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Denaturation of DNA in Ternary Mixed Solution of Water/Hydrophilic/Hydrophobic Organic Solvent

Denaturation of DNA in Ternary Mixed Solution of Water/Hydrophilic/Hydrophobic Organic Solvent

There was no evidence for the existence of a single-helix plasmid in the expe- riment; if a single-helix plasmid had existed, it would have migrated faster than the super-coiled one. However, as shown in Figure 3, we observed a 1.38-fold increase in the absorbance at 260 nm of the plasmid. This increase must be at- tributed to a denaturation bubble (partial change from double helix to single he- lix) [6] [7] in the ternary mixed solution.

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Your advantages: our pumps.

Your advantages: our pumps.

Due to a smaller rotor diameter, the seepex 6L geometry results in surface velocities, which are lower than the single helix conventional geometry by about 20 %, when operating at the same pump speed. This results in a significant extension to the service life of the rotor and stator. Due to the longer sealing line, the pressure and the conveying capacity can be kept constant over longer periods of time, even when wear and tear has reached an advanced stage.

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Statistical shape methodology for the analysis of helices

Statistical shape methodology for the analysis of helices

Consider a helix in three-dimensional space along which a sequence of equally spaced points is observed, subject to statistical noise. For data coming from a single helix, a two-stage algorithm based on a profile likelihood is devel- oped to compute the maximum likelihood estimate of the helix parameters. Statistical properties of the estimator are studied and comparisons are made to other estimators found in the literature. Next a likelihood ratio test is developed to test if there is a change point in the helix, splitting the data into two sub-helices. The shapes of protein α-helices are used to illustrate the methodology.
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The Relative Stream Function of the Uniformly Moving Helical Vortex Tube

The Relative Stream Function of the Uniformly Moving Helical Vortex Tube

and velocity fields induced by moving single-helix or multi-helix vortex filaments were given out by our previous paper [8][9] , in which the derivation of time-dependent velocity fields were changed into the derivation of time-independent velocity fields by the way of setting up moving cylindrical coordinate system together with the vortex filaments motion and postulating that the relative velocity fields were with the helical symmetry and time-independent field.

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Stable single α-helices are constant force springs in proteins.

Stable single α-helices are constant force springs in proteins.

Single ␣ -helix (SAH) domains are rich in charged residues (Arg, Lys, and Glu) and stable in solution over a wide range of pH and salt concentrations. They are found in many different pro- teins where they bridge two functional domains. To test the idea that their high stability might enable these proteins to resist unfolding along their length, the properties and unfolding behavior of the predicted SAH domain from myosin-10 were characterized. The expressed and purified SAH domain was highly helical, melted non-cooperatively, and was monomeric as shown by circular dichroism and mass spectrometry as expected for a SAH domain. Single molecule force spectroscopy experi- ments showed that the SAH domain unfolded at very low forces (<30 pN) without a characteristic unfolding peak. Molecular dynamics simulations showed that the SAH domain unfolds progressively as the length is increased and refolds progressively as the length is reduced. This enables the SAH domain to act as a constant force spring in the mechanically dynamic environ- ment of the cell.
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Biophysical characterization of recombinant proteins expressing the leucine zipper-like domain of the human immunodeficiency virus type 1 transmembrane protein gp41.

Biophysical characterization of recombinant proteins expressing the leucine zipper-like domain of the human immunodeficiency virus type 1 transmembrane protein gp41.

Since leucine zippers have been shown to mediate dimeriza- tion of several DNA-binding transcription factors (28, 34), it has been suggested that the zipper domain of gp41 may be responsible for multimerization of HIV-1 Env (15, 24). The assembly domain of gp160 has been mapped to a 62-residue region (residues 584 to 646 of gp160) located within the extra- cellular domain of gp41 and overlaps the last heptad repeat unit of the zipper-like motif (20). However, direct involvement of this latter motif in Env assembly oligomerization has yet to be demonstrated. In contrast, oligomerization of the gp41 zip- per domain has been shown to be critical for Env multimer- ization during the virus entry process (10, 11, 18, 51, 52). In synthetic peptide models evaluated by circular dichroism (51, 52), single helix-disrupting nonconservative substitutions (e.g., proline or serine) at an invariant isoleucine residue (position 578) centrally located in the gp41 zipper sequence abrogated coiled-coil formation, unlike the case for peptides containing a * Corresponding author. Mailing address: Department of Surgery,
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DNA binding and unwinding by Hel308 helicase requires dual functions of a winged helix domain

DNA binding and unwinding by Hel308 helicase requires dual functions of a winged helix domain

Figure S1. See also Figures 1A and 1B. Clustal omega alignments of amino acid sequences from archaeal Hel308 enzymes from the genera indicated. Also included is the sequence of a human Hel308 homologue, also called HelQ. The first approximately 300 amino acids of human HelQ are omitted from the alignment because they give no sequence homology to any other protein. Amino acid sequences corresponding to the WHD are highlighted by a black box, within which a red box indicates the solvent-exposed -helix (-20) referred to in the main results. 

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Structure of the C terminal domain of the Prokaryotic Sodium Channel Orthologue NsvBa

Structure of the C terminal domain of the Prokaryotic Sodium Channel Orthologue NsvBa

energetically less costly channel conformation change during gating. During channel gating, the neck could act like a spring or tether separating the stabilising coiled-coil from the moving S6 helixes. While the conflicting predictions for disorder and helical structure within the neck region of NsvBa support this hypothesis, such predictions were not observed in any other structurally characterised channel. Additionally, no evidence for a helix-to-disorder transition of this region in NsvBa was observed under the conditions of this study, even upon truncation of the coiled-coil, nor did the results suggest a mixed population of helical and disordered conformations of the neck region within the sample. However, under the conditions used (detergent micelles) there is no driving force such as an ion gradient, to initiate such a transition between conformational states, which would be the likely instigator for any change in the secondary structure within the CTD neck region. This lack of driving force for conformational change is also true for the other crystallographic or spectroscopic studies of the prokaryotic channels, as all of them also utilised detergent micelles or bicelles to maintain channel solubility. Detailed studies involving subtle changes such as the ones described in this work would not have been feasible in lipid bilayers due to
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Innovation today: the Triple Helix and research diversity

Innovation today: the Triple Helix and research diversity

The case of Germany is a powerful version of Triple Helix theory. It deserves to be carefully studied and debated by each mature economic and social system, certainly by French specialists in science and technology policy. ‘ Regionalization ’ has been a major policy in France since the late 1960s. It was the last reform introduced in 1969 by General de Gaulle. It was rejected by popular vote and de Gaulle chose to resign. The French population voted against this project because the majority of the voters did not consider that these regions would have the resources to develop economically, that in- equities between regions would rise, and that it would also reduce the capacity of the central government to balance these inequities. The Loi Deferre, the decentralization law voted in 1982, was a real transfer of sovereignty to the regions. Local governments were established. But this administrative transfer never went so far as to create or in- duce locally the will to establish the conditions for an endogenous regional dynamic, adapted to the local economic fabric and contrasted (not disconnected) from national policies. These French regions did take into account their specific geo-economical en- vironment, but with the exception of Alsace, they always stayed in the end within the framework of a national sovereignty. They never converted to the establishment of a full real trans-border growth area based on research and innovation activities, as ex- emplified by the Knowledge triangle Eindhoven-Leuven-Aachen. Soon, regional politics obscured the ambition and benefits of effective research policies. The French regions have reproduced the national political debate and administrative model. They seem unable and unwilling to emancipate from this model. They are for the moment unable to establish a regional Triple Helix, to establish research and innovation activities as a common regional platform for economic and social development s .
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Triple helix program

Triple helix program

The two-day programme, Entrepreneurial Networking in Industrial Linkages University- Industry Triple-Helix was organised from 3 th until 4 th September, 2012 at Kampus AKEPT, Bandar Enstek, Negeri Sembilan. The programme was conducted as a two days programme that filling with Talk, Workshop and Forum session. With general aim to provide a platform for the sharing of knowledge and experience among academics, researchers, entrepreneurs, government agencies and industrialists (SMEs and MNCs) in an effort to enhance innovation and entrepreneurship in the country via smart collaboration (Triple-Helix), this programme was organised by AKEPT Centre for Leadership Research and Innovation (ACLRI) in collaboration with Universiti Teknikal Malaysia Melaka (UTeM). There were four speakers with each of them was given one hour thirty minutes during the talk session. The workshop session and forum session were taken one hour and two hours thirty minutes, respectively. The participants were from policy makers, academics, researchers, entrepreneurs, government agencies and industrialists (SMEs and MNCs).
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Asymmetric Polymerization initiated by Cationic Zirconocene Complexes possessing Chiral Counter Anions

Asymmetric Polymerization initiated by Cationic Zirconocene Complexes possessing Chiral Counter Anions

Many research groups are interested in developing new methods for controlling the stereoregularity of synthetic polymers and generating single handed helical polymers. One of our research goals is to develop new methods for generating single handed helical polycarbodiimides. Several factors can influence helix-sense selectivity of the polymers including the ligands on the catalyst, chiral side chains, temperature, and solvents. In ionic systems there is also the possibility of having counterion and ion pairing effects. It has recently been demonstrated that ionic interactions in metal catalysis are not only important but can be utilized to influence chirality in reaction products. 1-4 Helix-sense selective anionic polymerizations of highly isotactic vinyl polymers by chiral counterion effects have been reported. 2,3 In this study we are interested in the effects of chiral counter anions in metal- catalyzed polymerizations of achiral carbodiimides.
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Structure of the Tetrahymena thermophila telomerase RNA helix II template boundary element

Structure of the Tetrahymena thermophila telomerase RNA helix II template boundary element

intense peaks and cross peaks for the U23·A33 and U25·A31 base pairs than for other Watson–Crick base pairs in the helical stem, consistent with the decreased RNase V1 cleavage in the upper portion of the stem compared with the terminal region. All of the guanine nucleotides in helix II were moderately cleaved by RNase T1 in the absence of TERT. G26 is single-stranded (in the pentaloop) and should be cleaved in both the free and bound TER unless it is a direct site for TERT binding. G32 is located between the two A·U base pairs in the upper stem which both exhibit only modest RNase V1 cleav- age suggesting weak hydrogen bonding. G21 is the nucleotide directly 5 0 to the staggered adenine nucleotides in the helical stem, and modest changes in the A-form helical structure in this region may expose the 3 0 side of G21 to increased RNase T1 cleavage. G37 is in the terminal base pair of the TBE helix, and modest RNase T1 cleavage is consistent with fraying of the base pairs at the helix terminus. Therefore, the positions of the guanine nucleotides in the TBE make them likely candid- ates for RNase T1 cleavage, even though the region is struc- tured. Thus, while structure probing results suggest that binding of TERT to TER may increase the stability of the helix or decrease accessibility, TERT binding is not a pre- requisite for helix II structure formation.
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Investigating helix helix interactions in the transmembrane domains of membrane proteins

Investigating helix helix interactions in the transmembrane domains of membrane proteins

Identifying helix-helix interactions and the structural determinants that drive α - helical membrane protein folding is a technically challenging problem due to their hydrophobicity. Of particular interest is accessing detailed structural information regarding the interacting side chains and hence enabling identification of the non- covalent bonds stabilising the association of the helices. Using current methods for studying TM interactions (e.g. TOXCAT, GALLEX, Cross-linking, FRET, AUC) it is possible to identify homo- and hetero- association between TM domains and to also determine their oligomeric state, as has been shown in the previous chapters of this work. Current studies on the hetero-association of TM domains have used the GALLEX assay, FRET experiments and immune- precipitation. Complementing these techniques, molecular modelling and mutagenesis studies can suggest residues that are important for the interactions. However, the results from these studies in our experience are often difficult to interpret conclusively. Furthermore, ultimately these methods, though powerful, do not provide information on the arrangements of atoms in these oligomers and ultimately the definitive test for any predictions made from such studies is to solve the atomic structure of the domains.
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Phylogenetic analysis of the human basic helix loop helix proteins

Phylogenetic analysis of the human basic helix loop helix proteins

orthologs (Scleraxis, Dermo-1 and S-Myc) were unsuccess- ful, suggesting that these orthologs either do not exist in humans or are not in the draft sequence. We were recently made aware that there is some incompatibility between the current version of BLAST and the human genome sequence (probably due to the large number of Ns (unassigned nucleotides) in the sequence), which makes BLAST unable to locate some of the best or even exact matches of small query sequences (J.A.M. Leunissen, personal communication). This may explain why we missed the four genes cited above, and also why, in a few cases, we were unable to find known cloned human genes in the genome sequence (see Table 2). We also found eight cases in which two human genes group together (with high statistical support) to the exclusion of any other genes and are often orthologs of a single mouse gene (Figure 2b and Additional data). Conversely, we found two cases in which two mouse genes are, collectively, orthologs of a single human gene (Figure 2d). This may reveal relatively recent duplications specific to the human or mouse lineage. In agreement with this, in all cases amino-acid identity between the two duplicates is high and is not confined to the bHLH. In addition, we found that in two cases (human sequences Q9UH92/N005106 and Q02363/N005999), one of the two duplicates lacks introns. The two copies are, fur- thermore, on different chromosomes. This strongly suggests that the duplications have occurred by retrotransposition, a type of event that appears to be rather frequent in humans [26]. In both cases, the copy lacking introns has stop codons in the bHLH, suggesting that it is a pseudogene.
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Unraveling Viral Interleukin-6 Binding to gp130 and Activation of STAT-Signaling Pathways Independently of the Interleukin-6 Receptor

Unraveling Viral Interleukin-6 Binding to gp130 and Activation of STAT-Signaling Pathways Independently of the Interleukin-6 Receptor

Human herpesvirus 8 encodes a viral version of interleukin-6 (vIL-6) which shows 25% sequence homology with human IL-6. In contrast to human IL-6, which first binds to the IL-6 receptor (IL-6R) and only subsequently associates with the signal transducing receptor subunit gp130, vIL-6 has been shown to directly bind to gp130 without the need of IL-6R. As a functional consequence, vIL-6 can activate far more target cells in the body since all cells express gp130, but only cells such as hepatocytes and some leukocytes express IL-6R. We sought to understand which amino acid sequences within the vIL-6 protein were responsible for its ability to bind and activate gp130 independent of IL-6R. As a first approach, we constructed chimeric IL-6 proteins in which all known gp130 interacting sites (sites II and III) were sequentially transferred from vIL-6 into the human IL-6 protein. To our surprise, human IL-6 carrying all gp130 interacting sites from vIL-6 did not show IL-6R-independent gp130 activation. Even more surprisingly, the loop between helix B and C of vIL-6, clearly shown in the crystal structure not to be in contact with gp130, is indispensable for direct binding to and activation of gp130. This points to an IL-6R induced change of site III conformation in human IL-6, which is already preformed in vIL-6. These data indicate a novel activation mechanism of human IL-6 by the IL-6R that will be important for the construction of novel hyperactive cytokine variants.
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A Simple Analysis of Helical Slow-Wave Structure Loaded by Dielectric Embedded Metal Segments for Wideband Traveling-Wave Tubes

A Simple Analysis of Helical Slow-Wave Structure Loaded by Dielectric Embedded Metal Segments for Wideband Traveling-Wave Tubes

In this paper, the authors have considered a practical wideband helical SWS where the helix is supported by three rectangular dielectric support rods partially embedded in the metal segments and the whole enclosed in a metal envelope (Fig. 1). This structure has merits not only from electromagnetic considerations but also from mechanical considerations in that the structure is thermally rugged, and easy to be fabricated by inserting the dielectric rod and metal segment assembly into the metal envelope. The similar structure has been analyzed by Lei et al. [11] using a tape helix model which, though it is rigorous, is involved and cumbersome. In the present paper, a simple analysis for this structure is presented in the tape helix model (THM) by incorporating into the THM analysis of a free-space helix [17] the dielectric loading factor (D LF ) obtained by a simpler
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DNA triple helix formation: A potential tool for genetic repair

DNA triple helix formation: A potential tool for genetic repair

DNA triple helices offer new perspectives towards oligonucleotide-directed gene regulation. Triple helix forming oligonucleotides, which bind to double-stranded DNA, are of special interest since they are targeted to the gene itself rather than to its mRNA product (as in the antisense strategy). However, the poor stability of some of these structures might limit their use under physiological conditions. Specific ligands can intercalate into DNA triple helices and stabilize them. This review summarizes recent advances in this field while also highlighting major obstacles that remain to be overcome, before the application of triplex technology to therapeutic gene repair can be achieved.
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Mechanochemistry of the kinesin 1 ATPase

Mechanochemistry of the kinesin 1 ATPase

rapid ADP release, but the resulting apo state then tends to denature. 6 In complex with microtubules, the story is very dif- ferent. Strong binding to microtubules activates the release of MgADP by up to three orders of magnitude, 7 and creates a sta- ble apo kinesin-microtubule complex. A closely related ground state complex with unpolymerized tubulin was recently visual- ized by X-ray crystallography at 2.19A resolution (4LNU, Ref. 8). In this structure, key residue–residue interactions identified by Muto and colleagues using tubulin mutagenesis 9–11 are present. Tubulin binding stabilizes the helix alpha 4 in an extended conformation, in which it gains 2.5 helical turns compared to its solution state. The switch 1 is melted, but the critical Sw1–Sw2 latch bridge remains connected. This shows that the formation of this critical latch bridge connection is not enough in itself to structure the Sw1, despite tubulin being bound and the helix 4 being thereby lengthened. Instead, Mg- nucleotide binding is required. Conversely, this structure also shows that nucleotide binding is not required to latch the criti- cal salt bridge. The 4LNU structure is related to but not identi- cal with the apo kinesin microtubule complex, because in 4LNU tubulin is in a curved configuration that differs from its conformation when built into microtubules. It seems clear that most of the kinesin–microtubule apo state interface is present in this structure, but it remains possible that extra contacts formed by the binding of apo-kinesin to straight (polymerized) tubulin might for example strain the motor domain suffi- ciently to disconnect the latch bridge and entirely decouple the Sw1 and Sw2.
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The basic helix loop helix transcription factor, dHAND, is required for vascular development

The basic helix loop helix transcription factor, dHAND, is required for vascular development

enchymal interactions during angiogenesis. Within the heart, Ang-1 secretion from the endocardium is also nec- essary for trabeculation of the neighboring myocardium (8). TGF-β and its receptors play a role in vascular stabi- lization and remodeling and function through the Smad family of transcription factors (11–14). In contrast to these molecules that function mainly during angiogen- esis, VEGF, a heparin-binding growth factor with high specificity for endothelial cells, is a central mediator of angiogenesis and vasculogenesis (4, 15). There are 5 iso- forms produced from a single VEGF gene by alternative splicing. VEGF induces endothelial proliferation, pro- motes cell migration, and inhibits apoptosis (3). Inhibi- tion of VEGF activity results in tumor regression, indi- cating that VEGF is necessary for the neovascularization associated with tumors (16). VEGF signals through its receptor tyrosine kinases, VEGFR-1/Flt-1 and VEGFR- 2/KDR/Flk-1, which are expressed specifically on the surface of vascular endothelial cells and are required for both vasculogenesis and angiogenesis (17–20). Endothe- lial cells of VEGFR-1 mutant mouse embryos differenti- ate, but do not assemble properly into vessels (18), whereas VEGFR-2 mutants display more severe defects of vasculogenesis (17). Recently, another VEGF receptor, VEGFR-3, has been shown to be important for the remodeling and maturation of primary vascular net- works into larger blood vessels (21). These data suggest that VEGF controls unique steps of vascular develop- ment through distinct receptors.
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MBAR enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation

MBAR enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation

More and larger simulations are needed to determine the relative stability of different possible TatA aggregates. The results presented in this work show that methods such as MBAR-enhanced MC [14] make it viable to model larger aggregates—at least when up to one helix is present. However our simulations showed that the acceptance rate for pull moves decreased substantially with

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