Determination by MAD-DM of the structure of the DNA duplex d[ACGTACG(5-BrU)]2 at 1.46 Å and 100 K

A four-wavelength MAD experiment on a new brominated octanucleotide is reported here. d[ACGTACG(5-BrU)], C77H81BrN30O32P7, (DNA) = 2235, tetragonal, P43212 (No. 96), a = 43.597, c = 26.268 Å, V = 49927.5 Å3, Z = 8, T = 100 K, R = 10.91% for 4312 reflections between 15.0 and 1.46 Å resolution. The self-complementary brominated octanucleotide d[ACGTACG(5-BrU)]2 has been crystallized and data measured to 1.45 Å at both 293 K and a second crystal flash frozen at 100 K. The latter data collection was carried out to the same resolution at the four wavelengths 0.9344, 0.9216, 0.9208 and 0.9003 Å, around the Br K edge at 0.92 Å and the structure determined from a map derived from a MAD data analysis using pseudo-MIR methodology, as implemented in the program MLPHARE. This is one of the first successful MAD phasing experiments carried out at Sincrotrone Elettra in Trieste, Italy. The structure was refined using the data measured at 0.9003 Å, anisotropic temperature factors and the restrained least-squares refinement implemented in the program SHELX96, and the helical parameters are compared with those previously determined for the isomorphous d(ACGTACGT)2 analogue. The asymmetric unit consists of a single strand of octamer with 96 water molecules. No countercations were located. The A-DNA helix geometry obtained has been analysed using the CURVES program.

Structure of the DNA octanucleotide d(ACGTACGT)2

d(ACGTACGT), C78H84N30O32P7.20H2O, Mr (DNA) = 2170, tetragonal, P43212 (No 96), a = 42.845 (1), b = 42.845(1), c = 24.804 (1) Å, V = 45532.5 (2) Å3, z = 8,(MoK) = 0.71069 Å,µ(MoK) = 0.10 mm-1, T = 295 K, R = 0.18 for 1994 unique reflections between 5.0 and 1.9 Å resolution. The self-complementary octanucleotide d(ACGTACGT)2 has been crystallized and its structure determined to a resolution of 1.9 Å. The asymmetric unit consists of a single strand of octamer with 20 water molecules. It is only the second example of an octanucleotide having terminal A·T base pairs whose structure has been determined by X-ray crystallography. The sequence adopts the modified A-type conformation found for all octanucleotide duplexes studied to date with the helix bent by approximately 15° and an average tilt angle of 0°. Unusually the data collection was carried out using a 3 kW molybdenum sealed-tube source. The conformational details are discussed in comparison with other closely related sequences.

Hydrogen-bonding-driven self-assembly of PEGylated organosilica nanoparticles with poly(acrylic acid) in aqueous solutions and in layer-by-layer deposition at solid surfaces

PEGylated organosilica nanoparticles have been synthesized through self-condensation of (3-mercaptopropyl)trimethoxysilane in dimethyl sulfoxide into thiolated nanoparticles with their subsequent reaction with methoxypoly(ethylene glycol) maleimide. The PEGylated nanoparticles showed excellent colloidal stability over a wide range of pH in contrast to the parent thiolated nanoparticles, which have a tendency to aggregate irreversibly under acidic conditions (pH < 3.0). Due to the presence of a poly(ethylene glycol)-based corona, the PEGylated nanoparticles are capable of forming hydrogen-bonded interpolymer complexes with poly(acrylic acid) in aqueous solutions under acidic conditions, resulting in larger aggregates. The use of hydrogen-bonding interactions allows more efficient attachment of the nanoparticles to surfaces. The alternating deposition of PEGylated nanoparticles and poly(acrylic acid) on silicon wafer surfaces in a layer-by-layer fashion leads to multilayered coatings. The self-assembly of PEGylated nanoparticles with poly(acrylic acid) in aqueous solutions and at solid surfaces was compared to the behavior of linear poly(ethylene glycol). The nanoparticle system creates thicker layers than the poly(ethylene glycol), and a thicker layer is obtained on a poly(acrylic acid) surface than on a silica surface, because of the effects of hydrogen bonding. Some implications of these hydrogen-bonding-driven interactions between PEGylated nanoparticles and poly(acrylic acid) for pharmaceutical formulations are discussed.

A genetic linkage map of an apple rootstock progeny anchored to the Malus genome sequence

An apple rootstock progeny raised from the cross between the very dwarfing ‘M.27’ and the more vigorous ‘M.116’ (‘M.M.106’ × ‘M.27’) was used for the construction of a linkage map comprising a total of 324 loci: 252 previously mapped SSRs, 71 newly characterised or previously unmapped SSR loci (including 36 amplified by 33 out of the 35 novel markers reported here), and the self-incompatibility locus. The map spanned the 17 linkage groups (LG) expected for apple covering a genetic distance of 1,229.5 cM, an estimated 91% of the Malus genome. Linkage groups were well populated and, although marker density ranged from 2.3 to 6.2 cM/SSR, just 15 gaps of more than 15 cM were observed. Moreover, only 17.5% of markers displayed segregation distortion and, unsurprisingly in a semi-compatible backcross, distortion was particularly pronounced surrounding the self-incompatibility locus (S) at the bottom of LG17. DNA sequences of 273 SSR markers and the S locus, representing a total of 314 loci in this investigation, were used to anchor to the ‘Golden Delicious’ genome sequence. More than 260 of these loci were located on the expected pseudo-chromosome on the ‘Golden Delicious’ genome or on its homeologous pseudo-chromosome. In total, 282.4 Mbp of sequence from 142 genome sequence scaffolds of the Malus genome were anchored to the ‘M.27’ × ‘M.116’ map, providing an interface between the marker data and the underlying genome sequence. This will be exploited for the identification of genes responsible for traits of agronomic importance such as dwarfing and water use efficiency.

Self-assembly of a peptide amphiphile containing l-carnosine and its mixtures with a multilamellar vesicle forming lipid

The self-assembly of the peptide amphiphile (PA) hexadecyl-(β-alaninehistidine) is examined in aqueous solution, along with its mixtures with multilamellar vesicles formed by DPPC (dipalmitoyl phosphatidylcholine). This PA, denoted C16-βAH, contains a dipeptide headgroup corresponding to the bioactive molecule L-carnosine. It is found to selfassemble into nanotapes based on stacked layers of molecules. Bilayers are found to coexist with monolayers in which the PA molecules pack with alternating up−down arrangement so that the headgroups decorate both surfaces. The bilayers become dehydrated as PA concentration increases and the number of layers in the stack decreases to produce ultrathin nanotapes comprised of 2−3 bilayers. Addition of the PA to DPPC multilamellar vesicles leads to a transition to well-defined unilamellar vesicles. The unique ability to modulate the stacking of this PA as a function of concentration, combined with its ability to induce a multilamellar to unilamellar thinning of DPPC vesicles, may be useful in biomaterials applications where the presentation of the peptide function at the surface of self-assembled nanostructures is crucial.

Structural and morphological studies of the dipeptide based L-Pro-L-Val organocatalytic gels and their rheological behaviour

Organocatalytic gels based on the dipeptide sequence L-Pro-L-Val have been studied by two different FTIR techniques. This suggests a different arrangement of the gelator molecules in the self-assembled fibers depending on the organic solvent employed. In acetonitrile and nitromethane the structure of the supramolecular aggregates is similar and provides similar catalytic properties (supramolecularenhancement of basicity). In contrast, the self-assembled fibers obtained in toluene clearly presented a different molecular arrangement consistent with its different catalytic behaviour (enamine-based catalysis). In addition these gels have been studied by microscopy and rheology.

Nano structures through self-assembly of protected hydrophobic amino acids: encapsulation of rhodamine B dye by proline-based nanovesicles

The development of novel molecules for the creation of nanometer structures with specific properties has been the current interest of this research. We have developed a set of molecules from hydrophobic omega- and alpha-amino acids by protecting the -NH(2) with Boc (t-butyloxycarbonyl) group and -CO(2)H with para-nitroanilide such as BocHN-Xx-CONH-(p-NO(2))center dot C(6)H(4), where Xx is gamma-aminobutyric acid (gamma-Abu), (L)-isoleucine, alpha-aminoisobutyric acid, proline, etc. These molecules generate various nanometer structures, such as nanofibrils, nanotubes and nanovesicles, in methanol/water through the self-assembly of bilayers in which the nitro benzene moieties are stacked in the middle and the Boc-protected amino acids parts are packed in the outer surface. The bilayers can be further stacked one over the other through hydrophobic interactions to form multilayer structure, which helps to generate different kinds of nanoscopic structures. The formation of the nanostructures has been facilitated through the participation of various noncovalent interactions, such as hydrophobic interactions, hydrogen bonding and aromatic p-stacking interactions. Fluorescence microscopy and UV studies reveal that the nanovesicles generated from pro-based molecule can encapsulate dye molecules which can be released by addition of acid (at pH 2). These single amino acid based molecules are both easy to synthesize and cost-effective and therefore offer novel scaffolds for the future design of nanoscale structures.

The R1441C mutation alters the folding properties of the ROC domain of LRRK2

LRRK2 is a 250 kDa multidomain protein, mutations in which cause familial Parkinson's disease. Previously, we have demonstrated that the R1441C mutation in the ROC domain decreases GTPase activity. Here we show that the R1441C alters the folding properties of the ROC domain, lowering its thermodynamic stability. Similar to small GTPases, binding of different guanosine nucleotides alters the stability of the ROC domain, suggesting that there is an alteration in conformation dependent on GDP or GTP occupying the active site. GTP/GDP bound state also alters the self-interaction of the ROC domain, accentuating the impact of the R1441C mutation on this property. These data suggest a mechanism whereby the R1441C mutation can reduce the GTPase activity of LRRK2, and highlights the possibility of targeting the stability of the ROC domain as a therapeutic avenue in LRRK2 disease.

An obscured tradition: the sonnet and its fourteen-line predecessors

The sonnet in English is usually located as a sixteenth-century innovation, firmly linked to Italian influences, and frequently associated with a distinctively modern consciousness. Yet the speed and comfort with which the form settled into English reflects the fact that the sonnet per se was preceded by a longstanding tradition of 14-line poems in English written in forms derived from French. Indeed, in terms of formal features, the earliest sonnets in English frequently fray into earlier forms, sharing more with the roundel than with later sonnets. This article considers a number of features of style and content that various writers on the sonnet have argued to be characteristic, sometimes definitive, of the sonnet. These features include repetition, formal unity/division of octave and sestet, use of the volta, asymmetry, argument and development, and a preoccupation with contradictions and the self. The article shows that, while it is true that these features are characteristic of many sonnets, they are not peculiarly characteristic of sonnets, and they can all be found in earlier 14-line poems. Furthermore, a number of the earliest sonnets in English do not themselves possess these ‘sonnet-like’ characteristics. The otherness and the modernity of the sonnet have thus been overstated.

Parsing the passive: comparing children with Specific Language Impairment to sequential bilingual children

25 monolingual (L1) children with Specific Language Impairment (SLI), 32 sequential bilingual (L2) children, and 29 L1 controls completed the Test of Active & Passive Sentences-Revised (van der Lely, 1996) and the self-paced listening task with picture verification for actives and passives (Marinis, 2007). These revealed important between-group differences in both tasks. The children with SLI showed difficulties in both actives and passives when they had to reanalyse thematic roles on-line. Their error pattern provided evidence for working memory limitations. The L2 children showed difficulties only in passives both on-line and off-line. We suggest that these relate to the complex syntactic algorithm in passives and reflect an earlier developmental stage due to reduced exposure to the L2. The results are discussed in relation to theories of SLI and can be best accommodated within accounts proposing that difficulties in the comprehension of passives stem from processing limitations.

Summertime stratospheric processes at northern mid-latitudes: comparisons between MANTRA balloon measurements and the Canadian Middle Atmosphere Model

In this paper we report on a study conducted using the Middle Atmospheric Nitrogen TRend Assessment (MANTRA) balloon measurements of stratospheric constituents and temperature and the Canadian Middle Atmosphere Model (CMAM). Three different kinds of data are used to assess the inter-consistency of the combined dataset: single profiles of long-lived species from MANTRA 1998, sparse climatologies from the ozonesonde measurements during the four MANTRA campaigns and from HALOE satellite measurements, and the CMAM climatology. In doing so, we evaluate the ability of the model to reproduce the measured fields and to thereby test our ability to describe mid-latitude summertime stratospheric processes. The MANTRA campaigns were conducted at Vanscoy, Saskatchewan, Canada (52◦ N, 107◦ W)in late August and early September of 1998, 2000, 2002 and 2004. During late summer at mid-latitudes, the stratosphere is close to photochemical control, providing an ideal scenario for the study reported here. From this analysis we find that: (1) reducing the value for the vertical diffusion coefficient in CMAM to a more physically reasonable value results in the model better reproducing the measured profiles of long-lived species; (2) the existence of compact correlations among the constituents, as expected from independent measurements in the literature and from models, confirms the self-consistency of the MANTRA measurements; and (3) the 1998 measurements show structures in the chemical species profiles that can be associated with transport, adding to the growing evidence that the summertime stratosphere can be much more disturbed than anticipated. The mechanisms responsible for such disturbances need to be understood in order to assess the representativeness of the measurements and to isolate longterm trends.

Film as literature, or the Truffaldian Malaise

This chapter looks at L’Homme qui aimait les femmes (1977) as a privileged instance of the self-effacing, obliquely disruptive, reflexive aesthetics that characterizes Truffaut’s cinema, by means of an intermedial approach. Although an original story, written by Truffaut in collaboration with Suzanne Schiffman and Michel Fermaud, the film’s subject is the writing of a book containing the protagonist’s story. More importantly, its mode of address presents this story as literature, through a complex network of flashbacks and voiceover narrations that comment on and make sense of the fragmentary present-tense action scenes. As well as a film, this method resulted in an actual novel, or cinéroman, this time authored exclusively by the director under the same title of L’Homme qui aimait les femmes, thus giving material form to the literary aim of the cinematic enterprise: a book.

Self-assembly of a model amphiphilic oligopeptide incorporating an arginine headgroup

The self-assembly in aqueous solution of the alanine-rich peptide A12R2 containing twelve alanine residues and two arginine residues has been investigated. This oligomeric peptide was synthesized via NCA-polymerization methods. The surfactant-like peptide is found via FTIR to form antiparallel dimers which aggregate into twisted fibrils, as revealed by cryogenic-transmission electron microscopy. The fibril substructure is probed via detailed X-ray scattering experiments, and are uniquely comprised of twisted tapes only 5 nm wide, set by the width of the antiparallel A12R2 dimers. The packing of the alanine residues leads to distinct “b-sheet” spacings compared to those for amyloid-forming peptides. For this peptide, b-sheet structure coexists with some a-helical content. These ultrafine amyloid fibrils present arginine at high density on their surfaces, and this may lead to applications in nanobiotechnology.

Near-infrared water vapour self-continuum at close to room temperature

The gaseous absorption of solar radiation within near-infrared atmospheric windows in the Earth's atmosphere is dominated by the water vapour continuum. Recent measurements by Baranov et al. (2011) [17] in 2500 cm−1 (4 μm) window and by Ptashnik et al. (2011) [18] in a few near-infrared windows revealed that the self-continuum absorption is typically an order of magnitude stronger than given by the MT_CKD continuum model prior to version 2.5. Most of these measurements, however, were made at elevated temperatures, which makes their application to atmospheric conditions difficult. Here we report new laboratory measurements of the self-continuum absorption at 289 and 318 K in the near-infrared spectral region 1300–8000 cm−1, using a multipass 30 m base cell with total optical path 612 m. Our results confirm the main conclusions of the previous measurements both within bands and in windows. Of particular note is that we present what we believe to be the first near-room temperature measurement using Fourier Transform Spectrometry of the self-continuum in the 6200 cm−1 (1.6 μm) window, which provides tentative evidence that, at such temperatures, the water vapour continuum absorption may be as strong as it is in 2.1 μm and 4 μm windows and up to 2 orders of magnitude stronger than the MT_CKD-2.5 continuum. We note that alternative methods of measuring the continuum in this window have yielded widely differing assessment of its strength, which emphasises the need for further measurements.

Self-assembly of palmitoyl lipopeptides used in skin care products

The self-assembly of three cosmetically active peptide amphiphiles C16-GHK, C16-KT, and C16-KTTKS (C16 denotes a hexadecyl, palmitoyl chain) used in commercial skin care products is examined. A range of spectroscopic, microscopic, and X-ray scattering methods is used to probe the secondary structure, aggregate morphology, and the nanostructure. Peptide amphiphile (PA) C16-KTTKS forms flat tapes and extended fibrillar structures with high β-sheet content. In contrast, C16-KT and C16-GHK exhibit crystal-like aggregates with, in the case of the latter PA, lower β-sheet content. All three PA samples show spacings from bilayer structures in small-angle X-ray scattering profiles, and all three have similar critical aggregation concentrations, this being governed by the lipid chain length. However, only C16-KTTKS is stained by Congo red, a diagnostic dye used to detect amyloid formation, and this PA also shows a highly aligned cross-β X-ray diffraction pattern consistent with the high β-sheet content in the self-assembled aggregates. These findings may provide important insights relevant to the role of self-assembled aggregates on the reported collagen-stimulating properties of these PAs.