Effect of methylene group insertions on the structural rigidity of Aib containing helices

Nonprotein amino acids are being extensively used in the design of synthetic peptides to create new structure mimics. In this study we report the effect of methylene group insertions in a heptapeptide Boc-Ala(1)-Leu(2)-Aib(3)-Xxx(4)-Ala(5)-Leu(6)-Aib(7)-OMe which nicely folds into a mixed 3(10)-/-helical structure when Xxx= Ala. Analogs of this peptide have been made and studied by replacing central Xxx(4) residue with Glycine (-residue), -Alanine (-la), -aminobutyric acid (Gaba), and epsilon-aminocaproic acid (epsilon-Aca). NMR and circular dichroism were used to study the solution structure of these peptides. Crystals of the peptides containing alanine, -la, and Gaba reveal that increasing the number of central methylene (-CH2-) groups introduces local perturbations even as the helical structure is retained. (c) 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 720-732, 2015.

Efficient density matrix renormalization group algorithm to study Y junctions with integer and half-integer spin

An efficient density matrix renormalization group (DMRG) algorithm is presented and applied to Y junctions, systems with three arms of n sites that meet at a central site. The accuracy is comparable to DMRG of chains. As in chains, new sites are always bonded to the most recently added sites and the superblock Hamiltonian contains only new or once renormalized operators. Junctions of up to N = 3n + 1 approximate to 500 sites are studied with antiferromagnetic (AF) Heisenberg exchange J between nearest-neighbor spins S or electron transfer t between nearest neighbors in half-filled Hubbard models. Exchange or electron transfer is exclusively between sites in two sublattices with N-A not equal N-B. The ground state (GS) and spin densities rho(r) = < S-r(z)> at site r are quite different for junctions with S = 1/2, 1, 3/2, and 2. The GS has finite total spin S-G = 2S(S) for even (odd) N and for M-G = S-G in the S-G spin manifold, rho(r) > 0(< 0) at sites of the larger (smaller) sublattice. S = 1/2 junctions have delocalized states and decreasing spin densities with increasing N. S = 1 junctions have four localized S-z = 1/2 states at the end of each arm and centered on the junction, consistent with localized states in S = 1 chains with finite Haldane gap. The GS of S = 3/2 or 2 junctions of up to 500 spins is a spin density wave with increased amplitude at the ends of arms or near the junction. Quantum fluctuations completely suppress AF order in S = 1/2 or 1 junctions, as well as in half-filled Hubbard junctions, but reduce rather than suppress AF order in S = 3/2 or 2 junctions.

Inhibition of p300 lysine acetyltransferase activity by luteolin reduces tumor growth in head and neck squamous cell carcinoma (HNSCC) xenograft mouse model

Chromatin acetylation is attributed with distinct functional relevance with respect to gene expression in normal and diseased conditions thereby leading to a topical interest in the concept of epigenetic modulators and therapy. We report here the identification and characterization of the acetylation inhibitory potential of an important dietary flavonoid, luteolin. Luteolin was found to inhibit p300 acetyltransferase with competitive binding to the acetyl CoA binding site. Luteolin treatment in a xenografted tumor model of head and neck squamous cell carcinoma (HNSCC), led to a dramatic reduction in tumor growth within 4 weeks corresponding to a decrease in histone acetylation. Cells treated with luteolin exhibit cell cycle arrest and decreased cell migration. Luteolin treatment led to an alteration in gene expression and miRNA profile including up-regulation of p53 induced miR-195/215, let7C; potentially translating into a tumor suppressor function. It also led to down regulation of oncomiRNAs such as miR-135a, thereby reflecting global changes in the microRNA network. Furthermore, a direct correlation between the inhibition of histone acetylation and gene expression was established using chromatin immunoprecipitation on promoters of differentially expressed genes. A network of dysregulated genes and miRNAs was mapped along with the gene ontology categories, and the effects of luteolin were observed to be potentially at multiple levels: at the level of gene expression, miRNA expression and miRNA processing.

Fourth order accurate compact scheme with group velocity control (GVC)

For solving complex flow field with multi-scale structure higher order accurate schemes are preferred. Among high order schemes the compact schemes have higher resolving efficiency. When the compact and upwind compact schemes are used to solve aerodynamic problems there are numerical oscillations near the shocks. The reason of oscillation production is because of non-uniform group velocity of wave packets in numerical solutions. For improvement of resolution of the shock a parameter function is introduced in compact scheme to control the group velocity. The newly developed method is simple. It has higher accuracy and less stencil of grid points.

Scheme Construction with Numerical Flux Residual Correction (NFRC) and Group Velocity Control (GVC)

For simulating multi-scale complex flow fields like turbulent flows, the high order accurate schemes are preferred. In this paper, a scheme construction with numerical flux residual correction (NFRC) is presented. Any order accurate difference approximation can be obtained with the NFRC. To improve the resolution of the shock, the constructed schemes are modified with group velocity control (GVC) and weighted group velocity control (WGVC). The method of scheme construction is simple, and it is used to solve practical problems.

Optimized Group Velocity Control Scheme and DNS of Decaying Compressible Turbulence of Relative High Turbulent Mach Number

To overcome the difficulty in the DNS of compressible turbulence at high turbulent Mach number, a new difference scheme called GVC8 is developed. We have succeeded in the direct numerical simulation of decaying compressible turbulence up to turbulent Mach number 0.95. The statistical quantities thus obtained at lower turbulent Mach number agree well with those from previous authors with the same initial conditions, but they are limited to simulate at lower turbulent Mach numbers due to the so-called start-up problem. The energy spectrum and coherent structure of compressible turbulent flow are analysed. The scaling law of compressible turbulence is studied. The computed results indicate that the extended self-similarity holds in decaying compressible turbulence despite the occurrence of shocklets, and compressibility has little effects on relative scaling exponents when turbulent Mach number is not very high.

The pottery from A and C-Group tombs at Serra West in the Museum of Natural History, La Plata

Abstract: The Museum of Natural History, La Plata, Argentina, houses a ceramic collection of the A-Group and C-Group cultures from Nubian tombs at Serra West (AA and ACS cemeteries), on the west bank of the Nile in Lower Nubia. It has been originated from the division after the excavations made by the Franco-Argentine Archaeological Expedition in Sudan between 1961 and 1963, as part of the UNESCO campaigns to save the Nubian monuments.

The Head-On Colliding Process Of Binary Liquid Droplets At Low Velocity: High-Speed Photography Experiments And Modeling

The experimental and theoretical studies are reported in this paper for the head-on collisions of a liquid droplet with another of the same fluid resting on a solid substrate. The droplet on the hydrophobic polydimethylsiloxane (PDMS) substrate remains in a shape of an approximately spherical segment and is isometric to an incoming droplet. The colliding process of the binary droplets was recorded with high-speed photography. Head-on collisions saw four different types of response in our experiments: complete rebound, coalescence, partial rebound With conglutination, and coalescence accompanied by conglutination. For a complete rebound, both droplets exhibited remarkable elasticity and the contact time of the two colliding droplets was found to be in the range of 10-20 ms. With both droplets approximately considered as elastic bodies, Hertz contact theory was introduced to estimate the contact time for the complete rebound case. The estimated result Was found to be on the same order of magnitude as the experimental data, which indicates that the present model is reasonable. (C) 2008 Elsevier Inc. All rights reserved.

Derivation Of A Nonlinear Reynolds Stress Model Using Renormalization Group Analysis And Two-Scale Expansion Technique

Adopting Yoshizawa's two-scale expansion technique, the fluctuating field is expanded around the isotropic field. The renormalization group method is applied for calculating the covariance of the fluctuating field at the lower order expansion. A nonlinear Reynolds stress model is derived and the turbulent constants inside are evaluated analytically. Compared with the two-scale direct interaction approximation analysis for turbulent shear flows proposed by Yoshizawa, the calculation is much more simple. The analytical model presented here is close to the Speziale model, which is widely applied in the numerical simulations for the complex turbulent flows.

The vector fields admitting one-parameter spatial symmetry group and their reduction

For a n-dimensional vector fields preserving some n-form, the following conclusion is reached by the method of Lie group. That is, if it admits an one-parameter, n-form preserving symmetry group, a transformation independent of the vector field is constructed explicitly, which can reduce not only dimesion of the vector field by one, but also make the reduced vector field preserve the corresponding ( n - 1)-form. In partic ular, while n = 3, an important result can be directly got which is given by Me,ie and Wiggins in 1994.

Renormalization group approach on nanostructured systems

The electronic spectra of one-dimensional nanostructured systems are calculated within the pure hopping model on the tight-binding Hamiltonian. By means of the renormalization group Green's function method, the dependence of the density of states on the distributions of nanoscaled grains and the changes of values of hopping integrals in nanostructured systems are studied. It is found that the frequency shifts are dependent rather on the changes of the hopping integrals at nanoscaled grains than the distribution of nanoscaled grains.

Tidal oscillations at the head of Monterey Submarine Canyon and their relation to oceanographic sampling and the circulation of water in Monterey Bay. Annual report, Part 6, September 1972

During a 25-hour hydrographic times series at two stations near the head of Monterey Submarine Canyon, an internal tide was observed with an amplitude of 80 to 115 m in water depths of 120 and 220 m respectively. These large oscillations produced daily variations in hydrographic and chemical parameters that were of the same magnitude as seasonal variations in Monterey Bay. Computed velocities associated with the internal tide were on the order of 10 em/sec, and this tidally induced circulation may have a significant role in the exchange of deep water between Monterey Submarine Canyon and the open ocean. (PDF contains 49 pages)

Report of the Study Group on “Ecosystem-Based Management Science and its application to the North Pacific”

EXECUTIVE SUMMARY INTRODUCTION OVERVIEW OF INTERNATIONAL EBM HISTORY References CANADA Overview Activities to date Integrated Management implementation in Canada Objectives, indicators and reference points Assessment approaches Research directions for the future Management directions for the future References JAPAN Overview Conservation and sustainable use of marine living resources Harvest control by TAC system Stock Recovery Plan and effort regulation system Stock enhancement by hatchery-produced juvenile release Conservation and sustainable develop-ment on coastal waters The implementation of ecosystem-based management PEOPLE’S REPUBLIC OF CHINA Overview Current actions Output control Input control Summer fishing ban Enhance ecosystem health REPUBLIC OF KOREA Initiatives and actions of ecosystem-based management in Korea Current ecosystem-based management initiatives in Korea Precautionary TAC-based fishery management Closed fishing season/areas Fish size- and sex-controls Fishing gear design restrictions Marine protected areas (MPA) RUSSIA Existing and anticipated ecosystem-based management initiatives Issues related to the implementation of ecosystem-based management UNITED STATES OF AMERICA Definitions and approaches to ecosystem-based fishery management in the United States Present U.S. legislative mandates relating to ecosystem-based fishery management Target species Bycatch species Threatened or endangered species Habitats Food webs Ecosystems Integration of legislative mandates into an ecosystem approach Scientific issues in implementing ecosystem-based approaches References DISCUSSION AND RECOMMENDATIONS APPENDICES Appendix 10.1 Study group membership and participants Appendix 10.2 Terminology definitions Appendix 10.3 Present state of implementing ecosystem-based fishery management in Alaska: Alaska groundfish fisheries Appendix 10.4 Present state of implementing ecosystem-based fishery management off the West Coast of the United States: Pacific Coast groundfish fisheries Appendix 10.5 Descriptions of multi-species and ecosystem models developed or under development in the U.S. North Pacific region that might be used to predict effects of fishing on ecosystems Appendix 10.6 A potential standard reporting format (developed by Australia, and currently being used by the U.S.A in their contribution to this report) (83 page document)

Report of the Study Group on “ Fisheries and Ecosystem Response to Recent Regime Shifts”

EXECUTIVE SUMMARY 1. DECADAL-SCALE CLIMATE EVENTS 1.1 Introduction 1.2 Basin-scale Patterns 1.3 Long Time Series in the North Pacific 1.4 Decadal Climate Variability in Ecological Regions of the North Pacific 1.5 Mechanisms 1.6 References 2. COHERENT REGIONAL RESPONSES 2.1 Introduction 2.2 Central North Pacific (CNP) 2.3 California Current System (CCS) 2.4 Gulf of Alaska (GOA) 2.5 Bering Sea and Aleutian Islands 2.6 Western North Pacific (WNP) 2.7 Coherence in Regional Responses to the 1998 Regime Shift 2.8 Climate Indicators for Detecting Regime Shifts 2.9 References 3. IMPLICATIONS FOR THE MANAGEMENT OF MARINE RESOURCES 3.1 Introduction 3.2 Response Time of Biota to Regime Shifts 3.3 Response Time of Management to Regime Shifts 3.4 Provision of Stock Assessment Advice 3.5 Decision Rules 3.6 References 4. SUGGESTED LITERATURE 4.1 Climate Regimes 4.2 Impacts on Lower Trophic Levels 4.3 Impacts on Fish and Higher Trophic Levels 4.4 Impacts on Ecosystems and Possible Mechanisms 4.5 Regimes and Fisheries Management APPENDIX 1: RECENT ECOSYSTEM CHANGES IN THE CENTRAL NORTH PACIFIC A1.1 Introduction A1.2 Physical Oceanography A1.3 Lower Trophic Levels A1.4 Invertebrates A1.5 Fishes A1.6 References APPENDIX 2: RECENT ECOSYSTEM CHANGES IN THE CALIFORNIA CURRENT SYSTEM A2.1 Introduction A2.2 Physical Oceanography A2.3 Lower Trophic Levels A2.4 Invertebrates A2.5 Fishes A2.6 References APPENDIX 3: RECENT ECOSYSTEM CHANGES IN THE GULF OF ALASKA A3.1 Introduction A3.2 Physical Oceanography A3.3 Lower Trophic Levels A3.4 Invertebrates A3.5 Fishes A3.6 Higher Trophic Levels A3.7 Coherence in Gulf of Alaska Fish A3.8 Combined Standardized Indices of Recruitment and Survival Rate A3.9 References APPENDIX 4: RECENT ECOSYSTEM CHANGES IN THE BERING SEA AND ALEUTIAN ISLANDS A4.1 Introduction A4.2 Bering Sea Environmental Variables and Physical Oceanography A4.3 Bering Sea Lower Trophic Levels A4.4 Bering Sea Invertebrates A4.5 Bering Sea Fishes A4.6 Bering Sea Higher Trophic Levels A4.7 Coherence in Bering Sea Fish Responses A4.8 Combined Standardized Indices of Bering Fish Recruitment and Survival Rate A4.9 Aleutian Islands A4.10 References APPENDIX 5: RECENT ECOSYSTEM CHANGES IN THE WESTERN NORTH PACIFIC A5.1 Introduction A5.2 Sea of Okhotsk A5.3 Tsushima Current Region and Kuroshio/Oyashio Current Region A5.4 Bohai Sea, Yellow Sea, and East China Sea A5.5 References (168 page document)