Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes

Plant resistance proteins (R proteins) recognize corresponding pathogen avirulence (Avr) proteins either indirectly through detection of changes in their host protein targets or through direct R-Avr protein interaction. Although indirect recognition imposes selection against Avr effector function, pathogen effector molecules recognized through direct interaction may overcome resistance through sequence diversification rather than loss of function. Here we show that the flax rust fungus AvrLS67 genes, whose products are recognized by the L5, L6, and L7 R proteins of flax, are highly diverse, with 12 sequence variants identified from six rust strains. Seven AvrL567 variants derived from Avr alleles induce necrotic responses when expressed in flax plants containing corresponding resistance genes (R genes), whereas five variants from avr alleles do not. Differences in recognition specificity between AvA567 variants and evidence for diversifying selection acting on these genes suggest they have been involved in a gene-specific arms race with the corresponding flax R genes. Yeast two-hybrid assays indicate that recognition is based on direct R-Avr protein interaction and recapitulate the interaction specificity observed in planta. Biochemical analysis of Escherichia coli-produced AvrL567 proteins shows that variants that escape recognition nevertheless maintain a conserved structure and stability, suggesting that the amino acid sequence differences directly affect the R-Avr protein interaction. We suggest that direct recognition associated with high genetic diversity at corresponding R and Avr gene loci represents an alternative outcome of plant-pathogen coevolution to indirect recognition associated with simple balanced polymorphisms for functional and nonfunctional R and Avr genes.

Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity:in silico bioinformatic step-by-step guide using quantitative structure-activity relationships

Quantitative structure-activity relationship (QSAR) analysis is a cornerstone of modern informatics. Predictive computational models of peptide-major histocompatibility complex (MHC)-binding affinity based on QSAR technology have now become important components of modern computational immunovaccinology. Historically, such approaches have been built around semiqualitative, classification methods, but these are now giving way to quantitative regression methods. We review three methods--a 2D-QSAR additive-partial least squares (PLS) and a 3D-QSAR comparative molecular similarity index analysis (CoMSIA) method--which can identify the sequence dependence of peptide-binding specificity for various class I MHC alleles from the reported binding affinities (IC50) of peptide sets. The third method is an iterative self-consistent (ISC) PLS-based additive method, which is a recently developed extension to the additive method for the affinity prediction of class II peptides. The QSAR methods presented here have established themselves as immunoinformatic techniques complementary to existing methodology, useful in the quantitative prediction of binding affinity: current methods for the in silico identification of T-cell epitopes (which form the basis of many vaccines, diagnostics, and reagents) rely on the accurate computational prediction of peptide-MHC affinity. We have reviewed various human and mouse class I and class II allele models. Studied alleles comprise HLA-A*0101, HLA-A*0201, HLA-A*0202, HLA-A*0203, HLA-A*0206, HLA-A*0301, HLA-A*1101, HLA-A*3101, HLA-A*6801, HLA-A*6802, HLA-B*3501, H2-K(k), H2-K(b), H2-D(b) HLA-DRB1*0101, HLA-DRB1*0401, HLA-DRB1*0701, I-A(b), I-A(d), I-A(k), I-A(S), I-E(d), and I-E(k). In this chapter we show a step-by-step guide into predicting the reliability and the resulting models to represent an advance on existing methods. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made are freely available online at the URL http://www.jenner.ac.uk/MHCPred.

Anisotropic surface energetics and wettability of macroscopic form I paracetamol crystals

Advancing (θA) and receding (θR) contact angles were measured with several probe liquids on the external facets (201), (001), (011), and (110) of macroscopic form I paracetamol crystals as well as the cleaved (internal) facet (010). For the external crystal facets, dispersive surface energies γd calculated from the contact angles were found to be similar (34 ± 1 mJ/m2), while the polar components varied significantly. Cleaving the crystals exposed a more apolar (010) surface with very different surface properties, including γd = 45 ± 1 mJ/m2. The relative surface polarity (γp/γ) of the facets in decreasing order was (001) > (011) > (201) > (110) > (010), which agreed with the fraction of exposed polar hydroxyl groups as determined from C and O 1s X-ray photoelectron spectroscopy (XPS) spectra, and could be correlated with the number of non-hydrogen-bonded hydroxyl groups per unit area present for each crystal facet, based on the known crystal structures. In conclusion, all facets of form I paracetamol crystals examined exhibited anisotropic wetting behavior and surface energetics that correlated to the presence of surface hydroxyl groups.  © 2006 American Chemical Society.

Incidentally Raised Cardiac Troponin I Has a Worse Prognosis in Older Patients Compared to Those with Normal Cardiac Troponin I and Patients with Acute Coronary Syndrome : A Cohort Study

Acknowledgement J.H.B.-S. was supported by the Norfolk and Norwich University Hospital (NNUH) Research and Development (R&D) research capability funds between July 2013 and December 2014.

The syntheses and characterization of nickel complexes; investigation of Ni(dppp)2 and [NiX(dppp)n]x, potentially catalytically active nickel(0)/(I) species for cross-coupling reactions

This thesis describes an investigation in which we compare Ni(0), Ni(I) and Ni(II) complexes containing 1,3-bis(diphenylphosphino)propane (dppp) as a phosphine ligand for their abilities to effect three types of cross-coupling reactions: Buchwald-Hartwig Amination, Heck-Mizoroki, and Suzuki-Miyaura cross-coupling reactions with different types of substrates. The Ni(0) complex Ni(dppp)2 is known and we have synthesized it via a new procedure involving zinc reduction of the known NiCl2(dppp) in the presence of an excess of dppp. The Ni(0) complex was characterized by NMR spectroscopy and X-ray crystallography. Since Ni(I) complexes of dppp seem unknown, we have synthesized what at this stage appear to be NiXdpppn/[NiX(dppp)n]x (X = Cl, Br, I; n = 1,2, x = 1, 2) by comproportionation of molar equivalents of Ni(dppp)2 and NiX2dppp, X= Cl, Br, I.

The Outer Solar Systems Origins Survey. I. Design and First-quarter Discoveries

We report the discovery, tracking, and detection circumstances for 85 trans-Neptunian objects (TNOs) from the first 42 deg2 of the Outer Solar System Origins Survey. This ongoing r-band solar system survey uses the 0.9 deg2 field of view MegaPrime camera on the 3.6 m Canada–France–Hawaii Telescope. Our orbital elements for these TNOs are precise to a fractional semimajor axis uncertainty <0.1%. We achieve this precision in just two oppositions, as compared to the normal three to five oppositions, via a dense observing cadence and innovative astrometric technique. These discoveries are free of ephemeris bias, a first for large trans-Neptunian surveys. We also provide the necessary information to enable models of TNO orbital distributions to be tested against our TNO sample. We confirm the existence of a cold "kernel" of objects within the main cold classical Kuiper Belt and infer the existence of an extension of the "stirred" cold classical Kuiper Belt to at least several au beyond the 2:1 mean motion resonance with Neptune. We find that the population model of Petit et al. remains a plausible representation of the Kuiper Belt. The full survey, to be completed in 2017, will provide an exquisitely characterized sample of important resonant TNO populations, ideal for testing models of giant planet migration during the early history of the solar system.

”By my Lords comand, I am to acquainte you”: An Edition of the Seventeenth-Century Correspondence of the Wentworth Family in the Folger Shakespeare Library

This thesis is an edition of the correspondence of the Yorkshirean Wentworth family. The aim of the edition is to provide these handwritten manuscripts to a wider audience by transcribing them. The material has been acquired from the Folger Shakespeare Library, and the transcriptions presented in this thesis are a part of their database called Early Modern Manuscripts Online. My material consists of fifteen documents from the early modern period which have been sent to or sent by members of the Wentworth family. Fourteen of these documents are letters, and one is a warrant written in the form of a letter. In the Folger Shakespeare Library the documents form the section 2.1. Correspondence of the Wentworth family in a larger collection called Papers of the Cavendish-Talbot family. The documents have been transcribed diplomatically in order to retain the character of the original manuscripts. In addition to the transcriptions, background chapters on letter writing, the historical and linguistic context, and palaeography are provided. Furthermore, each text includes a commentary containing a brief summary of the text and a description of the manuscript. Notes concerning specific words or concepts are also provided to make the texts easier to understand. Additionally, the transcriptions are encoded in XML for the purposes of the Folger Shakespeare Library. These earlier unedited manuscripts reassert the status of the Wentworth family in the early modern English society and provide information about letter writing conventions, language, and palaeographical conventions in early modern England. This edition can be used in further studies, for example as part of a larger corpus.

Poetyckie dialogi Czesława Miłosza i Tadeusza Różewicza

Wydział Filologii Polskiej i Klasycznej

I. Quantal effects in biochemical cooperativity and a proposed mechanism for the differentiation of calcium signaling in synaptic plasticity. II. Evolutionary algorithms for the optimization of methods in computational chemistry

In Part 1 of this thesis, we propose that biochemical cooperativity is a fundamentally non-ideal process. We show quantal effects underlying biochemical cooperativity and highlight apparent ergodic breaking at small volumes. The apparent ergodic breaking manifests itself in a divergence of deterministic and stochastic models. We further predict that this divergence of deterministic and stochastic results is a failure of the deterministic methods rather than an issue of stochastic simulations.

Ergodic breaking at small volumes may allow these molecular complexes to function as switches to a greater degree than has previously been shown. We propose that this ergodic breaking is a phenomenon that the synapse might exploit to differentiate Ca$^{2+}$ signaling that would lead to either the strengthening or weakening of a synapse. Techniques such as lattice-based statistics and rule-based modeling are tools that allow us to directly confront this non-ideality. A natural next step to understanding the chemical physics that underlies these processes is to consider \textit{in silico} specifically atomistic simulation methods that might augment our modeling efforts.

In the second part of this thesis, we use evolutionary algorithms to optimize \textit{in silico} methods that might be used to describe biochemical processes at the subcellular and molecular levels. While we have applied evolutionary algorithms to several methods, this thesis will focus on the optimization of charge equilibration methods. Accurate charges are essential to understanding the electrostatic interactions that are involved in ligand binding, as frequently discussed in the first part of this thesis.

I. Nickel-Exchanged Zincosilicate Catalysts for the Oligomerization of Propylene and II. Organic SDA-Free Catalysts for the Methanol-to-Olefins Reaction

Nickel-containing catalysts are developed to oligomerize light olefins. Two nickel-containing zincosilicates (Ni-CIT-6 and Ni-Zn-MCM-41) and two nickel-containing aluminosilicates (Ni-HiAl-BEA and Ni-USY) are synthesized as catalysts to oligomerize propylene into C_3n (C₆ and C₉) products. All catalysts oligomerize propylene, with the zincosilicates demonstrating higher average selectivities to C_3n products, likely due to the reduced acidity of the Zn heteroatom.

To test whether light alkanes can be incorporated into this oligomerization reaction, a supported homogeneous catalyst is combined with Ni-containing zincosilicates. The homogeneous catalyst is included to provide dehydrogenation/hydrogenation functions. When this tandem catalyst system is evaluated using a propylene/n-butane feed, no significant integration of alkanes are observed.

Ni-containing zincosilicates are reacted with 1-butene and an equimolar propylene/1-butene mixture to study other olefinic feeds. Further, other divalent metal cations such as Mn²⁺, Co²⁺, Cu²⁺, and Zn²⁺ are exchanged onto CIT-6 samples to investigate stability and potential use for other reactions. Co-CIT-6 oligomerizes propylene, albeit less effectively than Ni-CIT-6. The other M-CIT-6 samples, while not able to oligomerize light olefins, may be useful for other reactions, such as deNO_x.

Molecular sieves are synthesized, characterized, and used to catalyze the methanol-to-olefins (MTO) reaction. The Al concentration in SSZ-13 samples is varied to investigate the effect of Al number on MTO reactivity when compared to a SAPO-34 sample with only isolated Si Brønsted acid sites. These SSZ-13 samples display reduced transient selectivity behavior and extended reaction lifetimes as Si/Al increases; attributable to fewer paired Al sites. MTO reactivity for the higher Si/Al SSZ-13s resembles the SAPO-34 sample, suggesting that both catalysts owe their stable reaction behavior to isolated Brønsted acid sites.

Zeolites CHA and RHO are prepared without the use of organic structure-directing agents (OSDAs), dealuminated by steam treatments (500°C-800°C), and evaluated as catalysts for the MTO reaction. The effects of temperature and steam partial pressure during steaming are investigated. X-ray diffraction (XRD) and Ar physisorption show that steaming causes partial structural collapse of the zeolite, with degradation increasing with steaming temperature. ²⁷Al MAS NMR spectra of steamed materials reveal the presence of tetrahedral, pentacoordinate, and hexacoordinate aluminum.

Proton forms of as-synthesized CHA (Si/Al=2.4) and RHO (Si/Al=2.8) rapidly deactivate under MTO testing conditions (400°C, atmospheric pressure). CHA samples steamed at 600°C performed best among samples tested, showing increased olefin selectivities and catalyst lifetime. Acid washing these steamed samples further improved activity. Reaction results for RHO were similar to CHA, with the RHO sample steamed at 800°C producing the highest light olefin selectivities. Catalyst lifetime and C₂-C₃ olefin selectivities increase with increasing reaction temperature for both CHA-type and RHO-type steamed samples.

Essays on Financial Constraints, R&D Investments, and Competition

This dissertation consists of two chapters of theoretical studies that investigate the effect of financial constraints and market competition on research and development (R&D) investments. In the first chapter, I explore the impact of financial constraints on two different types of R&D investments. In the second chapter, I examine the impact of market competition on the relationship between financial constraints and R&D investments. In the first chapter, I develop a dynamic monopoly model to study a firm’s R&D strategy. Contrary to intuition, I show that a financially constrained firm may invest more aggressively in R&D projects than an unconstrained firm. Financial constraints introduce a risk that a firm may run out of money before its project bears fruit, which leads to involuntary termination on an otherwise positive-NPV project. For a company that relies on cash flow from assets in place to keep its R&D project alive, early success can be relatively important. I find that when the discovery process can be expedited by heavier investment (“accelerable” projects), a financially constrained company may find it optimal to “over”-invest in order to raise the probability of project survival. The over-investment will not happen if the project is only “scalable” (investment scales up payoffs). The model generates several testable implications regarding over-investment and project values. In the second chapter, I study the effects of competition on R&D investments in a duopoly framework. Using a homogeneous duopoly model where two unconstrained firms compete head to head in an R&D race, I find that competition has no effect on R&D investment if the project is not accelerable, and the competing firms are not constrained. In a heterogeneous duopoly model where a financially constrained firm competes against an unconstrained firm, I discover interesting strategic interactions that lead to preemption by the constrained firm in equilibrium. The unconstrained competitor responds to its constrained rival’s investment in an inverted-U shape fashion. When the constrained competitor has high cash flow risk, it accelerates the innovation in equilibrium, while the unconstrained firm invests less aggressively and waits for its rival to quit the race due to shortage of funds.