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At least 1,423 records · Page 79

Submonomer synthesis of sequence defined peptoids with diverse side-chains.

Peptoids are a diverse family of sequence-defined oligomers of N-substituted glycine monomers, that can be readily accessed by the solid-phase submonomer synthesis method. Due to the versatility and efficiency of this chemistry, and the easy access to hundreds of potential monomers, there is an enormous potential sequence space that can be explored. This has enabled researchers from many different fields to custom-design peptoid sequences tailored to a wide variety of problems in biomedicine, nanoscience and polymer science. Here we provide detailed protocols for the synthesis of peptoids, using optimized protocols that can be performed by non-chemists. The submonomer method is fully compatible with Fmoc-peptide synthesis conditions, so the method is readily automated on existing automated peptide synthesizers using protocols provided here. Although the submonomer synthesis for peptoids is well established, there are special considerations required in order to access many of the most useful and desirable sidechains. Here we provide methods to include most of the amino-acid-like side chains, some of the most important non-natural monomer classes, as well as the creation of peptoid conjugates and peptide-peptoid hybrids.

Connolly, Michael D↗

Measurement-induced disturbance and thermal negativity in 1D optical lattice chain

We study the measurement-induced disturbance (MID) in a 1D optical lattice chain with nonlinear coupling. Special attention is paid to the difference between the thermal entanglement and MID when considering the influences of the linear coupling constant, nonlinear coupling constant and external magnetic field. It is shown that MID is more robust than thermal entanglement against temperature T and external magnetic field B, and MID may reveal more properties about quantum correlations of the system, which can be seen from the point of view that MID can be nonzero when there is no thermal entanglement and MID can detect the critical point of quantum phase transition at finite temperature. - Highlights: Black-Right-Pointing-Pointer The nonlinear coupling constant can strengthen the quantum correlation. Black-Right-Pointing-Pointer MID is more robust than entanglement against temperature and magnetic field. Black-Right-Pointing-Pointer MID exhibits more information about quantum correlation than entanglement. Black-Right-Pointing-Pointer MID can detect the critical point of quantum phase transition at finite temperature.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The Haldane–Shastry spin chain and the topological basis realization

In this paper, based on the topological basis states, we investigate the Hamiltonian family (H{sub 2},H{sub 3},H{sub 4}) of a closed four-qubit Haldane–Shastry spin chain. Not only the two-qubit interaction form, but also the three-qubit interaction form and the four-qubit interaction form are presented in terms of spin operators. Meanwhile, we explore some particular properties of the topological basis states in these systems. With Yangian algebra, the symmetry of the systems and the transitions between the eigenstates have been investigated. We find a really useful effect of Y(sl(2)) operators (J{sub ±},J{sub 3}), which is that they can describe the transitions between the spin single state and the spin triple states. Furthermore, we construct a new Hamiltonian, whose energy degeneracies can be changed by adjusting the strengths of the two-qubit interactions, three-qubit interactions, four-qubit interactions, and the external magnetic field. -- Highlights: •We study the Haldane–Shastry model based on the topological basis realization. •Really useful effects of Yangian operators are found. •We explore some particular properties of the topological basis in these systems. •We construct a new Hamiltonian whose energy degeneracy can be changed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Semiclassical prediction of large spectral fluctuations in interacting kicked spin chains

While plenty of results have been obtained for single-particle quantum systems with chaotic dynamics through a semiclassical theory, much less is known about quantum chaos in the many-body setting. We contribute to recent efforts to make a semiclassical analysis of many-body systems feasible. This is nontrivial due to both the enormous density of states and the exponential proliferation of periodic orbits with the number of particles. As a model system we study kicked interacting spin chains employing semiclassical methods supplemented by a newly developed duality approach. We show that for this model the line between integrability and chaos becomes blurred. Due to the interaction structure the system features (non-isolated) manifolds of periodic orbits possessing highly correlated, collective dynamics. As with the invariant tori in integrable systems, their presence lead to significantly enhanced spectral fluctuations, which by order of magnitude lie in-between integrable and chaotic cases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Thermal quantum coherence and correlation in the extended XY spin chain

Quantum coherence and correlation of thermal states in the extended XY spin chain are studied in terms of the recently proposed l{sub 1} norm, skew information, and Bures distance of geometry discord (BGD), respectively. The entanglement measured via concurrence is calculated for reference. A two-dimensional susceptibility is introduced to explore their capability in highlighting the critical lines associated with quantum phase transitions in the model. It is shown that the susceptibility of the skew information and BGD is a genuine indicator of quantum phase transitions, and characterizes the factorization. However, the l{sub 1} norm is trivial for the factorization. An explicit scaling law of BGD is captured at low temperature in the XY model. In contrast to the entanglement, quantum coherence reveals a kind of long-range nonclassical correlation. Moreover, the obvious relation among model parameters is extracted for the factorized line in the extended model. Those are instructive for the understanding of quantum coherence and correlation in the theory of quantum information, and quantum phase transitions and factorization in condensed-matter physics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Correlation functions for a spin-(1/2) Ising-XYZ diamond chain: Further evidence for quasi-phases and pseudo-transitions

One-dimensional systems with short-range interactions cannot exhibit a long-range order at nonzero temperature. However, there are some particular one-dimensional models, such as the Ising–Heisenberg spin models with a variety of lattice geometries, which exhibit unexpected behavior similar to the discontinuous or continuous temperature-driven phase transition. Although these pseudo-transitions are not true temperature-driven transitions showing only abrupt changes or sharp peaks in thermodynamic quantities, they may be confused while interpreting experimental data. Here we consider the spin-(1/2) Ising-XYZ diamond chain in the regime when the model exhibits temperature-driven pseudo-transitions. We provide a detailed investigation of several correlation functions between distant spins that illustrates the properties of quasi-phases separated by pseudo-transitions. Inevitably, all correlation functions show the evidence of pseudo-transition, which are supported by the analytical solutions and, besides we provide a rigorous analytical investigation around the pseudo-critical temperature. It is worth to mention that the correlation functions between distant spins have an extremely large correlation length at pseudo-critical temperature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Diagonal entropy and topological phase transitions in extended Kitaev chains

We investigate the diagonal entropy for ground states of the extended Kitaev chains with extensive pairing and hopping terms. The systems contain rich topological phases equivalently represented by topological invariant winding numbers and Majorana zero modes. Both the finite size scaling law and block scaling law of the diagonal entropy are studied, which indicates that the diagonal entropy demonstrates volume effect. The parameter of volume term is regarded as the diagonal entropy density, which can identify the critical points of symmetry-protected topological phase transitions efficiently in the studied models, even for those with higher winding numbers. The formulation of block scaling law and the capability of diagonal entropy density in detecting topological phase transitions are independent of the chosen bases. In order to manifest the advantage of diagonal entropy, we also calculate the global entanglement, which cannot show clear signatures of the topological phase transitions. This work provides a new quantum-informatic approach to characterize the feature of the topologically ordered states and may motivate a deep understanding of the quantum coherence and diagonal entropy in various condensed matter systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Exact bounds for dynamical critical exponents of transverse-field Ising chains with a correlated disorder

Highlights: • Analytic results in disordered quantum systems are obtained. • Correlated disorder changes the universality class of quantum phase transitions. • The lower and upper bounds of the dynamical critical exponent are obtained. This study investigates the dynamical critical exponent of disordered Ising chains under transverse fields to examine the effect of a correlated disorder on quantum phase transitions. The correlated disorder, where the on-site transverse field depends on the nearest-neighbor coupling strengths connecting the site, gives a qualitatively different result from the uncorrelated disorder. In the uncorrelated disorder cases where the transverse field is either homogeneous over sites or random independently of the nearest-neighbor coupling strengths, the dynamical critical exponent is infinite. In contrast, in the presence of the correlated disorder, we analytically show that the dynamical critical exponent is finite. We also show that the dynamical critical exponent depends on the tuning process of the transverse field strengths.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The NDUFB6 subunit of the mitochondrial respiratory chain complex I is required for electron transfer activity: A proof of principle study on stable and controlled RNA interference in human cell lines

Highlights: {yields} NDUFB6 is required for activity of mitochondrial complex I in human cell lines. {yields} Lentivirus based RNA interference results in frequent off target insertions. {yields} Flp-In recombinase mediated miRNA insertion allows gene-specific extinction. -- Abstract: Molecular bases of inherited deficiencies of mitochondrial respiratory chain complex I are still unknown in a high proportion of patients. Among 45 subunits making up this large complex, more than half has unknown function(s). Understanding the function of these subunits would contribute to our knowledge on mitochondrial physiology but might also reveal that some of these subunits are not required for the catalytic activity of the complex. A direct consequence of this finding would be the reduction of the number of candidate genes to be sequenced in patients with decreased complex I activity. In this study, we tested two different methods to stably extinct complex I subunits in cultured cells. We first found that lentivirus-mediated shRNA expression frequently resulted in the unpredicted extinction of additional gene(s) beside targeted ones. This can be ascribed to uncontrolled genetic material insertions in the genome of the host cell. This approach thus appeared inappropriate to study unknown functions of a gene. Next, we found it possible to specifically extinct a CI subunit gene by direct insertion of a miR targeting CI subunits in a Flp site (HEK293 Flp-In cells). By using this strategy we unambiguously demonstrated that the NDUFB6 subunit is required for complex I activity, and defined conditions suitable to undertake a systematic and stable extinction of the different supernumerary subunits in human cells.

60 APPLIED LIFE SCIENCES↗

Analysis of various types of single-polypeptide-chain (sc) heterodimeric A{sub 2A}R/D{sub 2}R complexes and their allosteric receptor–receptor interactions

Highlights: • Various scA{sub 2A}R/D{sub 2}R constructs, with spacers between the two receptors, were created. • Using whole cell binding assay, constructs were examined for their binding activity. • Although the apparent ratio of A{sub 2A}R to D{sub 2}R binding sites should be 1, neither was 1. • Counter agonist-independent binding cooperativity occurred in context of scA{sub 2A}R/D{sub 2}R. - Abstract: Adenosine A{sub 2A} receptor (A{sub 2A}R) heteromerizes with dopamine D{sub 2} receptor (D{sub 2}R). However, these class A G protein-coupled receptor (GPCR) dimers are not fully formed, but depend on the equilibrium between monomer and dimer. In order to stimulate the heteromerization, we have previously shown a successful design for a fusion receptor, single-polypeptide-chain (sc) heterodimeric A{sub 2A}R/D{sub 2}R complex. Here, using whole cell binding assay, six more different scA{sub 2A}R/D{sub 2}R constructs were examined. Not only in scA{sub 2A}R/D{sub 2}R ‘liberated’ with longer spacers between the two receptors, which confer the same configuration as the prototype, the A{sub 2A}R-odr4TM-D{sub 2L}R, but differ in size (Forms 1–3), but also in scA{sub 2A}R/D{sub 2L}R (Form 6) fused with a transmembrane (TM) of another type II TM protein, instead of odr4TM, neither of their fixed stoichiometry (the apparent ratios of A{sub 2A}R to D{sub 2}R binding sites) was 1, suggesting their compact folding. This suggests that type II TM, either odr4 or another, facilitates the equilibrial process of the dimer formation between A{sub 2A}R and D{sub 2L}R, resulting in the higher-order oligomer formation from monomer of scA{sub 2A}R/D{sub 2L}R itself. Also, in the reverse type scA{sub 2A}R/D{sub 2L}R, i.e., the D{sub 2L}R-odr4TM-A{sub 2A}R, counter agonist-independent binding cooperativity (cooperative folding) was found to occur (Forms 4 and 5). In this way, the scA{sub 2A}R/D{sub 2L}R system has unveiled the cellular phenomenon as a snapshot of the molecular behavior in A{sub 2A}R/D{sub 2L}R dimer. Thus, these results indicate that the various designed types of functional A{sub 2A}R/D{sub 2}R exist even in living cells and that this fusion expression system would be useful to analyze as a model of the interaction between class A GPCRs.

60 APPLIED LIFE SCIENCES↗

Short-chain C6 ceramide sensitizes AT406-induced anti-pancreatic cancer cell activity

Our previous study has shown that AT406, a first-in-class small molecular antagonist of IAPs (inhibitor of apoptosis proteins), inhibits pancreatic cancer cell proliferation in vitro and in vivo. The aim of this research is to increase AT406's sensitivity by adding short-chain C6 ceramide. We show that co-treatment of C6 ceramide dramatically potentiated AT406-induced caspase/apoptosis activation and cytotoxicity in established (Panc-1 and Mia-PaCa-2 lines) and primary human pancreatic cancer cells. Reversely, caspase inhibitors largely attenuated C6 ceramide plus AT406-induced above cancer cell death. Molecularly, C6 ceramide downregulated Bcl-2 to increase AT406's sensitivity in pancreatic cancer cells. Intriguingly, C6 ceramide-mediated AT406 sensitization was nullified with Bcl-2 shRNA knockdown or pretreatment of the Bcl-2 inhibitor ABT-737. In vivo, liposomal C6 ceramide plus AT406 co-administration dramatically inhibited Panc-1 xenograft tumor growth in severe combined immunodeficient (SCID) mice. The combined anti-tumor activity was significantly more potent than either single treatment. Expressions of IAPs (cIAP1/XIAP) and Bcl-2 were downregulated in Panc-1 xenografts with the co-administration. Together, we demonstrate that C6 ceramide sensitizes AT406-mediated anti-pancreatic cancer cell activity possibly via downregulating Bcl-2. - Highlights: • C6 ceramide dramatically potentiates AT406-induced pancreatic cancer cell death. • C6 ceramide facilitates AT406-induced pancreatic cancer cell apoptosis. • C6 ceramide downregulates Bcl-2 to increase AT406's sensitivity in pancreatic cancer cells. • Liposomal C6 ceramide enhances AT406-induced anti-pancreatic cancer activity in vivo.

60 APPLIED LIFE SCIENCES↗

Tracking protons from respiratory chain complexes to ATP synthase c-subunit: The critical role of serine and threonine residues

F{sub 1}F{sub o}-ATP synthase is a multisubunit enzyme responsible for the synthesis of ATP. Among its multiple subunits (8 in E. coli, 17 in yeast S. cerevisiae, 16 in vertebrates), two subunits a and c are known to play a central role controlling the H{sup +} flow through the inner mitochondrial membrane which allows the subsequent synthesis of ATP, but the pathway followed by H{sup +} within the two proteins is still a matter of debate. In fact, even though the structure of ATP synthase is now well defined, the molecular mechanisms determining the function of both F{sub 1} and F{sub O} domains are still largely unknown. In this study, we propose a pathway for proton migration along the ATP synthase by hydrogen-bonded chain mechanism, with a key role of serine and threonine residues, by X-ray diffraction data on the subunit a of E. coli Fo.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A point mutation in the heavy chain complementarity-determining region 3 (HCDR3) significantly enhances the specificity of an anti-ROS1 antibody

The proto-oncogene tyrosine kinase ROS1 plays a key role in carcinogenesis through gene rearrangement to form a fusion protein with other genes, in which the C-terminal intracellular region of ROS1 participates. The possibility of wild type ROS1 overexpression through epigenetic regulation has been proposed. Here, we generated an antibody, 3B20, reactive to the N-terminal region of ROS1 to use it for the detection of wild type ROS1 in cancerous tissues. Using immunoblot and immunoprecipitation analyses, we found that 3B20 also reacted with heat shock proteins (Hsp)70s. Using homology searching, ROS1 and Hsp70s were found to share an identical amino acid sequence: DLGT. Using alanine mutagenesis of ROS1, the epitope was found to harbor this sequence. To modify the idiotope with the aim of selecting more specific antibodies, we introduced random mutations into the heavy chain complementarity-determining region 3 and successfully generated an antibody clone, 3B20-G1K, with a point mutation that only reacted with ROS1 in enzyme-linked immunosorbent assays, and in immunoblot and immunoprecipitation analysis. In immunohistochemical analysis using 3B20-G1K, ROS1 was found to be absent in normal lung tissues and was overexpressed in a case of lung adenocarcinoma. - Highlights: • An antibody to N-terminal region of ROS1 was generated. • Modification of HCDR3 dramatically enhanced the specificity of an anti-ROS1 antibody. • Full-length wild type ROS1 is not detected in normal lung tissue. • Full-length wild type ROS1 is overexpressed in 10% of lung adenocarcinoma.

60 APPLIED LIFE SCIENCES↗

Increased mortality from influenza infection in long-chain acyl-CoA dehydrogenase knockout mice

Highlights: • LCAD−/− mice show increased mortality after influenza infection. • LCAD−/− mice exhibit equal or less lung injury depending upon the influenza strain. • LCAD−/− mice lose more body weight and become more hypothermic during infection. We previously showed that the mitochondrial fatty acid oxidation enzyme long-chain acyl-CoA dehydrogenase (LCAD) is expressed in alveolar type II pneumocytes and that LCAD−/− mice have altered breathing mechanics and surfactant defects. Here, we hypothesized that LCAD−/− mice would be susceptible to influenza infection. Indeed, LCAD−/− mice demonstrated increased mortality following infection with 2009 pandemic influenza (A/CA/07/09). However, the mortality was not due to increased lung injury, as inflammatory cell counts, viral titers, and histology scores all showed non-significant trends toward milder injury in LCAD−/− mice. To confirm this, LCAD−/− were infected with a second, mouse-adapted H1N1 virus (A/PR/8/34), to which they responded with significantly less lung injury. While both strains become increasingly hypoglycemic over the first week post-infection, LCAD−/− mice lose body weight more rapidly than wild-type mice. Surprisingly, while acutely fasted LCAD−/− mice develop hepatic steatosis, influenza-infected LCAD−/− mice do not. They do, however, become more hypothermic than wild-type mice and demonstrate increased blood lactate values. We conclude that LCAD−/− mice succumb to influenza from bioenergetic starvation, likely due to increased reliance upon glucose for energy.

60 APPLIED LIFE SCIENCES↗

MicroRNA-139-5p suppresses myosin heavy chain I and IIa expression via inhibition of the calcineurin/NFAT signaling pathway

Highlights: • MiR-139-5p was higher in mouse slow-twitch than in fast-twitch muscle. • MiR-139-5p overexpression downregulated the expression of MyHC I and MyHC IIa. • CaN/NFAT signaling was notably inhibited by miR-139-5p overexpression. • MiR-139-5p suppressed MyHC I and IIa expression via inhibiting CaN/NFAT signaling. MicroRNAs (miRNAs) are a class of small non-coding RNAs that are widely involved in a variety of biological processes. Different skeletal muscle fiber type composition exhibits characteristic differences in functional properties and energy metabolism of skeletal muscle. However, the molecular mechanism by which miRNAs control the different type of muscle fiber formation is still not fully understood. In the present study, we characterized the role of microRNA-139-5p (miR-139-5p) in the regulation of myosin heavy chain (MyHC) isoform expression and its underlying mechanisms. Here we found that the expression of miR-139-5p was significantly higher in mouse slow-twitch muscle than in fast-twitch muscle. Overexpression of miR-139-5p downregulated the expression of MyHC I and MyHC IIa, whereas inhibition of miR-139-5p upregulated them. We also found that the levels of calcineurin (CaN), NFATc1, MEF2C and MCIP1.4, which are the components of CaN/NFAT signaling pathway that has shown to positively regulate slow fiber-selective gene expression, were notably inhibited by miR-139-5p overexpression. Furthermore, treatment of phenylephrine (PE), a α1-adrenoceptor agonist, abolished the inhibitory effect of miR-139-5p on MyHC I and MyHC IIa expression. Together, our findings indicated that the role of miR-139-5p in regulating the MyHC isoforms, especially MyHC I and MyHC IIa, may be achieved through inhibiting CaN/NFAT signaling pathway.

60 APPLIED LIFE SCIENCES↗

Molecular characterization of single-chain antibody variable fragments (scFv) specific to Pep27 from Streptococcus pneumoniae

Highlights: • Two antibody fragments specific to pneumococcal autolysis factor Pep27 are selected. • The antibody fragments show sub-micromolar affinity with good selectivity. • Molecular docking supports epitope on Pep27 identified by alanine scanning. Pep27 from Streptococcus pneumoniae is reported to initiate pneumococcal autolysis, thereby constituting a major virulence factor. Although a few antisera recognizing Pep27 have been reported, no monoclonal, well-characterized antibody for Pep27 has been developed. Here we screened two single-chain antibody variable fragments (scFv) using a phage display from a large human synthetic scFv library to select clones E2 and F9. Dissociation constants (K{sub d}) of E2 and F9 were 1.1 μM and 0.50 μM, respectively. E2 and F9 did not cross-react with other pneumococcal and unrelated proteins. The epitopes of Pep27 were localized to residues 24, 26 and 27 by alanine scanning. Molecular docking analysis supported the experimentally investigated epitope. The E2 and F9 clones specifically detected Pep27 in an environment mimicking in vivo conditions, demonstrated in human serum. The scFv clones characterized here represent molecular tools for the detection of pneumococcal diseases with potential for further improvement in affinity.

60 APPLIED LIFE SCIENCES↗

Targeted cancer cell ablation in mice by an α-particle-emitting astatine-211-labeled antibody against major histocompatibility complex class I chain-related protein A and B

Highlights: • MICA/B is expressed in several human cancer cells. • We generated an α-particle-emitting {sup 211}At-labelled antibody targeting MICA/B. • {sup 211}At-labelled antibody specifically killed human cancer cells expressing MICA/B. • {sup 211}At-labelled antibody targeting MICA/B showed anti-tumor activity in vivo. Major histocompatibility complex class I chain-related protein A and B (MICA/B) are ligands of the immune receptor, natural-killer group 2 member D. MICA/B expression is often found in several types of cancer but is restricted in normal tissues. Here, we show that an α-particle emitting astatine-211 ({sup 211}At)-labeled antibody targeting MICA/B ({sup 211}At-anti MICA/B Ab) efficiently ablates cancer cells in vitro and in vivo. We generated {sup 211}At-anti MICA/B Ab, an anti-MICA/B antibody conjugated with a highly cytotoxic α-particle emitting radionuclide {sup 211}At. {sup 211}At-anti MICA/B Ab binds to human osteosarcoma SaOS2 and U2OS cells that exhibit high levels of MICA/B expression and efficiently kills those cells in vitro. Biodistribution analysis using xenograft mouse models of HCT116 p53{sup −/−} positive for MICA/B expression, showed increased {sup 211}At in the xenografts for up to 22 h after injection as time proceeded. A single dose of {sup 211}At-anti MICA/B Ab (1 MBq) showed significant reduction in the tumor growth rate of HCT116 p53{sup −/−} xenografts compared to {sup 211}At-labeled mouse IgG (1 MBq) at 21 days after injection. No body weight loss and erythrocytopenia was evident in mice that received {sup 211}At-anti MICA/B. Leukocytopenia and thrombocytopenia were observed within a week after {sup 211}At-anti MICA/B injection, but counts of red blood cells and platelets were recovered to control levels at about 3–4 weeks after injection. Taken together, these data strongly demonstrate that targeted α-particle therapy using {sup 211}At-anti-MICA/B Ab emitting highly cytotoxic α-particles is a potential new therapeutic option for several types of cancer.

60 APPLIED LIFE SCIENCES↗

Human health benefits of very-long-chain polyunsaturated fatty acids from microalgae

Microalgae are single-cell, photosynthetic organisms whose biodiversity places them at the forefront of biological producers of high-value molecules including lipids and pigments. Some of these organisms particular are capable of synthesizing n-3 very long chain polyunsaturated fatty acids (VLC-PUFAs), known to have beneficial effects on human health. Indeed, VLC-PUFAs are the precursors of many signaling molecules in humans involved in the complexities of inflammatory processes. Herein, this mini-review provides an inventory of knowledge on the synthesis of VLC-PUFAs in microalgae and on the diversity of signaling molecules (prostanoids, leukotrienes, SPMs, EFOX, isoprostanoids) that arise in humans from VLC-PUFAs.

59 BASIC BIOLOGICAL SCIENCES↗