Replacement of RNA hairpins by in vitro selected tetranucleotides

An in vitro selection method based on the autolytic cleavage of yeast tRNAPhe by Pb2+ was applied to obtain tRNA derivatives with the anticodon hairpin replaced by four single-stranded nucleotides. Based on the rates of the site-specific cleavage by Pb2+ and the presence of a specific UV-induced crosslink, certain tetranucieotide sequences allow proper folding of the rest of the tRNA molecule, wheras others do not. One such successful tetramer sequence was also used to replace the acceptor stem of yeast tRNAPhe and the anticodon hairpin of E.coli tRNAPhe without disrupting folding. These experiments suggest that certain tetramers may be able to replace structurally non essential hairpins in any RNA.

The "refoldability" of selected proteins in ionic liquids as a stabilization criterion, leading to a conjecture on biogenesis

The folding of proteins is usually studied in dilute aqueous solutions of controlled pH, but it has recently been demonstrated that reversible unfolding can occur in other media. Particular stability is conferred on the protein (folded or unfolded) when the process occurs in ‘protic ionic liquids’ (pILs) of controlled proton activity. This activity (‘effective pH’) is determined by the acid and base components of the pIL and is characterized in the present study by the proton chemical shift of the N–H proton. Here we propose a ‘refoldability’ or ‘refolding index’ (RFI) metric for assessing the stability of folded biomolecules in different solvent media, and demarcate high RFI zones in hydrated pIL media using ribonuclease A and hen egg white lysozyme as examples. Then we show that, unexpectedly, the same high RFIs can be obtained in pIL media that are 90% inorganic in character (simple ammonium salts). This leads us to a conjecture related to the objections that have been raised to ‘primordial soup’ theories for biogenesis, objections that are based on the observation that all the bonds involved in biomacromolecule formation are hydrolyzed in ordinary aqueous solutions unless specifically protected. The ingredients for primitive ionic liquids (NH3, CO, HCN, CO2, and water) were abundant in the early earth atmosphere, and many experiments have shown how amino acids could form from them also. Cyclical concentration in evaporating inland seas could easily produce the type of ambient-temperature, non-hydrolyzing, media that we have demonstrated here may be hospitable to biomolecules, and that may be actually encouraging of biopolymer assembly. Thus a plausible variant of the conventional ‘primordial soup’ model of biogenesis is suggested.

Structure–energy relations in hen egg white lysozyme observed during refolding from a quenched unfolded state

We use infrared spectroscopy to study the evolution of protein folding intermediate structures on arbitrarily slow time scales by rapidly quenching thermally unfolded hen egg white lysozyme in a glassy matrix, followed by reheating of the protein to refold; upon comparison with differential scanning calorimetric experiments, low-temperature structural changes that precede the formation of energetic native contacts are revealed.

Identifying foldable regions in protein sequence from the hydrophobic signal

Structural genomics initiatives aim to elucidate representative 3D structures for the majority of protein families over the next decade, but many obstacles must be overcome. The correct design of constructs is extremely important since many proteins will be too large or contain unstructured regions and will not be amenable to crystallization. It is therefore essential to identify regions in protein sequences that are likely to be suitable for structural study. Scooby-Domain is a fast and simple method to identify globular domains in protein sequences. Domains are compact units of protein structure and their correct delineation will aid structural elucidation through a divide-and-conquer approach. Scooby-Domain predictions are based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure. The prediction method employs an A*-search to identify sequence regions that form a globular structure and those that are unstructured. On a test set of 173 proteins with consensus CATH and SCOP domain definitions, Scooby-Domain has a sensitivity of 50% and an accuracy of 29%, which is better than current state-of-the-art methods. The method does not rely on homology searches and, therefore, can identify previously unknown domains.

Impact response and energy absorption of aluminium foam-filled tubes

The effect of foam fillers on the impact behaviour and energy absorption of an aluminium tube is investigated. Both experimental test and computational simulation are employed in current study. For comparison, hollow tubes and foams are also tested, respectively. Foam filler is found to be ineffective in increasing the crushing loads of the composite tubes over the simple superposition of the crushing loads of hollow tube and foam. Also, foam filler increases the tendency for the concertina mode of folding. The foam fillers of tubes additionally result in increasing the SAE values over those of hollow tubes.

Histological and global gene expression analysis of the ‘lactating’ pigeon crop

Background: Both male and female pigeons have the ability to produce a nutrient solution in their crop for the nourishment of their young. The production of the nutrient solution has been likened to lactation in mammals, and hence the product has been called pigeon ‘milk’. It has been shown that pigeon ‘milk’ is essential for growth and development of the pigeon squab, and without it they fail to thrive. Studies have investigated the nutritional value of pigeon ‘milk’ but very little else is known about what it is or how it is produced. This study aimed to gain insight into the process by studying gene expression in the ‘lactating’ crop.
Results: Macroscopic comparison of ‘lactating’ and non-’lactating’ crop reveals that the ‘lactating’ crop is enlarged and thickened with two very obvious lateral lobes that contain discrete rice-shaped pellets of pigeon ‘milk’. This was characterised histologically by an increase in the number and depth of rete pegs extending from the basal layer of the epithelium to the lamina propria, and extensive proliferation and folding of the germinal layer into the superficial epithelium. A global gene expression profile comparison between ‘lactating’ crop and non-’lactating’ crop showed that 542 genes are up-regulated in the ‘lactating’ crop, and 639 genes are down-regulated. Pathway analysis revealed that genes up-regulated in ‘lactating’ crop were involved in the proliferation of melanocytes, extracellular matrix-receptor interaction, the adherens junction and the wingless (wnt) signalling pathway. Gene ontology analysis showed that antioxidant response and microtubule transport were enriched in ‘lactating’ crop.
Conclusions: There is a hyperplastic response in the pigeon crop epithelium during ‘lactation’ that leads to localised cellular stress and expression of antioxidant protein-encoding genes. The differentiated, cornified cells that form the pigeon ‘milk’ are of keratinocyte lineage and contain triglycerides that are likely endocytosed as very low density lipoprotein (VLDL) and repackaged as triglyceride in vesicles that are transported intracellularly by microtubules. This mechanism is an interesting example of the evolution of a system with analogies to mammalian lactation, as pigeon ‘milk’ fulfils a similar function to mammalian milk, but is produced by a different mechanism.

Proline residues within spacer peptide p1 are important for human immunodeficiency virus type 1 infectivity, protein processing, and genomic RNA dimer stability

The full-length human immunodeficiency virus type 1 (HIV-1) mRNA encodes two precursor polyproteins, Gag and GagProPol. An infrequent ribosomal frameshifting event allows these proteins to be synthesized from the same mRNA in a predetermined ratio of 20 Gag proteins for each GagProPol. The RNA frameshift signal consists of a slippery sequence and a hairpin stem-loop whose thermodynamic stability has been shown in in vitro translation systems to be critical to frameshifting efficiency. In this study we examined the frameshift region of HIV-1, investigating the effects of altering stem-loop stability in the context of the complete viral genome and assessing the role of the Gag spacer peptide p1 and the GagProPol transframe (TF) protein that are encoded in this region. By creating a series of frameshift region mutants that systematically altered the stability of the frameshift stem-loop and the protein sequences of the p1 spacer peptide and TF protein, we have demonstrated the importance of stem-loop thermodynamic stability in frameshifting efficiency and viral infectivity. Multiple changes to the amino acid sequence of p1 resulted in altered protein processing, reduced genomic RNA dimer stability, and abolished viral infectivity. The role of the two highly conserved proline residues in p1 (position 7 and 13) was also investigated. Replacement of the two proline residues by leucines resulted in mutants with altered protein processing and reduced genomic RNA dimer stability that were also noninfectious. The unique ability of proline to confer conformational constraints on a peptide suggests that the correct folding of p1 may be important for viral function.

Ecology / economy

This work speaks to ideas of nurturing and embodiment. In one half of the screen we see a father massaging his child with coconut oil, a common practice in Fijian families, and an early investment in the health and spiritual wellbeing of the child. In the next frame we see the other end of the life cycle and an imagined re-enactment of the folding of the Fijian flag, as in the American military tradition for fallen service people. Here Bolatagici refers to the number of Fijians fighting for foreign armies, including the United States.

Solvent induced changes in the conformational state of β-lactoglobulin and the influence of protic ionic liquids

The protic ionic liquids (pILs), triethylammonium acetate, triethylammonium trifluoroacetate, triethylammonium mesylate and trimethylammonium sulfate were used to induce various native and non-native conformational states of the protein β-lactoglobulin (βLG). Changes in the secondary structure of βLG were observed on moving from a high water content to a high pIL content. We examined the stability of various pIL induced states via thermal unfolding and refolding, where it was found that at a given pIL concentration a highly stable non-native conformation was formed. The βLG non-native conformation was characterized by a high α-helical content. Additionally, pIL conditions that promoted amyloid fibril formation were identified and characterized by CD, a Thioflavin T binding assay and transmission electron microscopy (TEM). This work highlights the use of pILs as solvents in the study of protein folding using βLG as a model system.

Distinct disulfide isomers of μ-Conotoxins KIIIA and KIIIB block voltage-gated sodium channels

In the preparation of synthetic conotoxins containing multiple disulfide bonds, oxidative folding can produce numerous permutations of disulfide bond connectivities. Establishing the native disulfide connectivities thus presents a significant challenge when the venom-derived peptide is not available, as is increasingly the case when conotoxins are identified from cDNA sequences. Here, we investigate the disulfide connectivity of μ-conotoxin KIIIA, which was predicted originally to have a [C1–C9,C2–C15,C4–C16] disulfide pattern based on homology with closely related μ-conotoxins. The two major isomers of synthetic μ-KIIIA formed during oxidative folding were purified and their disulfide connectivities mapped by direct mass spectrometric collision-induced dissociation fragmentation of the disulfide-bonded polypeptides. Our results show that the major oxidative folding product adopts a [C1–C15,C2–C9,C4–C16] disulfide connectivity, while the minor product adopts a [C1–C16,C2–C9,C4–C15] connectivity. Both of these peptides were potent blockers of NaV1.2 (Kd values of 5 and 230 nM, respectively). The solution structure for μ-KIIIA based on nuclear magnetic resonance data was recalculated with the [C1–C15,C2–C9,C4–C16] disulfide pattern; its structure was very similar to the μ-KIIIA structure calculated with the incorrect [C1–C9,C2–C15,C4–C16] disulfide pattern, with an α-helix spanning residues 7–12. In addition, the major folding isomers of μ-KIIIB, an N-terminally extended isoform of μ-KIIIA identified from its cDNA sequence, were isolated. These folding products had the same disulfide connectivities as μ-KIIIA, and both blocked NaV1.2 (Kd values of 470 and 26 nM, respectively). Our results establish that the preferred disulfide pattern of synthetic μ-KIIIA and μ-KIIIB folded in vitro is 1–5/2–4/3–6 but that other disulfide isomers are also potent sodium channel blockers. These findings raise questions about the disulfide pattern(s) of μ-KIIIA in the venom of Conus kinoshitai; indeed, the presence of multiple disulfide isomers in the venom could provide a means of further expanding the snail’s repertoire of active peptides.

Gamma-irradiated carbon nanotube yarn as substrate for high-performance fiber supercapacitors

As an electrical double layer capacitor, dry-spun carbon nanotube yarn possesses relatively low specific capacitance. This can be significantly increased as a result of the pseudocapacitance of functional groups on the carbon nanotubes developed by oxidation using a gamma irradiation treatment in the presence of air. When coated with high-performance polyaniline nanowires, the gamma-irradiated carbon nanotube yarn acts as a high-strength reinforcement and a high-efficiency current collector in two-ply yarn supercapacitors for transporting charges generated along the long electrodes. The resulting supercapacitors demonstrate excellent electrochemical performance, cycle stability, and resistance to folding-unfolding that are required in wearable electronic textiles.

X is not the same as X

X is not the same as X is an installation that disturbs consumer identity and power relations. In the gallery at Melbourne Central the installation enacts a folding of the outside into the inside, and vice versa. Bishop & Reis entrap the viewer in a 2/3 size room – a slightly distorted replica of a space through which the viewer has recently passed. Inside this shaky interior, behind our own reflection, the viewer devolves into something else, an everyman who in The West Wing is presented as both one and many Santa. To warp a well-known phrase: the white hair follicles of the long beard marks a deterritorialisation of the fur, mouth and snout of the animal.

Different thermal analysis technique application in determination of fold surface-free energy

In this work, the crystallization rates and spherulitic growth rate of miscible blends of poly(vinylidene fluoride) (PVDF) and acrylic rubber (ACM) were determined using differential scanning calorimetry (DSC), real-time FTIR, and optical microscopy. FTIR results suggest that blending does not induce the creation of polymorphic crystalline forms of PVDF. SAXS data demonstrate the formation of interlamellar structure after blending. The fold surface-free energy (σ e) was analyzed and compared using different thermal analysis techniques. The isothermal crystallization curves obtained using real-time FTIR and DSC explored in two different methods: t 1/2 or Avrami equation. While the Avrami equation is more widespread and precise, both analytical methods gave similar free energy of folding values. However, it was found that the direct optical method of measuring spherulitic growth rate yields σ e values 30-50 % lower than those obtained from the overall crystallization rate data. Conversely, the σ e values were found to increase with increasing amorphous ACM phase content regardless of the analytical methods.