Identification of genes controlling milk production in dairy cattle

Siirretty Doriast

Climate-ready conservation objectives: a scoping study

AbstractAnticipated future climate change is very likely to have a wide range of different types of ecological impact on biodiversity across the whole of Australia. There is a high degree of confidence that these changes will be significant, affecting almost all species, ecosystems and landscapes. However, because of the complexity of ecological systems and the multiple ways climate change will affect them, the details of the future change are less certain for any given species or location. The nature of the changes means that the multiple ways biodiversity is experienced, used and valued by society will be affected in different ways. The likely changes present a significant challenge to any societal aspiration to preserve biodiversity in its current state, for example, to maintain a species in its current abundance and distribution. Preserving biodiversity ‘as is’ may have been feasible in a stationary climate (one that is variable but not changing), but this will not be possible with the widespread, pervasive and large ecological changes anticipated under significant levels of climate change. This makes the impacts of climate change quite unlike other threats to biodiversity, and they challenge, fundamentally, what it actually means to conserve biodiversity under climate change: what should the objectives of biodiversity conservation be under climate change? And what are the barriers to recalibrating conservation objectives?Based on key insights from the scientific literature on climate change and biodiversity, the project developed three adaptation propositions about managing biodiversity:Conservation strategies accommodate large amounts of ecological change and the likelihood of significant climate change–induced loss in biodiversity. Strategies remain relevant and feasible under a range of possible future trajectories of ecological change.Strategies seek to conserve the multiple different dimensions of biodiversity that are experienced and valued by society. Together these propositions summarise the challenge of future climate change for biodiversity conservation, and define a new way of framing conservation we called the ‘climate ready’ approach. In the near term, conservation strategies may be able to include some consideration of these propositions. However, under significant levels of climate change many of the current approaches to conservation will become increasingly difficult and ineffective (e.g. maintaining community types in their current locations). This challenge is fundamentally different from that posed by other threats to biodiversity, and the climate-ready approach is akin to a paradigm shift in conservation.The project used a review of 26 conservation strategy documents (spanning scales from international to local) and four case studies with conservation agencies to test and refine the climate-ready approach. The project found the approach to be robust and highly relevant; in the majority of situations, if adopted, it would lead to significant changes in the objectives and priorities of conservation. There were also many ‘green shoots’ of elements of the new approach in existing conservation practice. However, the project found there are currently substantial barriers to fully adopting a climate-ready approach. These include the need for: further development of ecological characterisation of ecosystem health and human activities in landscapesmuch better understanding of how society values different aspects of biodiversity, including ecosystems and landscapesdevelopment of policy tools to codify and implement new ecologically robust and socially endorsed objectives.  Anticipated future climate change is very likely to have a wide range of different types of ecological impact on biodiversity across the whole of Australia. There is a high degree of confidence that these changes will be significant, affecting almost all species, ecosystems and landscapes. However, because of the complexity of ecological systems and the multiple ways climate change will affect them, the details of the future change are less certain for any given species or location. The nature of the changes means that the multiple ways biodiversity is experienced, used and valued by society will be affected in different ways. The likely changes present a significant challenge to any societal aspiration to preserve biodiversity in its current state, for example, to maintain a species in its current abundance and distribution. Preserving biodiversity ‘as is’ may have been feasible in a stationary climate (one that is variable but not changing), but this will not be possible with the widespread, pervasive and large ecological changes anticipated under significant levels of climate change. This makes the impacts of climate change quite unlike other threats to biodiversity, and they challenge, fundamentally, what it actually means to conserve biodiversity under climate change: what should the objectives of biodiversity conservation be under climate change? And what are the barriers to recalibrating conservation objectives?Based on key insights from the scientific literature on climate change and biodiversity, the project developed three adaptation propositions about managing biodiversity:Conservation strategies accommodate large amounts of ecological change and the likelihood of significant climate change–induced loss in biodiversity. Strategies remain relevant and feasible under a range of possible future trajectories of ecological change.Strategies seek to conserve the multiple different dimensions of biodiversity that are experienced and valued by society. Together these propositions summarise the challenge of future climate change for biodiversity conservation, and define a new way of framing conservation we called the ‘climate ready’ approach. In the near term, conservation strategies may be able to include some consideration of these propositions. However, under significant levels of climate change many of the current approaches to conservation will become increasingly difficult and ineffective (e.g. maintaining community types in their current locations). This challenge is fundamentally different from that posed by other threats to biodiversity, and the climate-ready approach is akin to a paradigm shift in conservation.The project used a review of 26 conservation strategy documents (spanning scales from international to local) and four case studies with conservation agencies to test and refine the climate-ready approach. The project found the approach to be robust and highly relevant; in the majority of situations, if adopted, it would lead to significant changes in the objectives and priorities of conservation. There were also many ‘green shoots’ of elements of the new approach in existing conservation practice. However, the project found there are currently substantial barriers to fully adopting a climate-ready approach. These include the need for: further development of ecological characterisation of ecosystem health and human activities in landscapesmuch better understanding of how society values different aspects of biodiversity, including ecosystems and landscapesdevelopment of policy tools to codify and implement new ecologically robust and socially endorsed objectives. Please cite this report as: Dunlop M, Parris, H, Ryan, P, Kroon, F 2013 Climate-ready conservation objectives: a scoping study, National Climate Change Adaptation Research Facility, Gold Coast, pp. 102

Development of fluorogenic RNA aptamers for cellular imaging of RNA and genomic loci

In recent years, there has been an explosion of SELEX-evolved fluorescent RNA aptamers, such as Spinach, Broccoli, Corn and Mango. Fluorogenic RNA aptamers have sparked a lot of interest and hold great potential to enable background-free visualisation of RNA molecules in cellular environments. However, their application has been limited by relatively inefficient folding in vivo and fluorescent stability. Therefore, evolving new RNA aptamers with improved brightness and stability should better their use in cellular imaging. Three new Mango-based aptamers have recently been selected from the original Mango RNA SELEX pool using microfluidic- assisted in vitro compartmentalization and fluorescence-activated sorting. This thesis demonstrates the use of these new aptamer variants to image small non-coding RNAs (such as 5S rRNA, U6 snRNA and mgU2-47 scaRNA) in both fixed and live human cells with improved sensitivity and resolution. Upon expression the modified RNAs subcellular localisation pattern is conserved, as validated using immunofluoresence. Recent work with tandem Mango arrays shows increased sensitivity, which enables the visualization of single mRNA molecules in live and fixed cells. Furthermore, it is shown that the tandem Mango arrays don’t affect the expected localization of a cytoplasmic mRNA (β-actin) and the nuclear long non- coding RNA (NEAT-1). Furthermore, these RNA aptamers can also be used to label genomic loci via CRISPR/Cas9 mediated genome targeting with improved contrast. This allows for the targeting of short genomic repeats in a less invasive manner with regards to current methodologies. Taken together this data shows that new Mango aptamers are vastly improved for cellular imaging over previous RNA aptamers, and can in principle be incorporated into a wide range of coding and non-coding RNAs.Open Acces

Cooperative Radio Communications for Green Smart Environments

The demand for mobile connectivity is continuously increasing, and by 2020 Mobile and Wireless Communications will serve not only very dense populations of mobile phones and nomadic computers, but also the expected multiplicity of devices and sensors located in machines, vehicles, health systems and city infrastructures. Future Mobile Networks are then faced with many new scenarios and use cases, which will load the networks with different data traffic patterns, in new or shared spectrum bands, creating new specific requirements. This book addresses both the techniques to model, analyse and optimise the radio links and transmission systems in such scenarios, together with the most advanced radio access, resource management and mobile networking technologies. This text summarises the work performed by more than 500 researchers from more than 120 institutions in Europe, America and Asia, from both academia and industries, within the framework of the COST IC1004 Action on "Cooperative Radio Communications for Green and Smart Environments". The book will have appeal to graduates and researchers in the Radio Communications area, and also to engineers working in the Wireless industry. Topics discussed in this book include: • Radio waves propagation phenomena in diverse urban, indoor, vehicular and body environments• Measurements, characterization, and modelling of radio channels beyond 4G networks• Key issues in Vehicle (V2X) communication• Wireless Body Area Networks, including specific Radio Channel Models for WBANs• Energy efficiency and resource management enhancements in Radio Access Networks• Definitions and models for the virtualised and cloud RAN architectures• Advances on feasible indoor localization and tracking techniques• Recent findings and innovations in antenna systems for communications• Physical Layer Network Coding for next generation wireless systems• Methods and techniques for MIMO Over the Air (OTA) testin

Rate-limiting Steps in Transcription Initiation are Key Regulatory Mechanisms of Escherichia coli Gene Expression Dynamics

In all living organisms, the “blueprints of life” are documented in the genetic material. This material is composed of genes, which are regions of DNA coding for proteins. To produce proteins, cells read the information on the DNA with the help of molecular machines, such as RNAp holoenzymes and a factors. Proteins carry out the cellular functions required for survival and, as such, cells deal with challenging environments by adjusting their gene expression pattern. For this, cells constantly perform decision- making processes of whether or not to actively express a protein, based on intracellular and environmental cues. In Escherichia coli, gene expression is mostly regulated at the stage of transcription initiation. Although most of its regulatory molecules have been identified, the dynamics and regulation of this step remain elusive. Due to a limited number of specific regulatory molecules in the cells, the stochastic fluctuations of these molecular numbers can result in a sizeable temporal change in the numbers of transcription outputs (RNA and proteins) and have consequences on the phenotype of the cells. To understand the dynamics of this process, one should study the activity of the gene by tracking mRNA and protein production events at a detailed level. Recent advancements in single-molecule detection techniques have been used to image and track individually labeled fluorescent macromolecules of living cells. This allows investigating the intermolecular dynamics under any given condition. In this thesis, by using in vivo, single-RNA time-lapse microscopy techniques along with stochastic modelling techniques, we studied the kinetics of multi-rate limiting steps in the transcription process of multiple promoters, in various conditions. Specifically, first, we established a novel method of dissecting transcription in Escherichia coli that combines state-of-the-art microscopy measurements and model fitting techniques to construct detailed models of the rate-limiting steps governing the in vivo transcription initiation of a synthetic Lac-ara-1 promoter. After that, we estimated the duration of the closed and open complex formation, accounting for the rate of reversibility of the first step. From this, we also estimated the duration of periods of promoter inactivity, from which we were able to determine the contribution from each step to the distribution of intervals between consecutive RNA productions in individual cells. Second, using the above method, we studied the a factor selective mechanisms for indirect regulation of promoters whose transcription is primarily initiated by RNAp holoenzymes carrying a70. From the analysis, we concluded that, in E. coli, a promoter’s responsiveness to indirect regulation by a factor competition is determined by its sequence-dependent, dynamically regulated multi-step initiation kinetics. Third, we investigated the effects of extrinsic noise, arising from cell-to-cell variability in cellular components, on the single-cell distribution of RNA numbers, in the context of cell lineages. For this, first, we used stochastic models to predict the variability in the numbers of molecules involved in upstream processes. The models account for the intake of inducers from the environment, which acts as a transient source of variability in RNA production numbers, as well as for the variability in the numbers of molecular species controlling transcription of an active promoter, which acts as a constant source of variability in RNA numbers. From measurement analysis, we demonstrated the existence of lineage-to-lineage variability in gene activation times and mean transcription rates. Finally, we provided evidence that this can be explained by differences in the kinetics of the rate-limiting steps in transcription and of the induction scheme, from which it is possible to conclude that these variabilities differ between promoters and inducers used. Finally, we studied how the multi-rate limiting steps in the transcription initiation are capable of tuning the asymmetry and tailedness of the distribution of time intervals between consecutive RNA production events in individual cells. For this, first, we considered a stochastic model of transcription initiation and predicted that the asymmetry and tailedness in the distribution of intervals between consecutive RNA production events can differ by tuning the rate-limiting steps in transcription. Second, we validated the model with measurements from single-molecule RNA microscopy of transcription kinetics of multiple promoters in multiple conditions. Finally, from our results, we concluded that the skewness and kurtosis in RNA and protein production kinetics are subject to regulation by the kinetics of the steps in transcription initiation and affect the single-cell distributions of RNAs and, thus, proteins. We further showed that this regulation can significantly affect the probability of RNA and protein numbers to cross specific thresholds. Overall, the studies conducted in this thesis are expected to contribute to a better understanding of the dynamic process of bacterial gene expression. The advanced data and image analysis techniques and novel stochastic modeling approaches that we developed during the course of these studies, will allow studying in detail the in vivo regulation of multi-rate limiting steps of transcription initiation of any given promoter. In addition, by tuning the kinetics of the rate-limiting steps in the transcription initiation as executed here should allow engineering new promoters, with predefined RNA and, thus, protein production dynamics in Escherichia coli

Identification Of Metabolite Biomarkers In Epilepsy Using 1h Mrs

Epilepsy is a serious neurological disorder that affects 1% percent of the global population. Despite its status as one of the oldest neurological disorders known to man, its mechanisms remain poorly understood. Available medications are not curative but provide symptomatic management and do not work for well for more than 30 percent of patients. Because it is nearly impossible to predict on an individual level who will eventually develop epilepsy, it is also a disorder that can only be diagnosed after the patient has experienced established seizure activity, eliminating any possibility of stopping the disorder in its prodromal phase, before the patients are symptomatic. Availability of a reliable and non-invasive biomarker tool that can predict and identify the development of epilepsy would dramatically change how the disorder is detected, monitored, managed, and treated. In this project, we tested the potential of 1H MRS to provide metabolite biomarkers of epilepsy and epileptogenesis, both in human neocortical tissue obtained from intractable epilepsy patients who underwent resective surgery and also in a longitudinal rat model of epileptogenesis, using interictal epileptiform discharges as a surrogate indicator of disease progression. Using 1H MRS, we found unique metabolite differences that are highly predictive of epileptic and non-epileptic neocortex in humans that also partially overlaps with findings from our rat model. These findings provide evidence that 1H MRS is capable of identifying metabolite changes specific to epilepsy and may lead to reliable and non-invasive biomarkers of epilepsy and epileptogenesis in the future

Cell Engineering and Molecular Pharming for Biopharmaceuticals

Biopharmaceuticals are often produced by recombinant E. coli or mammalian cell lines. This is usually achieved by the introduction of a gene or cDNA coding for the protein of interest into a well-characterized strain of producer cells. Naturally, each recombinant production system has its own unique advantages and disadvantages. This paper examines the current practices, developments, and future trends in the production of biopharmaceuticals. Platform technologies for rapid screening and analyses of biosystems are reviewed. Strategies to improve productivity via metabolic and integrated engineering are also highlighted