Enumeration, identification and characterisation of methanogens colonising pre-ruminant calves : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science at Massey University, Palmerston North, New Zealand

Methane-producing archaea, methanogens, in ruminant animals are a major source of anthropogenic methane. With a global warming potential 23 times greater than carbon dioxide, methane has been targeted for reduction under the Kyoto protocol. In New Zealand methane emissions from ruminant animals are major contributor to the national greenhouse gas inventory. For this reason agricultural industries are challenged with reducing methane emissions from ruminants. This investigation on methanogens in young dairy calves was carried out to obtain information on methanogen colonisation and establishment in the rumen because little is known about this process. In this study, methanogen colonisation occurred within two days after birth in four calves that were raised in the absence of cows. Anaerobic culture techniques were used to enumerate methanogens in gut samples and showed that methanogen numbers increased over time, but dropped below detection limits in two of four calves between six and 11 days after birth. Methanogens in these two calves then reappeared at day 13. By three weeks of age methanogen densities in all four calves were approximately 108 cells ml -1. These densities are similar to those found by other workers for 3-week old and mature ruminants. Colonies picked from anaerobic agar roll-tubes prepared from enumeration cultures yielded 31 methanogenic isolates and 28 isolates that utilised hydrogen but did not produce methane. Eleven of the 31 methanogenic isolates were selected for purification. Despite extensive efforts only four methanogens were able to be purified from the eleven isolates because of persistent non-methanogenic eubacteria also present in cultures. A phylogenetic analysis of 16S rRNA gene sequences from purified and partially-purified methanogen isolates was carried out and dendograms constructed to identify methanogens. Some phenotypic characteristics of purified methanogens were determined. This revealed a number of methanogen species previously not found in the rumen. The results showed Methanofollis liminatans (three isolates), Methanoculleus palmolei (three isolates) or Methanosarcina barkeri (one isolate) were the predominant culturable methanogens colonising the rumen two days after birth. The three isolates identified as M. liminatans were only 96.0% identical at the 16S rRNA gene level to the M. liminatans type strain, DSM 4140, and appear to be a new methanogen species. In gut samples collected 3-5 days after birth, Methanobacterium bryantii (three isolates) was found to be a predominant methanogen in some calves apparently replacing the first methanogens colonising the developing rumen. Twenty two days after birth Methanobrevibacter thaueri (one isolate) was identified as a predominant methanogen in one calf. These results are the first to suggest that there is a successional change in the methanogen populations as the rumen develops in young ruminants. Consideration of the colonising species showed that Mcl. palmolei were obtained from only two calves (calves 10 and 12) and that Mfl. liminatans-like isolates were obtained only from a different cohort of calves penned separately to calves 10 and 12. These methanogens, previously found only in terrestrial or aquatic environments, are probably the primary colonising methanogens because there were no mature ruminants to provide alternative inocula. It appears that the developing rumen of young calves provides a niche suitable for opportunistic hydrogenotrophic methanogens. A PCR investigation using targeted primers specific for seven groupings of methanogens was carried out on all rumen samples to obtain information not dependant on culturing. This analysis on DNA extracts showed methanogens belonging to the Methanobacteriales were present in almost every sample. Methanogens belonging to the Methanosarcinales and Methanomicrobiales were not detected in any sample. At the end of the trial (22 days), PCR analysis showed the presence of Methanobacterium spp. and Methanobrevibacter spp. in all four calves. Although there were some disagreements with results for isolates cultured, overall, PCR results confirmed the concept of successional changes in methanogen populations in pre-ruminant calves

Resource modalities in game semantics

The description of resources in game semantics has never achieved the simplicity and precision of linear logic, because of a misleading conception: the belief that linear logic is more primitive than game semantics. We advocate instead the contrary: that game semantics is conceptually more primitive than linear logic. Starting from this revised point of view, we design a categorical model of resources in game semantics, and construct an arena game model where the usual notion of bracketing is extended to multi- bracketing in order to capture various resource policies: linear, affine and exponential

Posterior propriety in Bayesian extreme value analyses using reference priors

The Generalized Pareto (GP) and Generalized extreme value (GEV) distributions play an important role in extreme value analyses, as models for threshold excesses and block maxima respectively. For each of these distributions we consider Bayesian inference using "reference" prior distributions (in the general sense of priors constructed using formal rules) for the model parameters, specifically a Jeffreys prior, the maximal data information (MDI) prior and independent uniform priors on separate model parameters. We investigate the important issue of whether these improper priors lead to proper posterior distributions. We show that, in the GP and GEV cases, the MDI prior, unless modified, never yields a proper posterior and that in the GEV case this also applies to the Jeffreys prior. We also show that a sample size of three (four) is sufficient for independent uniform priors to yield a proper posterior distribution in the GP (GEV) case.Comment: 20 pages, 2 figures; typo corrected on page 5 (line -2, Euler's constant corrected to approx. 0.57722). The final publication is available at http://www3.stat.sinica.edu.tw/preprint/SS-14-034_preprint.pdf or http://dx.doi.org/10.5705/ss.2014.03

The development and calibration of a generic dynamic absorption chiller model

Although absorption cooling has been available for many years, the technology has typically been viewed as a poorly performing alternative to vapour compression refrigeration. Rising energy prices and the requirement to improve energy efficiency is however driving renewed interest in the technology, particularly within the context of combined cooling, heat and power systems (CCHP) for buildings. In order to understand the performance of absorption cooling, numerous models are available in the literature. However, the complexities involved in the thermodynamics of absorption chillers have so far restricted researchers to creating steady state or dynamic models reliant on data measurements of the internal chiller state, which require difficult-to-obtain, intrusive measurements. The pragmatic, yet fully-dynamic model described in this paper is designed to be easily calibrated using data obtained from the measurements of inflows and outflows to a chiller, without resorting to intrusive measurements. The model comprises a series of linked control volumes featuring both performance maps and lumped mass volumes, which reflect the underlying physical structure of the device. The model was developed for the ESP-r building simulation tool. This paper describes the modelling approach, theory and limitations, along with its calibration and the application of the model to a specific example

Cross-validatory extreme value threshold selection and uncertainty with application to ocean storm severity

Designs conditions for marine structures are typically informed by threshold-based extreme value analyses of oceanographic variables, in which excesses of a high threshold are modelled by a generalized Pareto (GP) distribution. Too low a threshold leads to bias from model mis-specification; raising the threshold increases the variance of estimators: a bias-variance trade-off. Many existing threshold selection methods do not address this trade-off directly, but rather aim to select the lowest threshold above which the GP model is judged to hold approximately. In this paper Bayesian cross-validation is used to address the trade-off by comparing thresholds based on predictive ability at extreme levels. Extremal inferences can be sensitive to the choice of a single threshold. We use Bayesian model-averaging to combine inferences from many thresholds, thereby reducing sensitivity to the choice of a single threshold. The methodology is applied to significant wave height datasets from the northern North Sea and the Gulf of Mexico.Comment: 24 pages, 15 figures. Confidence intervals in Figure 2 corrected. The final publication is available at Wiley via http://dx.doi.org/10.1111/rssc.1215

A short note on passivity, complete passivity and virtual temperatures

We give a simple and intuitive proof that the only states which are completely passive, i.e. those states from which work cannot be extracted even with infinitely many copies, are Gibbs states at positive temperatures. The proof makes use of the idea of virtual temperatures, i.e. the association of temperatures to pairs of energy levels (transitions). We show that (i) passive states are those where every transition is at a positive temperature, and (ii) completely passive states are those where every transition is at the same positive temperature.Comment: 3 pages, no figures. v2: Published versio

Technology Adoption, Social Learning, and Economic Policy

We study a two-player dynamic investment model with information externalities and provide necessary and sufficient conditions for a unique switching equilibrium. When the public information is sufficiently high and a social planer therefore expects an investment boom, investments should be taxed. Conversely, any positive investment tax is suboptimally high if the public information is sufficiently unfavorable.We also show that an investment tax may increase overall investment activity

Growth limiting conditions and denitrification govern extent and frequency of volume detachment of biofilms

This study aims at evaluating the mechanisms of biofilm detachment with regard of the physical properties of the biofilm. Biofilms were developed in Couette–Taylor reactor under controlled hydrodynamic conditions and under different environmental growth conditions. Five different conditions were tested and lead to the formation of two aerobic heterotrophic biofilms (aeHB1 and aeHB2), a mixed autotrophic and heterotrophic biofilm (MAHB) and two anoxic heterotrophic biofilms (anHB1 and anHB2). Biofilm detachment was evaluated by monitoring the size of the detached particles (using light-scattering) as well as the biofilm physical properties (using CCD camera and image analysis). Results indicate that volume erosion of large biofilm particles with size ranging from 50 to 500 lm dominated the biomass loss for all biofilms. Surface erosion of small particles with size lower than 20 lm dominates biofilm detachment in number. The extent of the volume detachment events was governed by the size of the biofilm surface heterogeneities (i.e., the absolute biofilm roughness) but never impacted more than 80% of the mean biofilm thickness due to the highly cohesive basal layer. Anoxic biofilms were smoother and thinner than aerobic biofilms and thus associated with the detachment of smaller particles. Our results contradict the simplifying assumption of surface detachment that is considered in many biofilm models and suggest that discrete volume events should be considered