Influence of Cooling Rate on the Enthalpy Relaxation and Fragility of a Metallic Glass

Structural relaxation behavior of a rapidly quenched (RQ) and a slowly cooled Pd40Cu30Ni10P20 metallic glass was investigated and compared. Differential scanning calorimetry was employed to monitor the relaxation enthalpies at the glass transition temperature, T-g , and the Kolrausch-Williams-Watts (KWW) stretched exponential function was used to describe its variation with annealing time. It was found that the rate of enthalpy recovery is higher in the ribbon, implying that the bulk is more resistant to relaxation at low temperatures of annealing. This was attributed to the possibility of cooling rate affecting the locations where the glasses get trapped within the potential energy landscape. The RQ process traps a larger amount of free volume, resulting in higher fragility, and in turn relaxes at the slightest thermal excitation (annealing). The slowly cooled bulk metallic glass (BMG), on the other hand, entraps lower free volume and has more short-range ordering, hence requiring a large amount of perturbation to access lower energy basins.

Multiple conformational states in crystals and in solution in alpha gamma hybrid peptides. Fragility of the C-12 helix in short sequences

The conformational properties of foldamers generated from alpha gamma hybrid peptide sequences have been probed in the model sequence Boc-Aib-Gpn-Aib-Gpn-NHMe. The choice of alpha-aminoisobutyryl (Aib) and gabapentin (Gpn) residues greatly restricts sterically accessible coil formational space. This model sequence was anticipated to be a short segment of the alpha gamma C-12 helix, stabilized by three successive 4 -> 1 hydrogen bonds, corresponding to a backbone-expanded analogue of the alpha polypeptide 3(10)-helix. Unexpectedly, three distinct crystalline polymorphs were characterized in the solid state by X-ray diffraction. In one form, two successive C-12 hydrogen bonds were obtained at the N-terminus, while a novel C-17 hydrogen-bonded gamma alpha gamma turn was observed at the C-terminus. In the other two polymorphs, isolated C-9 and C-7 hydrogen-bonded turns were observed at Gpn (2) and Gpn (4). Isolated C-12 and C-9 turns were also crystallographically established in the peptides Boc-Aib-Gpn-Aib-OMe and Boc-Gpn-Aib-NHMe, respectively. Selective line broadening of NH resonances and the observation of medium range NH(i)<-> NH(i+2) NOEs established the presence of conformational heterogeneity for the tetrapeptide in CDCl3 solution. The NMR results are consistent with the limited population of the continuous C-12 helix conformation. Lengthening of the (alpha gamma)(n) sequences in the nonapeptides Boc-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Xxx (Xxx = Aib, Leu) resulted in the observation of all of the sequential NOEs characteristic of an alpha gamma C-12 helix. These results establish that conformational fragility is manifested in short hybrid alpha gamma sequences despite the choice of conformationally constrained residues, while stable helices are formed on chain extension.

Mechanism of Fragility at BCL2 Gene Minor Breakpoint Cluster Region during t(14;18) Chromosomal Translocation

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Breaks in chromosome 18 are localized at the 3'-UTR of BCL2 gene or downstream and are mainly clustered in either the major breakpoint region or the minor breakpoint cluster region (mcr). The recombination activating gene (RAG) complex induces breaks at IgH locus of chromosome 14, whereas the mechanism of fragility at BCL2 mcr remains unclear. Here, for the first time, we show that RAGs can nick mcr; however, the mechanism is unique. Three independent nicks of equal efficiency are generated, when both Mg2+ and Mn2+ are present, unlike a single nick during V(D)J recombination. Further, we demonstrate that RAG binding and nicking at the mcr are independent of nonamer, whereas a CCACCTCT motif plays a critical role in its fragility, as shown by sequential mutagenesis. More importantly, we recapitulate the BCL2 mcr translocation and find that mcr can undergo synapsis with a standard recombination signal sequence within the cells, in a RAG-dependent manner. Further, mutation to the CCACCTCT motif abolishes recombination within the cells, indicating its vital role. Hence, our data suggest a novel, physiologically relevant, nonamer-independent mechanism of RAG nicking at mcr, which may be important for generation of chromosomal translocations in humans.

Potential G-quadruplex formation at breakpoint regions of chromosomal translocations in cancer may explain their fragility

Genetic alterations like point mutations, insertions, deletions, inversions and translocations are frequently found in cancers. Chromosomal translocations are one of the most common genomic aberrations associated with nearly all types of cancers especially leukemia and lymphoma. Recent studies have shown the role of non-B DNA structures in generation of translocations. In the present study, using various bioinformatic tools, we show the propensity of formation of different types of altered DNA structures near translocation breakpoint regions. In particular, we find close association between occurrence of G-quadruplex forming motifs and fragile regions in almost 70% of genes involved in rearrangements in lymphoid cancers. However, such an analysis did not provide any evidence for the occurrence of G-quadruplexes at the close vicinity of translocation breakpoint regions in nonlymphoid cancers. Overall, this study will help in the identification of novel non-B DNA targets that may be responsible for generation of chromosomal translocations in cancer. (C) 2012 Elsevier Inc. All rights reserved.

Sequence and structural basis for chromosomal fragility during translocations in cancer

Chromosomal aberration is considered to be one of the major characteristic features in many cancers. Chromosomal translocation, one type of genomic abnormality, can lead to deregulation of critical genes involved in regulating important physiological functions such as cell proliferation and DNA repair. Although chromosomal translocations were thought to be random events, recent findings suggest that certain regions in the human genome are more susceptible to breakage than others. The possibility of deviation from the usual B-DNA conformation in such fragile regions has been an active area of investigation. This review summarizes the factors that contribute towards the fragility of these regions in the chromosomes, such as DNA sequences and the role of different forms of DNA structures. Proteins responsible for chromosomal fragility, and their mechanism of action are also discussed. The effect of positioning of chromosomes within the nucleus favoring chromosomal translocations and the role of repair mechanisms are also addressed.

G-Quadruplex Structures Formed at the HOX11 Breakpoint Region Contribute to Its Fragility during t(10;14) Translocation in T-Cell Leukemia

The t(10;14) translocation involving the HOX11 gene is found in several T-cell leukemia patients. Previous efforts to determine the causes of HOX11 fragility were not successful. The role of non-B DNA structures is increasingly becoming an important cause of genomic instability. In the present study, bioinformatics analysis revealed two G-quadruplex-forming motifs at the HOX11 breakpoint cluster. Gel shift assays showed formation of both intra- and intermolecular G-quadruplexes, the latter being more predominant. The structure formation was dependent on four stretches of guanines, as revealed by mutagenesis. Circular dichroism analysis identified parallel conformations for both quadruplexes. The non-B DNA structure could block polymerization during replication on a plasmid, resulting in consistent K K+-dependent pause sites, which were abolished upon mutation of G-motifs, thereby demonstrating the role of the stretches of guanines even on double-stranded DNA. Extrachromosomal assays showed that the G-quadruplex motifs could block transcription, leading to reduced expression of green fluorescent protein (GFP) within cells. More importantly, sodium bisulfite modification assay showed the single-stranded character at regions I and II of HOX11 in the genome. Thus, our findings suggest the occurrence of G-quadruplex structures at the HOX11 breakpoint region, which could explain its fragility during the t(10;14) translocation.

Fragility correlates thermodynamic and kinetic properties of glass forming liquids

In our earlier communication we proposed a simple fragility determining function, (NBO]/(VmTg)-T-3), which we have now used to analyze several glass systems using available thermal data. A comparison with similar fragility determining function, Delta C-p/C-p(1), introduced by Chryssikos et al. in their investigation of lithium borate glasses has also been performed and found to be more convenient quantity for discussing fragilities. We now propose a new function which uses both Delta C-p and Delta T and which gives a numerical fragility parameter, F whose value lies between 0 and 1 for glass forming liquids. F can be calculated through the use of measured thermal parameters Delta C-p, C-p(1), T-g and T-m. Use of the new fragility values in reduced viscosity equation reproduces the whole range of viscosity curves of the Angell plot. The reduced viscosity equation can be directly compared with the Adam-Gibbs viscosity equation and a heat capacity function can be formulated which reproduces satisfactorily the Delta C-p versus In(T-r) curves and hence the configurational entropy. (C) 2014 Elsevier Ltd. All rights reserved.

Fragility correlates thermodynamic and kinetic properties of glass forming liquids

In our earlier communication we proposed a simple fragility determining function, (NBO]/(VmTg)-T-3), which we have now used to analyze several glass systems using available thermal data. A comparison with similar fragility determining function, Delta C-p/C-p(1), introduced by Chryssikos et al. in their investigation of lithium borate glasses has also been performed and found to be more convenient quantity for discussing fragilities. We now propose a new function which uses both Delta C-p and Delta T and which gives a numerical fragility parameter, F whose value lies between 0 and 1 for glass forming liquids. F can be calculated through the use of measured thermal parameters Delta C-p, C-p(1), T-g and T-m. Use of the new fragility values in reduced viscosity equation reproduces the whole range of viscosity curves of the Angell plot. The reduced viscosity equation can be directly compared with the Adam-Gibbs viscosity equation and a heat capacity function can be formulated which reproduces satisfactorily the Delta C-p versus In(T-r) curves and hence the configurational entropy. (C) 2014 Elsevier Ltd. All rights reserved.

Unusual Fragility and Cooperativity in Glass-Forming and Crystalline PVDF/PMMA Blends in the Presence of Multiwall Carbon Nanotubes

Poly(vinylidene fluoride) (PVDF) and poly(methyl methacrylate) (PMMA) are completely miscible below 50 wt % PVDF in the blends. In this work, an attempt was made to understand the fragility/cooperativity relation in glass-forming and crystalline blends of PVDF/PMMA and in the presence of a heteronucleating agent, multiwall carbon nanotubes (CNTs). Hence, three representative blends were chosen: a completely amorphous (10/90 by wt, PVDF/PMMA), on the verge of amorphous miscibility (50/50 by wt, PVDF/PMMA), and crystalline (60/40 by wt, PVDF/PMMA) blends. The intermolecular cooperativity/coupling, fragility, and configurational entropy near the glass transition temperature (T-g) were studied using differential scanning calorimetry (DSC) and broadband dielectric relaxation spectroscopy (DRS). It was observed that the blends with higher concentration of PMMA were more fragile (fragility index m = 141) and those with higher concentration of PVDF were more strong (m = 78). Interestingly, the coupling was less in the glass-forming blends (10/90 by wt, PVDF/PMMA) than the crystalline blends as manifested from DRS. This observation was also supported by DSC measurements which reflected that the cooperative rearranging region (CRR) existed over a smaller length scales in fragile blends as compared to strong blends, possibly due to restricted amorphous mobility. This effect was more prominent in the presence of CNTs, in particular for 50/50 (by wt) and 60/40 (by wt) PVDF/PMMA blends. Further, the configurational entropy, as manifested from DRS, decreased significantly in the strong blends in striking contrast to the fragile blends, supported by DSC, which manifested in an increase in the volume of cooperativity in the strong blends. The higher coupling in the crystalline blends can be attributed to good packing of the amorphous regions. While this is understood for crystalline blends (60/40 by wt, PVDF/PMMA), it is envisaged that enhanced dynamic heterogeneity is accountable for increased coupling in the case of blends which are on the verge of amorphous miscibility (50/50 by wt, PVDF/PMMA). The latter is also supported by broad relaxations near the T-g in DRS. Interestingly, the intermolecular coupling in the blends in the presence of CNTs has reduced, though the potential energy barrier hindering the rearrangement of CRR is lower than the blends without CNTs. In addition, the amorphous packing is not as effective as the blends without CNTs. This is manifested from reduced volume of cooperativity in particular, for 50/50 (by wt) and 60/40 (by wt) blends.

ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water

Using electron spin resonance spectroscopy (ESR), we measure the rotational mobility of probe molecules highly diluted in deeply supercooled bulk water and negligibly constrained by the possible ice fraction. The mobility increases above the putative glass transition temperature of water, T-g = 136 K, and smoothly connects to the thermodynamically stable region by traversing the so called "no man's land" (the range 150-235 K), where it is believed that the homogeneous nucleation of ice suppresses the liquid water. Two coexisting fractions of the probe molecules are evidenced. The 2 fractions exhibit different mobility and fragility; the slower one is thermally activated (low fragility) and is larger at low temperatures below a fragile-to-strong dynamic cross-over at approximate to 225 K. The reorientation of the probe molecules decouples from the viscosity below approximate to 225 K. The translational diffusion of water exhibits a corresponding decoupling at the same temperature [Chen S-H, et al. (2006) The violation of the Stokes-Einstein relation in supercooled water. Proc Natl Acad Sci USA 103:12974-12978]. The present findings are consistent with key issues concerning both the statics and the dynamics of supercooled water, namely the large structural fluctuations [Poole PH, Sciortino F, Essmann U, Stanley HE (1992) Phase behavior of metastable water. Nature 360: 324-328] and the fragile-to-strong dynamic cross-over at approximate to 228 K [Ito K, Moynihan CT, Angell CA (1999) Thermodynamic determination of fragility in liquids and a fragile-tostrong liquid transition in water. Nature 398: 492-494].

Acute toxicity of methyl isocyanate in rabbit: In vitro and in vivo effects on rabbit erythrocyte membrane

Methyl isocyanate (MIC) interaction with the rabbit erythrocyte membrane increased the fluidity of the membrane and decreased the osmotic fragility of erythrocytes both in vitro and in vivo in rabbits intoxicated with MIC subcutaneously. MIC inhibited both acetylcholinesterase (AChE) and adenosine triphosphatase (ATPase) activities of erythrocytes dose-dependently in vitro, while in vivo a decreased trend in ATPase activity with unaltered AChE activity was observed. MIC also caused significant decrease in plasma sodium level with corresponding increase in potassium level in rabbits. The observed effects are due to MIC, per se, as the hydrolysis products of MIC, methylamine and N,Nprime-dimethylurea did not affect the erythrocyte fluidity and enzymes activities both in vitro and in vivo while they increased the osmotic fragility of erythrocytes in vivo in rabbits administered subcutaneously in equimolar concentration to MIC dosage. Inhibition of Na+-K+-dependent ATPase with altered permeability to cations and also probably water transport of plasma membrane due to MIC interaction are envisaged.

Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3'-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.

Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3'-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.

A chemical approach to understand fragilities of glass-forming liquids

Fragility is viewed as a measure of the loss of rigidity of a glass structure above its glass transition temperature. It is attributed to the weakness of directional bonding and to the presence of a high density of low-energy configurational states. An a priori fragility function of electronegativities and bond distances is proposed which quite remarkably reproduces the entire range of reported fragilities and demonstrates that the fragility of a melt is indeed encrypted in the chemistry of the parent material. It has also been shown that the use of fragility-modified activation barriers in the Arrhenius function account for the whole gamut of viscosity behavior of liquids. It is shown that fragility can be a universal scaling parameter to collapse all viscosity curves on to a master plot.

Molecular Dynamics of Thermotropic Liquid Crystals: Anomalous relaxation dynamics of calamitic and discotic liquid crystals

Recent optical kerr effect (OKE) studies have demonstrated that orientational relaxation of rod-like nematogens exhibits temporal power law decay at intermediate times not only near the isotropic–nematic (I–N) phase boundary but also in the nematic phase. Such behaviour has drawn an intriguing analogy with supercooled liquids. We have investigated both collective and single-particle orientational dynamics of a family of model system of thermotropic liquid crystals using extensive computer simulations. Several remarkable features of glassy dynamics are on display including non-exponential relaxation, dynamical heterogeneity, and non-Arrhenius temperature dependence of the orientational relaxation time. Over a temperature range near the I–N phase boundary, the system behaves remarkably like a fragile glass-forming liquid. Using proper scaling, we construct the usual relaxation time versus inverse temperature plot and explicitly demonstrate that one can successfully define a density dependent fragility of liquid crystals. The fragility of liquid crystals shows a temperature and density dependence which is remarkably similar to the fragility of glass forming supercooled liquids. Energy landscape analysis of inherent structures shows that the breakdown of the Arrhenius temperature dependence of relaxation rate occurs at a temperature that marks the onset of the growth of the depth of the potential energy minima explored by the system. A model liquid crystal, consisting of disk-like molecules, has also been investigated in molecular dynamics simulations for orientational relaxation along two isobars starting from the high temperature isotropic phase. The isobars have been so chosen that the phase sequence isotropic (I)–nematic (N)–columnar (C) appears upon cooling along one of them and the sequence isotropic (I)–columnar(C) along the other. While the orientational relaxation in the isotropic phase near the I–N phase transition shows a power law decay at short to intermediate times, such power law relaxation is not observed in the isotropic phase near the I–C phase boundary. The origin of the power law decay in the single-particle second-rank orientational time correlation function (OTCF) is traced to the growth of the orientational pair distribution functions near the I–N phase boundary. As the system settles into the nematic phase, the decay of the single-particle second-rank orientational OTCF follows a pattern that is similar to what is observed with calamitic liquid crystals and supercooled molecular liquids.