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DEDICATION
This project is dedicated to Almighty God for his protection, kindness, strength over my life throughout the period and also to my --- for his financial support and moral care towards me.Also to my mentor --- for her academic advice she often gives to me. May Almighty God shield them from the peril of this world and bless their entire endeavour Amen.
ACKNOWLEDGEMENT
The successful completion of this project work could not have been a reality without the encouragement of my --- and other people. My immensely appreciation goes to my humble and able supervisor mr. --- for his kindness in supervising this project.
My warmest gratitude goes to my parents for their moral, spiritual and financial support throughout my study in this institution.
My appreciation goes to some of my lecturers among whom are Mr. ---, and Dr. ---. I also recognize the support of some of the staff of --- among whom are: The General Manager, Deputy General manager, the internal Auditor Mr. --- and the ---. Finally, my appreciation goes to my elder sister ---, my lovely friends mercy ---, ---, --- and many others who were quite helpful.
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System approaches to elucidate ecosystem functioning constitute an emerging area of research within microbial ecology. Such approaches aim at investigating all levels of biological information (DNA, RNA, proteins and metabolites) to capture the functional interactions occurring in a given ecosystem and track down characteristics that could not be accessed by the study of isolated components. In this context, the study of the proteins collectively expressed by all the microorganisms present within an ecosystem (metaproteomics) is not only crucial but can also provide insights into microbial functionality. Overall, the success of metaproteomics is closely linked to metagenomics, and with the exponential increase in the availability of metagenome sequences, this field of research is starting to experience generation of an overwhelming amount of data, which requires systematic analysis. Metaproteomics has been employed in very diverse environments, and this review discusses the recent advances achieved in the context of human biology, soil, marine and freshwater environments as well as natural and bioengineered systems.
Keyword: environmental proteomics, ecosystem function, marine and freshwater environment, soil, aquatic environment.
TABLE OF CONTENTS
TITLE PAGE
APPROVAL PAGE
DEDICATION
ACKNOWLEDGEMENT
ABSTRACT
TABLE OF CONTENT
CHAPTER ONE
- INTRODUCTION
- BACKGROUND OF THE STUDY
- PROBLEM STATEMENT
- AIM OF THE STUDY
- SIGNIFICANCE OF THE STUDY
- SCOPE OF THE STUDY
CHAPTER TWO
LITERATURE REVIEW
2.0 LITERATURE REVIEW
2.1 REVIEW OF THE STUDY
2.2 AN OVERVIEW OF METAPROTEOMICS
2.3 PROTEOMIC OF MICROBIAL COMMUNITY
2.4 METAPROTEOMICS AND THE HUMAN INTESTINAL MICROBIOME
2.5 METAPROTEOMICS IN ENVIRONMENTAL MICROBIOME STUDIES
CHAPTER THREE
3.0 METHODS
3.1 PROTEIN EXPRESSION IN THE HUMAN MICROBIOME
3.2 PROTEIN EXPRESSION IN SOIL
3.3 PROTEIN EXPRESSION IN MARINE AND FRESHWATER
CHAPTER FOUR
4.0 RESULT
CHAPTER FIVE
- CONCLUSIONS
- RECOMMENDATION
5.3 REFERENCES
CHAPTER ONE
1.0 INTRODUCTION
1.1 BACKGROUND OF THE STUDY
Microorganisms occupy virtually every habitat on our planet, and their activities largely determine the environmental conditions of today's world. Indeed, microorganisms are heavily involved in biogeochemistry, ensuring the recycling of elements such as carbon and nitrogen (Madsen, 2011). In addition, microorganisms are extensively used to degrade anthropogenic waste prior to release into the environment (Hussain et al., 2010). In their natural habitat, microorganisms coexist in mixed communities, the complexity of which is specific to each environment, for example from six estimated individual taxa for an acid mine drainage biofilm (Ram et al., 2005), up to 106 estimated taxa per gram of soil. As most of the microorganisms present in the environment have not been cultured, their investigation requires the use of molecular techniques that bypass the traditional isolation and cultivation of individual species (Amann et al., 1995). Moreover, even when isolation is possible, a single species removed from its natural environment might not necessarily display the same characteristics under laboratory conditions as it does within its ecological niche. Therefore, the study of mixed microbial communities within their natural environment is key to the investigation of the diverse roles played by microorganisms, and to the identification of the microbial potential for biotechnological application, including but not limited to: pharmaceutical, diagnostics, waste treatment, bioremediation and renewable energy generation. An emerging field of research in microbial ecology encompasses system approaches, whereby all levels of biological information are investigated (DNA, RNA, proteins and metabolites) to capture the functional interactions occurring in a given ecosystem and identify characteristics that could not be accessed by the study of isolated components (Röling et al., 2010). Recent technological advances, including the development of high-throughput ‘omics’ methods, make such system approaches possible, where mixed microbial communities are viewed as one meta-organism. Metaproteomics are employed to determine respectively the DNA sequences of the meta-organism under study, the collectively transcribed RNA, the translated proteins and the metabolites resulting from cellular processes. All of the generated data can then be used to identify the metabolic pathways and cellular processes at work within an ecosystem.
1.2 Problem statement
Aquatic ecosystems support a substantial source of the earth’s biological diversity. They are an essential reservoir and share an enormous proportion of earth’s biological productivity. Both aquatic resources and its biodiversity are interrelated to each other and they perform a myriad of functions and are valuable and essential for the sustainability of biotic communities. Aquatic biodiversity in both freshwater and marine environments are under continuous decline because of overexploitation of species, introduced exotic plant or animal, pollution sources from cities, industries and agricultural zones, loss and changes in ecological niche. Their conservation and management in the form of bio reserve points and bioregional management and worldwide monitoring are needed for the protection of the aquatic biodiversity. This study is presenting information on biodiversity in aquatic habitats and their resources, in marine and fresh water ecosystems, their importance conservation and restoration mechanisms using metaproteomics methods.
1.3 Aim of the study
The main aim of the study is to develop and apply metaproteomic platforms to better understand environmental systems and their robustness to change.
1.4 Scope of the study
The scope of this study covers studying the quantity of the molecular cellular components (e.g. DNA, mRNA, proteins and metabolites) in environmental samples can reveal significant information on ecosystem function.
1.5 Significance of the study
This study will provide a means we can gain a much more comprehensive understanding of environmental responses to processes such as climate change or pollution etc. The field known as Environmental Omics is mostly dominated by DNA sequencing. However, proteins are the functional entities in cells and therefore identifying and quantifying proteins gives a much more accurate insight into how ecosystems respond to environmental perturbations. Gaining a snapshot of ecosystem function through measuring the proteins in an environmental sample is referred to as metaproteomics.
The project would suit ideally a biosciences/chemistry graduate with a strong interest in novel and multidisciplinary approaches to environmental engineering, analytics, or mapping ecological responses using new, cutting edge technologies.
This study will serve as a training in quantitative analytical techniques e.g. high performance liquid, mass spectrometry. This includes experimental design and analysis of large amounts of data with bioinformatics pipelines. They will become experts in handling proteins and interpreting complex data. Metaproteomics is a tool that can be transferred to many different fields so flexibility within the project is high.
Metaproteomics is just one of many omics tools which are gaining momentum in their application in the laboratory and the field. The candidate will be developing skills that can be applied for research and development in many different field including the use of cutting edge analytical equipment.
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