Feeding specialization and host-derived chemical defense in Chrysomeline leaf beetles did not lead to an evolutionary dead end

Combination of molecular phylogenetic analyses of Chrysomelina beetles and chemical data of their defensive secretions indicate that two lineages independently developed, from an ancestral autogenous metabolism, an energetically efficient strategy that made the insect tightly dependent on the chemistry of the host plant. However, a lineage (the interrupta group) escaped this subordination through the development of a yet more derived mixed metabolism potentially compatible with a large number of new host-plant associations. Hence, these analyses on leaf beetles document a mechanism that can explain why high levels of specialization do not necessarily lead to “evolutionary dead ends.”

Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy

The Escherichia coli protein DbpA is unique in its subclass of DEAD box RNA helicases, because it possesses ATPase-specific activity toward the peptidyl transferase center in 23S rRNA. Although its remarkable ATPase activity had been well defined toward various substrates, its RNA helicase activity remained to be characterized. Herein, we show by using biochemical assays and atomic force microscopy that DbpA exhibits ATP-stimulated unwinding activity of RNA duplex regardless of its primary sequence. This work presents an attempt to investigate the action of DEAD box proteins by a single-molecule visualization methodology. Our atomic force microscopy images enabled us to observe directly the unwinding reaction of a DEAD box helicase on long stretches of double-stranded RNA. Specifically, we could differentiate between the binding of DbpA to RNA in the absence of ATP and the formation of a Y-shaped intermediate after its progression through double-stranded RNA in the presence of ATP. Recent studies have questioned the designation of DbpA, in particular, and DEAD box proteins in general as RNA helicases. However, accumulated evidence and the results reported herein suggest that these proteins are indeed helicases that resemble in many aspects the DNA helicases.

Life in the end-Permian dead zone

The fossil record of land plants is an obvious source of information on the dynamics of mass extinctions in the geological past. In conjunction with the end-Permian ecological crisis, ≈250 million years ago, palynological data from East Greenland reveal some unanticipated patterns. We document the significant time lag between terrestrial ecosystem collapse and selective extinction among characteristic Late Permian plants. Furthermore, ecological crisis resulted in an initial increase in plant diversity, instead of a decrease. Paradoxically, these floral patterns correspond to a “dead zone” in the end-Permian faunal record, characterized by a paucity of marine invertebrate megafossils. The time-delayed, end-Permian plant extinctions resemble modeled “extinction debt” responses of multispecies metapopulations to progressive habitat destruction.

A eukaryotic enzyme that can disjoin dead-end covalent complexes between DNA and type I topoisomerases.

The covalent joining of topoisomerases to DNA is normally a transient step in the reaction cycle of these important enzymes. However, under a variety of circumstances, the covalent complex is converted to a long-lived or dead-end product that can result in chromosome breakage and cell death. We have discovered and partially purified an enzyme that specifically cleaves the chemical bond that joins the active site tyrosine of topoisomerases to the 3' end of DNA. The reaction products made by the purified enzyme on a variety of model substrates indicate that the enzyme cleanly hydrolyzes the tyrosine-DNA phosphodiester linkage, thereby liberating a DNA terminated with a 3' phosphate. The wide distribution of this phosphodiesterase in eukaryotes and its specificity for tyrosine linked to the 3' end but not the 5' end of DNA suggest that it plays a role in the repair of DNA trapped in complexes involving eukaryotic topoisomerase I.

The "DEAD box" protein DbpA interacts specifically with the peptidyltransferase center in 23S rRNA.

The Escherichia coli DEAD (Asp-Glu-Ala-Asp) box protein DbpA is a putative RNA helicase and established RNA-dependent ATPase and is the only member of the DEAD box protein family for which a specific RNA substrate, bacterial 23S rRNA, has been identified. We have investigated the nature of this specificity in depth and have localized by deletion mutagenesis and PCR a single region of 93 bases (bases 2496-2588) in 23S rRNA that is both necessary and sufficient for complete activation of ATPase activity of DbpA. This target region forms part of the peptidyltransferase center and includes many bases involved in interaction with the 3' terminal adenosines of both A- and P-site tRNAs. Deletion of stem loops within the 93-base segment abolished ATPase activation. Similarly, point mutations that disrupt base pairing within stem structures ablated stimulation of ATPase activity. These data are consistent with roles for DbpA either in establishing and/or maintaining the correct three-dimensional structure of the peptidyltransferase center in 23S rRNA during ribosome assembly or in the peptidyltransferase reaction.

Are drawings dead? …and performance over aesthetics?

When the act of 'drawing' became what can only be called formalised, (whose growth can be said to have blossomed during the Renaissance), there developed a separation between the drawing and its procurement. Recently, David Ross Scheer, in his book ‘The Death of Drawing, Architecture in the Age of Simulation’ wrote: ‘…whereas architectural drawings exist to represent construction, architectural simulations exist to anticipate building performance.’ Meanwhile, Paolo Belardi, in his work ‘Why Architects Still Draw’ likens a drawing to an acorn, where he says: ‘It is the paradox of the acorn: a project emerges from a drawing – even from a sketch, rough and inchoate - just as an oak tree emerges from an acorn.’ He tells us that Giorgio Vasari would work late at night ‘seeking to solve the problems of perspective’ and he makes a passionate plea that this reflective process allows the concept to evolve, grow and/or develop. However, without belittling Belardi, the virtual model now needs this self-same treatment where it is nurtured, coaxed and encouraged to be the inchoate blueprint of the resultant oak tree. The model now too can embrace the creative process going through the first phase of preparation, where it focuses on the problem. The manipulation of the available material can then be incubated so that it is reasoned and generates feedback. This paper serves to align this shift in perception, methodologies and assess whether the 2D paper abstraction still has a purpose and role in today’s digital world!

A Map of the Dead Sea, Low plains and Gulf of Eloth, [1812 May 4]

A pen-and-ink map of the Dead Sea from Jericho to the Gulf of Eloth on a grid. The map accompanied a letter by Winthrop (HUG 1203.5 Box 1, Folder 13).

[Map of the Dead Sea before the Biblical destruction of Sodom, 1812 May 4]

A pen-and-ink and watercolor map of the Dead Sea noting the "Course of Jordan before the destruction of Sodom." The map accompanied a letter by Winthrop (HUG 1203.5 Box 1, Folder 13).

The concept of 'economic activity' in the EU treaty: from ideological dead-ends to workable judicial concepts. Research Paper in Law 06/2011

[From the Introduction]. The economic rules, or put more ambitiously, the economic constitution of the Treaty,1 only apply to economic activities. This general principle remains valid, even if some authors strive to demonstrate that certain Treaty rules also apply in the absence of an economic activity,2 and despite the fact that non-economic (horizontal) Treaty provisions (e.g. principle of nondiscrimination, rules on citizenship) are also applicable in the absence of any economic activity.3 Indeed, the exercise of some economic activity transcends the concepts of ‘goods’ (having positive or negative market value),4 workers (even if admitted in an extensive manner),5 and services (offered for remuneration).6 It is also economic activity or ‘the activity of offering goods and services into the market’7 that characterises an ‘undertaking’ thus making the competition rules applicable. Further, it is for regulating economic activity that Article 115 TFEU, Article 106(3) TFEU and most other legal bases in the TFEU provide harmonisation powers in favour of the EU. Last but not least, Article 14 TFEU on the distinction between services of general economic interest (SGEIs) and non-economic services of general interest (NESGIs), as well as Protocol n. 26 on Services of General Interest (SGIs) confirm the constitutional significance of the distinction between economic and non-economic: a means of dividing competences between the EU and the member states. The distinction between economic and non-economic activities is fraught with legal and technical intricacies – the latter being generated by dynamic technological advances and regulatory experimentation. More importantly, however, the distinction is overcharged with political and ideological significations and misunderstandings and, even, terminological confusions.8

Why the regulatory witch-hunt for ‘closet trackers’ is a dead-end. CEPS Commentary, 9 December 2014

ESMA, the European watchdog of securities markets, has announced its intention to take a closer look at so-called ‘closet trackers’, with a view to identify whether there is a potential need for a coordinated pan-European policy response to these particular funds, which are supposedly actively managed but in reality closely track their benchmarks. In this commentary, Jean Pierre Casey suggests that more work needs to be done to demonstrate that a market failure exists. He also cautions on some of the difficulties associated with a potential regulatory intervention. In his view, the perceived problem is best tackled through transparency and competition.

Down-core distribution of live and dead benthic foraminifera in deep sea sediments from the Weddell Sea and the Californian continental borderland

Five short cores sub-sampled from box cores from three sites in the eastern Weddell Sea off Antarctica and in the eastern Pacific off southern California, covering a range in water depth from 500 to 2000 m, were analysed for the down-core distribution of live (stained with Rose Bengal) and dead benthic foraminifera. In the California continental borderland, Planulina ariminensis, Rosalina columbiensis and Trochammina spp. live attached to agglutinated polychaetes tubes that rise above the sedimentwater interface. Bolivina spissa lives exclusively in or on the uppermost sediment. Stained specimens of Chilostomella ovoidea are found down to 6 cm within the sediment and specimens of Globobulimina pacifica down to a maximum of 8 cm. Delta13C values of live G. pacifica decrease with increasing depth from the sediment surface down to 7 cm core depth, indicating that this infaunal species utilizes13C-depleted carbon from pore waters. In the dead, predominantly calcareous benthic forminiferal assemblage, selective dissolution of small delicate tests in the upper sediment column causes a continuous variation in species proportions. In the eastern Weddell Sea, the calcareous Bulimina aculeata lives in a carbonate corrosive environment exclusively in or on the uppermost sediment. The arenaceous Cribrostomoides subglobosum, Recurvoides contortus and some Reophax species are frequently found within the top 4 cm of the sediment, whereas stained specimens of Haplophragmoides bradyi, Glomospira charoides and Cribrostomoides wiesneri occur in maximum abundance below the uppermost 1.5 cm. Species proportions in the dead, predominantly arenaceous, benthic foraminiferal assemblage change in three distinct steps. The first change is caused by calcite dissolution at the sediment-water interface, the second coincides with the lower boundary of intense bioturbation, and the third results from the geochemical shift from oxidizing to reducing conditions below a compacted ash layer.