EASI—enrichment of alternatively spliced isoforms

Alternative splicing produces more than one protein from the majority of genes and the rarer forms can have dominant functions. Instability of alternative transcripts can also hinder the study of regulation of gene expression by alternative splicing. To investigate the true extent of alternative splicing we have developed a simple method of enriching alternatively spliced isoforms (EASI) from PCRs using beads charged with Thermus aquaticus single-stranded DNA-binding protein (T.Aq ssb). This directly purifies the single-stranded regions of heteroduplexes between alternative splices formed in the PCR, enabling direct sequencing of all the rare alternative splice forms of any gene. As a proof of principle the alternative transcripts of three tumour suppressor genes, TP53, MLH1 and MSH2, were isolated from testis cDNA. These contain missing exons, cryptic splice sites or include completely novel exons. EASI beads are stable for months in the fridge and can be easily combined with standard protocols to speed the cloning of novel transcripts

Interception and Offshore Processing of Asylum Seekers: The International Law Dimensions

For decades the international community has conducted a delicate and politically charged balancing act trying to reconcile the inexorable increase in refugees-and the need to find permanent homes for them with the fundamental right of all countries to have secure frontiers. While the notion of non-refoulement remains fundamental to the treatment of asylum seekers, their rights vis A vis the states in which they seek asylum are significantly circumscribed by their alien status. States have a right to control entry to their territories. In the development of asylum law and policy, the central difficulty for states, and indeed the international community, is how to construct an appropriate balance between the urgent humanitarian demands to protect those who are genuinely in need of asylum, and the exclusion of those who do not qualify for humanitarian protection

Wavelet-based Faraday Rotation Measure Synthesis

Faraday Rotation Measure (RM) Synthesis, as a method for analyzing multi-channel observations of polarized radio emission to investigate galactic magnetic fields structures, requires the definition of complex polarized intensity in the range of the negative lambda square. We introduce a simple method for continuation of the observed complex polarized intensity into this domain using symmetry arguments. The method is suggested in context of magnetic field recognition in galactic disks where the magnetic field is supposed to have a maximum in the equatorial plane. The method is quite simple when applied to a single Faraday-rotating structure on the line of sight. Recognition of several structures on the same line of sight requires a more sophisticated technique. We also introduce a wavelet-based algorithm which allows us to consider a set of isolated structures. The method essentially improves the possibilities for reconstruction of complicated Faraday structures using the capabilities of modern radio telescopes.Comment: 5 pages, 5 figures, accepted for publication in MNRAS Letter

Development of Vegetation Communities in a Retrogressive Thaw Slump near Mayo, Yukon Territory : A 10-year Assessment

The vegetation in a retrogressive thaw slump, first surveyed and documented in 1987, was revisited 10 years later to investigate its subsequent development and to test a chronosequence-based successional model. The thaw slump stabilized in 1994, when the headwall became covered by organic and mineral debris. As a result, the meltwater supply from headwall ablation ceased. Alteration of environmental conditions due to stabilization of the headwall diverted the vegetation succession from the chronosequence determined in 1987. Areas that were marshy in 1987 dried up, and an area dominated by Polygonum alaskanum appeared close to the headwall. Much of the thaw slump was dominated by Salix spp. in 1997, rather than the Equisteum of 1987. However, the ground more than 200 m from the headwall, over a decade old in 1987, experienced less change in edaphic conditions, and the communities there continued to develop a structure approaching the surrounding undisturbed forest.La végétation située dans un décrochement de fonte régressif, étudiée et documentée pour la première fois en 1987, a fait l'objet d'une autre étude sur place dix ans plus tard pour examiner son évolution et tester un modèle de succession fondé sur la chronoséquence. Le décrochement de fonte s'est stabilisé en 1994, quand le mur de rimaye s'est couvert de débris organiques et minéraux. Il en a résulté que l'alimentation en eau de fonte venant de l'ablation du mur de rimaye a cessé. Le changement dans les conditions environnementales dû à la stabilisation du mur a détourné la succession végétale de la chronoséquence établie en 1987. Des zones qui étaient marécageuses en 1987 se sont asséchées, et une étendue où dominait Polygonum alaskanum apparue près du mur. En 1997, une grande partie de la zone du décrochement de fonte était dominée par des espèces Salix, plutôt qu'Equisteum, comme c'était le cas en 1987. Toutefois, le sol situé à plus de 200 m du mur de rimaye, sol vieux de dix ans en 1987, a subi moins de changement dans les conditions édaphiques, et les communautés y ont continué à évoluer vers une structure qui se rapproche de la forêt non perturbée située à la périphérie

The formation of Jupiter by hybrid pebble-planetesimal accretion

The standard model for giant planet formation is based on the accretion of solids by a growing planetary embryo, followed by rapid gas accretion once the planet exceeds a so-called critical mass. The dominant size of the accreted solids (cm-size particles named pebbles or km to hundred km-size bodies named planetesimals) is, however, unknown. Recently, high-precision measurements of isotopes in meteorites provided evidence for the existence of two reservoirs in the early Solar System. These reservoirs remained separated from ~1 until ~ 3 Myr after the beginning of the Solar System's formation. This separation is interpreted as resulting from Jupiter growing and becoming a barrier for material transport. In this framework, Jupiter reached ~20 Earth masses within ~1 Myr and slowly grew to ~50 Earth masses in the subsequent 2 Myr before reaching its present-day mass. The evidence that Jupiter slowed down its growth after reaching 20 Earth masses for at least 2 Myr is puzzling because a planet of this mass is expected to trigger fast runaway gas accretion. Here, we use theoretical models to describe the conditions allowing for such a slow accretion and show that Jupiter grew in three distinct phases. First, rapid pebble accretion brought the major part of Jupiter's core mass. Second, slow planetesimal accretion provided the energy required to hinder runaway gas accretion during 2 Myr. Third, runaway gas accretion proceeded. Both pebbles and planetesimals therefore have an important role in Jupiter's formation.Comment: Published in Nature Astronomy on August 27, 201

In Vitro Production of Ergothioneine Isotopologues

Ergothioneine is an emerging component of the redox homeostasis system in human cells and in microbial pathogens, such as Mycobacterium tuberculosis and Burkholderia pseudomallei. The synthesis of stable isotope-labeled ergothioneine derivatives may provide important tools for deciphering the distribution, function, and metabolism of this compound in vivo. We describe a general protocol for the production of ergothioneine isotopologues with programmable 2 H, 15 N, 13 C, 34 S, and 33 S isotope labeling patterns. This enzyme-based approach makes efficient use of commercial isotope reagents and is also directly applicable to the synthesis of radio-isotopologues

An inverse modeling approach to obtain P-T conditions of metamorphic stages involving garnet growth and resorption

This contribution presents an approach and a computer program (GRTMOD) for numerical simulation of garnet evolution based on compositions of successive growth zones in natural samples. For each garnet growth stage, a new local effective bulk composition is optimized, allowing for resorption and/or fractionation of previously crystallized garnet. The successive minimizations are performed using the Nelder-Mead algorithm; a heuristic search method. An automated strategy including two optimization stages and one refinement stage is described and tested. This program is used to calculate pressure-temperature (P-T) conditions of crystal growth as archived in garnet from the Sesia Zone (Western Alps). The compositional variability of successive growth zones is characterized using standardized X-ray maps and the program XMapTools. The model suggests that Permian garnet cores crystallized under granulite-facies conditions at T>800 °C and P = 6 kbar. During Alpine times, a first garnet rim grew at eclogite-facies conditions (650 °C, 16 kbar) at the expense of the garnet core. A second rim was added at lower P (∼11 kbar) and 630 °C. In total, garnet resorption is modeled to amount to ∼9 vol% during the Alpine evolution; this value is supported by our observations in X-ray compositional maps