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

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

Couplers for Non-Locality Swapping

Studying generalized non-local theories brings insight to the foundations of quantum mechanics. Here we focus on non-locality swapping, the analogue of quantum entanglement swapping. In order to implement such a protocol, one needs a coupler that performs the equivalent of quantum joint measurements on generalized `box-like' states. Establishing a connection to Bell inequalities, we define consistent couplers for theories containing an arbitrary amount of non-locality, which leads us to introduce the concepts of perfect and minimal couplers. Remarkably, Tsirelson's bound for quantum non-locality naturally appears in our study.Comment: 16 pages, 3 figure

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

Motion Planning for Kinematic systems

In this paper, we present a general theory of motion planning for kinematic systems. This theory has been developed for long by one of the authors in a previous series of papers. It is mostly based upon concepts from subriemannian geometry. Here, we summarize the results of the theory, and we improve on, by developping in details an intricated case: the ball with a trailer, which corresponds to a distribution with flag of type 2,3,5,6. This paper is dedicated to Bernard Bonnard for his 60th birthday

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

Equilibria in a Dynamic Global Game: The Role of Cohort Effects

We introduce strategic waiting in a global game setting with irreversible investment. Players can wait in order to make a better informed decision. We allow for cohort effects and discuss when they arise endogenously in technology adoption problems with positive contemporaneous network effects. Formally, cohort effects lead to intra-period network effects being greater than inter-period network effects. Depending on the nature of the cohort effects, the dynamic game may or may not satisfy dynamic strategic complementarity. If it does, our model has a unique rationalizable outcome. Otherwise, there exists parameter values for which multiple equilibria arise because player have a strong incentive to invest at the same point in time others do. ZUSAMMENFASSUNG - (Gleichgewichte in einem Dynamischen Globalen Spiel: Die Rolle von Kohorteneffekten) Koordinationsspiele haben typischerweise multiple Nashgleichgewichte mit sich selbsterfüllenden Erwartungen. Die Theorie der globalen Spiele führt Unsicherheit und private Informationen in statischen Koordinationsspielen ein und zeigt die Bedingungen auf, unter denen dies zu einem eindeutigen Gleichgewicht führt. In diesem Beitrag untersuchen wir ein Zweiperiodenspiel, in welchem die Spieler eine irreversible Investitionsentscheidung mit einer positiven Netwerkexternalität treffen. In der ersten Periode wählen die Spieler, ob sie sofort investieren oder auf bessere Informationen über das Projekt warten. Wir zeigen, dass Kohorteneffekte bei Technologiewahlproblemen mit positiven Netzwerkexternalitäten auftreten und untersuchen ihre Auswirkungen. Kohorteneffekte führen dazu, dass die Intraperioden-Netzwerkeffekte größer sind als die Interperioden-Netzwerkeffekte. Aus technischer Sicht bestimmen die Kohorteneffekte, ob das globale Spiel die Eigenschaft der dynamischen strategischen Komplemantarität erfüllt. Diese Eigenschaft wiederum impliziert, dass unser Modell eine eindeutige rationalisierbare Lösung hat. Ist diese Eigenschaft nicht erfüllt, so hat jeder Spieler einen hohen Anreiz zum gleichen Zeitpunkt wie die andern Spieler zu investieren. In diesem Fall exstieren Parameterwerte für welche unser Spiel multiple Nashgleichgewichtslösungen hat.Global Game, Strategic Waiting, Coordination, Strategic Complementarities, Period-specific Network Effects, Equilibrium Selection