Farhana R. Pinu

Bio: Farhana R. Pinu is an academic researcher from Plant & Food Research. The author has contributed to research in topics: Wine & Winemaking. The author has an hindex of 16, co-authored 25 publications receiving 944 citations. Previous affiliations of Farhana R. Pinu include Stamford University Bangladesh & University of Auckland.

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community.

Abstract: The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches. However, due to their inherent data differences, integrating multiple omics platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with the integration of these complex multi-omics data sets. The question is, how? Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics integration that was held at the recent 'Australian and New Zealand Metabolomics Conference' (ANZMET 2018) in Auckland, New Zealand (Sept. 2018). We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies. We also believe that these ideas may allow the full promise of integrated multi-omics research and, ultimately, of systems biology to be realized.

Review of recent developments in GC-MS approaches to metabolomics-based research.

Abstract: Metabolomics aims to identify the changes in endogenous metabolites of biological systems in response to intrinsic and extrinsic factors. This is accomplished through untargeted, semi-targeted and targeted based approaches. Untargeted and semi-targeted methods are typically applied in hypothesis-generating investigations (aimed at measuring as many metabolites as possible), while targeted approaches analyze a relatively smaller subset of biochemically important and relevant metabolites. Regardless of approach, it is well recognized amongst the metabolomics community that gas chromatography-mass spectrometry (GC–MS) is one of the most efficient, reproducible and well used analytical platforms for metabolomics research. This is due to the robust, reproducible and selective nature of the technique, as well as the large number of well-established libraries of both commercial and ‘in house’ metabolite databases available. This review provides an overview of developments in GC–MS based metabolomics applications, with a focus on sample preparation and preservation techniques. A number of chemical derivatization (in-time, in-liner, offline and microwave assisted) techniques are also discussed. Electron impact ionization and a summary of alternate mass analyzers are highlighted, along with a number of recently reported new GC columns suited for metabolomics. Lastly, multidimensional GC–MS and its application in environmental and biomedical research is presented, along with the importance of bioinformatics. The purpose of this review is to both highlight and provide an update on GC–MS analytical techniques that are common in metabolomics studies. Specific emphasis is given to the key steps within the GC–MS workflow that those new to this field need to be aware of and the common pitfalls that should be looked out for when starting in this area.

Translational Metabolomics: Current Challenges and Future Opportunities.

Abstract: Metabolomics is one of the latest omics technologies that has been applied successfully in many areas of life sciences. Despite being relatively new, a plethora of publications over the years have exploited the opportunities provided through this data and question driven approach. Most importantly, metabolomics studies have produced great breakthroughs in biomarker discovery, identification of novel metabolites and more detailed characterisation of biological pathways in many organisms. However, translation of the research outcomes into clinical tests and user-friendly interfaces has been hindered due to many factors, some of which have been outlined hereafter. This position paper is the summary of discussion on translational metabolomics undertaken during a peer session of the Australian and New Zealand Metabolomics Conference (ANZMET 2018) held in Auckland, New Zealand. Here, we discuss some of the key areas in translational metabolomics including existing challenges and suggested solutions, as well as how to expand the clinical and industrial application of metabolomics. In addition, we share our perspective on how full translational capability of metabolomics research can be explored.

Analysis of Intracellular Metabolites from Microorganisms: Quenching and Extraction Protocols.

Abstract: Sample preparation is one of the most important steps in metabolome analysis. The challenges of determining microbial metabolome have been well discussed within the research community and many improvements have already been achieved in last decade. The analysis of intracellular metabolites is particularly challenging. Environmental perturbations may considerably affect microbial metabolism, which results in intracellular metabolites being rapidly degraded or metabolized by enzymatic reactions. Therefore, quenching or the complete stop of cell metabolism is a pre-requisite for accurate intracellular metabolite analysis. After quenching, metabolites need to be extracted from the intracellular compartment. The choice of the most suitable metabolite extraction method/s is another crucial step. The literature indicates that specific classes of metabolites are better extracted by different extraction protocols. In this review, we discuss the technical aspects and advancements of quenching and extraction of intracellular metabolite analysis from microbial cells.

Extracellular Microbial Metabolomics: The State of the Art

Abstract: Microorganisms produce and secrete many primary and secondary metabolites to the surrounding environment during their growth. Therefore, extracellular metabolites provide important information about the changes in microbial metabolism due to different environmental cues. The determination of these metabolites is also comparatively easier than the extraction and analysis of intracellular metabolites as there is no need for cell rupture. Many analytical methods are already available and have been used for the analysis of extracellular metabolites from microorganisms over the last two decades. Here, we review the applications and benefits of extracellular metabolite analysis. We also discuss different sample preparation protocols available in the literature for both types (e.g., metabolites in solution and in gas) of extracellular microbial metabolites. Lastly, we evaluate the authenticity of using extracellular metabolomics data in the metabolic modelling of different industrially important microorganisms.

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community.

Abstract: The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches. However, due to their inherent data differences, integrating multiple omics platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with the integration of these complex multi-omics data sets. The question is, how? Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics integration that was held at the recent 'Australian and New Zealand Metabolomics Conference' (ANZMET 2018) in Auckland, New Zealand (Sept. 2018). We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies. We also believe that these ideas may allow the full promise of integrated multi-omics research and, ultimately, of systems biology to be realized.

Review of recent developments in GC-MS approaches to metabolomics-based research.

Abstract: Metabolomics aims to identify the changes in endogenous metabolites of biological systems in response to intrinsic and extrinsic factors. This is accomplished through untargeted, semi-targeted and targeted based approaches. Untargeted and semi-targeted methods are typically applied in hypothesis-generating investigations (aimed at measuring as many metabolites as possible), while targeted approaches analyze a relatively smaller subset of biochemically important and relevant metabolites. Regardless of approach, it is well recognized amongst the metabolomics community that gas chromatography-mass spectrometry (GC–MS) is one of the most efficient, reproducible and well used analytical platforms for metabolomics research. This is due to the robust, reproducible and selective nature of the technique, as well as the large number of well-established libraries of both commercial and ‘in house’ metabolite databases available. This review provides an overview of developments in GC–MS based metabolomics applications, with a focus on sample preparation and preservation techniques. A number of chemical derivatization (in-time, in-liner, offline and microwave assisted) techniques are also discussed. Electron impact ionization and a summary of alternate mass analyzers are highlighted, along with a number of recently reported new GC columns suited for metabolomics. Lastly, multidimensional GC–MS and its application in environmental and biomedical research is presented, along with the importance of bioinformatics. The purpose of this review is to both highlight and provide an update on GC–MS analytical techniques that are common in metabolomics studies. Specific emphasis is given to the key steps within the GC–MS workflow that those new to this field need to be aware of and the common pitfalls that should be looked out for when starting in this area.

OUP accepted manuscript

Abstract: Abstract Metabolomics is a field of systems biology that draws on the scientific methods of other groups to qualitatively or quantitatively characterize small molecule metabolites in organisms, revealing their interconnections with the state of the organism at an overall relative macroscopic level. Diabetic kidney disease (DKD) is well known as a chronic metabolic disease, and metabolomics provides an excellent platform for its clinical study. A growing number of metabolomic analyses have revealed that individuals with DKD have metabolic disturbances of multiple substances in their bodies. With the continuous development and improvement of metabolomic analysis technology, the application of metabolomics in the clinical research of DKD is also expanding. This review discusses the recent progress of metabolomics in the early diagnosis, disease prognosis, and pathogenesis of DKD at the level of small molecule metabolites in vivo.

Metabolomics: A New Tool to Reveal the Nature of Diabetic Kidney Disease.

Abstract: Metabolomics is a field of systems biology that draws on the scientific methods of other groups to qualitatively or quantitatively characterize small molecule metabolites in organisms, revealing their interconnections with the state of the organism at an overall relative macroscopic level. Diabetic kidney disease (DKD) is well known as a chronic metabolic disease, and metabolomics provides an excellent platform for its clinical study. A growing number of metabolomic analyses have revealed that individuals with DKD have metabolic disturbances of multiple substances in their bodies. With the continuous development and improvement of metabolomic analysis technology, the application of metabolomics in the clinical research of DKD is also expanding. This review discusses the recent progress of metabolomics in the early diagnosis, disease prognosis, and pathogenesis of DKD at the level of small molecule metabolites in vivo.