass spectrometry to better understand the formation processes of the organic-rich dark layers and to reconstruct the paleoenvironmental changes. The molecular distributions of n-alkanes and fatty alcohols indicate that terrigenous organic matter largely contributed to both types of sediments. Significant amounts of hopanoid hydrocarbons, such as diploptene and hop-17(21)-ene, however, were detected characteristically in the dark sediments, which suggests that prokaryotes such as methane-oxidizing bacteria or cyanobacteria may have significantly contributed to the formation of these organic-rich, dark sediments. These results indicate that the bottom waters of the Norway Basin had been subjected to anoxic conditions during the early Miocene.