Combinatorial Crystal Synthesis: Structural Landscape of Phloroglucinol:1,2-bis(4-pyridyl)ethylene and Phloroglucinol:Phenazine

A large number of crystal forms, polymorphs and pseudopolymorphs, have been isolated in the phloroglucinol-dipyridylethylene (PGL:DPE) and phloroglucinol-phenazine (PGL:PHE) systems. An understanding of the intermolecular interactions and synthon preferences in these binary systems enables one to design a ternary molecular solid that consists of PGL, PHE, and DPE, and also others where DPE is replaced by other heterocycles. Clean isolation of these ternary cocrystals demonstrates synthon amplification during crystallization. These results point to the lesser likelihood of polymorphism in multicomponent crystals compared to single-component crystals. The appearance of several crystal forms during crystallization of a multicomponent system can be viewed as combinatorial crystal synthesis with synthon selection from a solution library. The resulting polymorphs and pseudopolymorphs that are obtained constitute a crystal structure landscape.

Mapping Post-translational Modifications of Mammalian Testicular Specific Histone Variant TH2B in Tetraploid and Haploid Germ Cells and Their Implications on the Dynamics of Nucleosome Structure

Histones regulate a variety of chromatin templated events by their post-translational modifications (PTMs). Although there are extensive reports on the PTMs of canonical histones, the information on the histone variants remains very scanty. Here, we report the identification of different PTMs, such as acetylation, methylation, and phosphorylation of a major mammalian histone variant TH2B. Our mass spectrometric analysis has led to the identification of both conserved and unique modifications across tetraploid spermatocytes and haploid spermatids. We have also computationally derived the 3-dimensional model of a TH2B containing nucleosome in order to study the spatial orientation of the PTMs identified and their effect on nucleosome stability and DNA binding potential. From our nucleosome model, it is evident that substititution of specific amino acid residues in TH2B results in both differential histone-DNA and histone-histone contacts. Furthermore, we have also observed that acetylation on the N-terminal tail of TH2B weakens the interactions with the DNA. These results provide direct evidence that, similar to somatic H2B, the testis specific histone TH2B also undergoes multiple PTMs, suggesting the possibility of chromatin regulation by such covalent modifications in mammalian male germ cells.

Exploring the Crystal Structure Landscape with a Heterosynthon Module: Fluorobenzoic Acid:1,2-Bis(4-pyridyl)ethylene 2:1 Cocrystals

The crystal structure landscape of the 2:1 benzoic acid:dipyridylethylene cocrystal (BA:DPE-I) is explored experimentally with fluoro-substituted benzoic acids and extended with studies employing the Cambridge Structural Database (CSD). The interpretation of the cocrystal landscape is facilitated by considering the kinetically favored and robust acidpyridine heterosynthon as a modular unit. Information based on high-throughput crystallography shows that polymorphs and pseudopolymorphs may belong to the same landscape but arise from different crystallization pathways because of complex and different kinetic features, and secondary synthon preferences. Using the CSD as a guide, the coformer was changed from 1,2-bis(4-pyridyl)ethylene (DPE-I) to 1,2-bis(4-pyridyl)ethane (DPE-II) and this provides an extended interpretation of the BA:DPE-I cocrystal landscape, also highlighting the complexity of the kineticthermodynamic dichotomy during the molecule-to-crystal progression.

LANDSCAPE DYNAMICS MODELING THROUGH INTEGRATED MARKOV, FUZZY-AHP AND CELLULAR AUTOMATA

Multi temporal land use information were derived using two decades remote sensing data and simulated for 2012 and 2020 with Cellular Automata (CA) considering scenarios, change probabilities (through Markov chain) and Multi Criteria Evaluation (MCE). Agents and constraints were considered for modeling the urbanization process. Agents were nornmlized through fiizzyfication and priority weights were assigned through Analytical Hierarchical Process (AHP) pairwise comparison for each factor (in MCE) to derive behavior-oriented rules of transition for each land use class. Simulation shows a good agreement with the classified data. Fuzzy and AHP helped in analyzing the effects of agents of growth clearly and CA-Markov proved as a powerful tool in modelling and helped in capturing and visualizing the spatiotemporal patterns of urbanization. This provided rapid land evaluation framework with the essential insights of the urban trajectory for effective sustainable city planning.

Reversible induction of translational isoforms of p53 in glucose deprivation

Tumor suppressor protein p53 is a master transcription regulator, indispensable for controlling several cellular pathways. Earlier work in our laboratory led to the identification of dual internal ribosome entry site (IRES) structure of p53 mRNA that regulates translation of full-length p53 and Delta 40p53. IRES-mediated translation of both isoforms is enhanced under different stress conditions that induce DNA damage, ionizing radiation and endoplasmic reticulum stress, oncogene-induced senescence and cancer. In this study, we addressed nutrient-mediated translational regulation of p53 mRNA using glucose depletion. In cell lines, this nutrient-depletion stress relatively induced p53 IRES activities from bicistronic reporter constructs with concomitant increase in levels of p53 isoforms. Surprisingly, we found scaffold/matrix attachment region-binding protein 1 (SMAR1), a predominantly nuclear protein is abundant in the cytoplasm under glucose deprivation. Importantly under these conditions polypyrimidine-tract-binding protein, an established p53 ITAF did not show nuclear-cytoplasmic relocalization highlighting the novelty of SMAR1-mediated control in stress. In vivo studies in mice revealed starvation-induced increase in SMAR1, p53 and Delta 40p53 levels that was reversible on dietary replenishment. SMAR1 associated with p53 IRES sequences ex vivo, with an increase in interaction on glucose starvation. RNAi-mediated-transient SMAR1 knockdown decreased p53 IRES activities in normal conditions and under glucose deprivation, this being reflected in changes in mRNAs in the p53 and Delta 40p53 target genes involved in cell-cycle arrest, metabolism and apoptosis such as p21, TIGAR and Bax. This study provides a new physiological insight into the regulation of this critical tumor suppressor in nutrient starvation, also suggesting important functions of the p53 isoforms in these conditions as evident from the downstream transcriptional target activation.

Crystal landscape in the orcinol:4,4 `-bipyridine system: synthon modularity, polymorphism and transferability of multipole charge density parameters

Polymorphism in the orcinol: 4,4'-bipyridine cocrystal system is analyzed in terms of a robust convergent modular phenol...pyridine supramolecular synthon. Employing the Synthon Based Fragments Approach (SBFA) to transfer the multipole charge density parameters, it is demonstrated that the crystal landscape can be quantified in terms of intermolecular interaction energies in the five crystal forms so far isolated in this complex system. There are five crystal forms. The first has an open, divergent O-H...N based structure with alternating orcinol and bipyridine molecules. The other four polymorphs have different three-dimensional packing but all of them are similar at an interaction level, and are based on a modular O-H...N mediated supramolecular synthon that consists of two orcinol and two bipyridine molecules in a closed, convergent structure. The SBFA method, which depends on the modularity of synthons, provides good agreement between experiment and theory because it takes into account the supramolecular contribution to charge density. The existence of five crystal forms in this system shows that polymorphism in cocrystals need not be considered to be an unusual phenomenon. Studies of the crystal landscape could lead to an understanding of the kinetic pathways that control the crystallization processes, in other words the valleys in the landscape. These pathways are traditionally not considered in exercises pertaining to computational crystal structure prediction, which rather monitors the thermodynamics of the various stable forms in the system, in other words the peaks in the landscape.

Relationship between entropy and diffusion: A statistical mechanical derivation of Rosenfeld expression for a rugged energy landscape

Diffusion-a measure of dynamics, and entropy-a measure of disorder in the system are found to be intimately correlated in many systems, and the correlation is often strongly non-linear. We explore the origin of this complex dependence by studying diffusion of a point Brownian particle on a model potential energy surface characterized by ruggedness. If we assume that the ruggedness has a Gaussian distribution, then for this model, one can obtain the excess entropy exactly for any dimension. By using the expression for the mean first passage time, we present a statistical mechanical derivation of the well-known and well-tested scaling relation proposed by Rosenfeld between diffusion and excess entropy. In anticipation that Rosenfeld diffusion-entropy scaling (RDES) relation may continue to be valid in higher dimensions (where the mean first passage time approach is not available), we carry out an effective medium approximation (EMA) based analysis of the effective transition rate and hence of the effective diffusion coefficient. We show that the EMA expression can be used to derive the RDES scaling relation for any dimension higher than unity. However, RDES is shown to break down in the presence of spatial correlation among the energy landscape values. (C) 2015 AIP Publishing LLC.

Effects of Translational Nonequilibrium on Performance of Flowing Chemical Oxygen-Iodine Laser

The effect of the translational nonequilibrium on performance modeling of flowing chemical oxygen-iodine lasers (COIL) is emphasized in this paper. The spectral line broadening (SLB) model is a basic factor for predicting the performances of flowing COIL. The Voigt profile function is a well-known SLB model and is usually utilized. In the case of gas pressure in laser cavity less than 5 torr, a low pressure limit expression of the Voigt profile function is used. These two SLB models imply that ail lasing particles can interact with monochromatic laser radiation. Basically, the inhomogeneous broadening effects are not considered in these two SLB models and they cannot predict the spectral content. The latter requires consideration of finite translational relaxation rate. Unfortunately, it is rather difficult to solve simultaneously the Navier-Stokes (NS) equations and the conservation equations of the number of lasing particles per unit volume and per unit frequency interval. In the operating condition of flowing COIL, it is possible to obtain a perturbational solution of the conservational equations for lasing particles and deduce a new relation between the gain and the optical intensity, i.e., a new gain-saturation relation. By coupling the gain-saturation relation with other governing equations (such as the NS equations, chemical reaction equations and the optical model of gain-equal-loss), We have numerically calculated the performances of flowing COIL. The present results are compared with those obtained by the common rate-equation (RE) model, in which the Voigt profile function and its low pressure limit expression are used. The difference of different model's results is great. For instance, in the case of lasing frequency coinciding with the central frequency of line profile and very low gas pressure, the gain-saturation relation of the present model is quite different with that of the RE model.

Landscape valuation through discrete choice experiments: Current practice and future research reflections

This work has been presented in: V Conference AERNA, Faro (Portugal), 30 May 2012-1 June 2012 and IV Workshop on Valuation Methods in Agro-food and Environmental Economics, Castelldefels (Barcelona, Spain), 12 July 2012-13 July 2012.

Phylogeography and non-invasive landscape genetics of the European pine marten ("martes martes" L. 1758) : insights into ancient and contemporary processes shaping genetic variation

283 p. : graf., map.

Influence of seagrass landscape structure on the juvenile blue crab habitat-survival function

Organismal survival in marine habitats is often positively correlated with habitat structural complexity at local (within-patch) spatial scales. Far less is known, however, about how marine habitat structure at the landscape scale influences predation and other ecological processes, and in particular, how these processes are dictated by the interactive effect of habitat structure at local and landscape scales. The relationship between survival and habitat structure can be modeled with the habitat-survival function (HSF), which often takes on linear, hyperbolic, or sigmoid forms. We used tethering experiments to determine how seagrass landscape structure influenced the HSF for juvenile blue crabs Callinectes sapidus Rathbun in Back Sound, North Carolina, USA. Crabs were tethered in artificial seagrass plots of 7 different shoot densities embedded within small (1 – 3 m2) or large (>100 m2) seagrass patches (October 1999), and within 10 × 10 m landscapes containing patchy (<50% cover) or continuous (>90% cover) seagrass (July 2000). Overall, crab survival was higher in small than in large patches, and was higher in patchy than in continuous seagrass. The HSF was hyperbolic in large patches and in continuous seagrass, indicating that at low levels of habitat structure, relatively small increases in structure resulted in substantial increases in juvenile blue crab survival. However, the HSF was linear in small seagrass patches in 1999 and was parabolic in patchy seagrass in 2000. A sigmoid HSF, in which a threshold level of seagrass structure is required for crab survival, was never observed. Patchy seagrass landscapes are valuable refuges for juvenile blue crabs, and the effects of seagrass structural complexity on crab survival can only be fully understood when habitat structure at larger scales is considered.

How do you change the learning landscape?

Analysis of the Changing the Learning Landscape strategic conversations with senior managers, staff and students in 58 institutions was undertaken in order to identify trends and direction of change in relation to technology-enhanced learning (TEL) and the student experience.

A view of the Assessment and Feedback Landscape: baseline analysis of policy and practice from the JISC Assessment and Feedback programme

Assessment and feedback lies at the heart of the learning experience, and forms a significant part of both academic and administrative workload. It remains however the single biggest source of student dissatisfaction with the higher education experience. The JISC Assessment and Feedback programme (Sept 2011-Aug 2014) is supporting large-scale changes in assessment and feedback practice, supported by technology, with the aim of enhancing the learning and teaching process and delivering efficiencies and quality improvements. This report summarises baseline reviews undertaken by a number of institutions as part of their programme activity.