Unlocking the M13 (F1) virion : investigation into the role of pIII C domain of F specific filamentous bacteriophage in infection : a thesis presented in partial fulfillment of the requirements for the degree of Master of Science in Biochemistry at Massey University, Palmerston North, New Zealand

Filamentous phage adsorb to the host cells by binding of the N2 domain of pIII to the tip of the F pilus. Binding of N1 domain of pIII to the secondary receptor (Tol A), triggers the opening of the virion by a poorly understood mechanism. Filamentous phage assembly is a secretion-like process. The assembly is terminated and virion released from the membranes by C domain of pIII. Because the infection is a reversal of assembly, it can be hypothesized that the C domain of pIII plays an active role in the infection. To test this hypothesis, we have set up a system in which virions carried a mixture of two types of mutant pIII molecules: i) functional N1N2 domains fused to a short C domain that can be incorporated but cannot terminate assembly and release the phage from the membrane: ii) C domain only, which can terminate phage assembly, but lacks the receptor-binding domains N1N2. The infectivity of the particles was as low as 0.21% that of the positive control setup in which virions carried a mixture of wild-type pIII and C domain. Therefore, a functional C domain covalently linked to the receptor domain N1N2 is required for infection. These findings suggest that simple binding of N1 domain of pIII to the periplasmic receptor TolA is not sufficient for infection. Rather, this interaction may, via functional C domain of pIII, trigger a conformational change required for the downstream events which result in the virion uncoating and DNA entry. To add further weight to this model, a "microphage" producing system was designed to produce short phage particles suitable for Cryo-EM structural analysis

Carbon dioxide emissions intensity convergence: Evidence from central American countries

This paper extends the literature on the convergence of carbon dioxide emissions intensity and its determinants (energy intensity and the carbonization index) for six Central American countries over the period 1971 to 2014. Using the Phillips-Sul club convergence approach, the results indicate two distinct convergence clubs with respect to carbon dioxide emissions intensity and energy intensity with the first convergence club consisting of Costa Rica, El Salvador, Guatemala, and Honduras and the second convergence club consisting of Nicaragua and Panama. However, in the case of the carbonization index, only one convergence club emerges that includes Costa Rica, El Salvador, Guatemala, Honduras, and Nicaragua with Panama exhibiting non-convergent behavior.N/

Native vegetation of the southern forests : south-east highlands, Australian alps, south-west Slopes, and SE Corner bioregions

The Southern Forests study area covers an area of about six million hectares of south-eastern New South Wales, south of Oberon and Kiama and east of Albury and Boorowa (latitude 33° 02’–37 ° 06’ S; longitude 146° 56’ – 147° 06’ E). The total area of existing vegetation mapped was three million hectares (3 120 400 hectares) or about 50% of the study area. Terrestrial, wetland and estuarine vegetation of the Southern Forests region were classified into 206 vegetation groups and mapped at a scale between 1: 25 000 and 1: 100 000. The classification was based on a cluster analysis of detailed field surveys of vascular plants, as well as field knowledge in the absence of field survey data. The primary classification was based on 3740 vegetation samples with full floristics cover abundance data. Additional classifications of full floristics presence-absence and tree canopy data were carried out to guide mapping in areas with few full floristic samples. The mapping of extant vegetation was carried out by tagging vegetation polygons with vegetation codes, guided by expert knowledge, using field survey data classified into vegetation groups, remote sensing, and other environmental spatial data. The mapping of pre-1750 vegetation involved tagging of soils mapping with vegetation codes at 1: 100 000 scale, guided by spatial modelling of vegetation groups using generalised additive statistical models (GAMS), and expert knowledge. Profiles of each of the vegetation groups on the CD-ROM* provide key indicator species, descriptions, statistics and lists of informative plant species. The 206 vegetation groups cover the full range of natural vegetation, including rainforests, moist eucalypt forests, dry shrub forests, grassy forests, mallee low forests, heathlands, shrublands, grasslands and wetlands. There are 138 groups of Eucalyptus forests or woodlands, 12 rainforest groups, and 46 non-forest groups. Of the 206 groups, 193 were classified and mapped in the study area. Thirteen vegetation groups were not mapped because of their small size and lack of samples, or because they fell outside the study area. Updated regional extant and pre-1750 vegetation maps of southern New South Wales have been produced in 2005, based on those originally prepared in 2000 for the southern Regional Forest Agreement (RFA). Further validation and remapping of extant vegetation over 10% of the study area has subsequently improved the quality of the vegetation map, and removed some of the errors in the original version. The revised map provides a reasonable representation of native vegetation at a scale between 1: 25 000 and 1: 100 000 across the study area. In 2005 native vegetation covers 50% of the study area. Environmental pressures on the remaining vegetation include clearing, habitat degradation from weeds and nutrification, severe droughts, changing fire regimes, and urbanisation. Grassy woodlands and forests, temperate grasslands, and coastal and riparian vegetation have been the most reduced in areal extent. Over 90% of the grassy woodlands and temperate grasslands have been lost. Conservation of the remaining vegetation in these formations is problematic because of the small, discontinuous, and degraded nature of the remaining patches of vegetation

Marquette Interchange Perpetual Pavement Instrumentation Project - Phase II

This report presents findings from the second phase of the Marquette Interchange instrumentation project and focuses on the maintenance of data recordation systems, development of computer programs to analyze data, and development of data packages for redistribution. The product of this research is a set of data which includes dynamic pavement response due to live traffic, vehicle information (weight, class, length, et cetera), and environmental data for the test site. The tasks within this project were not oriented for findings regarding pavement performance, but important and helpful conclusions can be drawn for similar future projects. The recordation systems have been maintained and recordation has been continuous. A handful of sensors did require attention and only a fraction of the critical strain sensors have ceased to function, making the project a success. The results of the computer programs written to analyze data show that reasonable accuracy has been achieved. Future work can help to generate more intricate programming making the processes more accurate

Enumeration of idempotents in planar diagram monoids

We classify and enumerate the idempotents in several planar diagram monoids: namely, the Motzkin, Jones (a.k.a. Temperley-Lieb) and Kauffman monoids. The classification is in terms of certain vertex- and edge-coloured graphs associated to Motzkin diagrams. The enumeration is necessarily algorithmic in nature, and is based on parameters associated to cycle components of these graphs. We compare our algorithms to existing algorithms for enumerating idempotents in arbitrary (regular *-) semigroups, and give several tables of calculated values.Comment: Majorly revised (new title, new abstract, one additional author), 24 pages, 6 figures, 8 tables, 5 algorithm

Non-triviality conditions for integer-valued polynomial rings on algebras

Let $D$ be a commutative domain with field of fractions $K$ and let $A$ be a torsion-free $D$-algebra such that $A \cap K = D$. The ring of integer-valued polynomials on $A$ with coefficients in $K$ is \Int_K(A) = \{f \in K[X] \mid f(A) \subseteq A\}, which generalizes the classic ring \Int(D) = \{f \in K[X] \mid f(D) \subseteq D\} of integer-valued polynomials on $D$. The condition $A \cap K$ implies that D[X] \subseteq \Int_K(A) \subseteq \Int(D), and we say that \Int_K(A) is nontrivial if \Int_K(A) \ne D[X]. For any integral domain $D$, we prove that if $A$ is finitely generated as a $D$-module, then \Int_K(A) is nontrivial if and only if \Int(D) is nontrivial. When $A$ is not necessarily finitely generated but $D$ is Dedekind, we provide necessary and sufficient conditions for \Int_K(A) to be nontrivial. These conditions also allow us to prove that, for $D$ Dedekind, the domain \Int_K(A) has Krull dimension 2

Dynamics of Monetary Policy Uncertainty and the Impact on the Macroeconomy

A large literature lauds the benefits of central bank transparency and credibility, but when a central bank like the U.S. Federal Reserve has a dual mandate, is not specific to the extent it targets employment versus price stability, and is not specific to the magnitude interest rates should change in response to these targets, market participants must depend largely on past data to form expectations about monetary policy. We suppose market participants estimate a Taylor-like regression equation to understand the conduct of monetary policy, which likely guides their short-run and long-run expectations. When the Federal Reserve's actions deviate from its historical targets for macroeconomic variables, an environment of greater uncertainty may be the result. We quantify this degree of uncertainty by measuring and aggregating recent deviations of the federal funds rate from econometric forecasts predicted by constant gain learning. We incorporate this measure of uncertainty into a VAR model with ARCH shocks to measure the effect monetary policy uncertainty has on inflation, output growth, unemployment, and the volatility of these variables. We find that a higher degree of uncertainty regarding monetary policy is associated with greater volatility of output growth and unemployment.Uncertainty; learning; volatility; Taylor rule; vector autoregression; ARCH.