scholarly journals Combining Genomics, Metabolome Analysis, and Biochemical Modelling to Understand Metabolic Networks

2001 ◽  
Vol 2 (3) ◽  
pp. 155-168 ◽  
Author(s):  
Oliver Fiehn
Keyword(s):  
Metabolic Networks ◽  
Analytical Techniques ◽  
Cellular Responses ◽  
Protein Profiling ◽  
Gene Products ◽  
Metabolome Analysis ◽  
Genome Sequences ◽  
Potential Applications ◽  
Analytical Approaches ◽  
Accurate Quantification

Now that complete genome sequences are available for a variety of organisms, the elucidation of gene functions involved in metabolism necessarily includes a better understanding of cellular responses upon mutations on all levels of gene products, mRNA, proteins, and metabolites. Such progress is essential since the observable properties of organisms – the phenotypes – are produced by the genotype in juxtaposition with the environment. Whereas much has been done to make mRNA and protein profiling possible, considerably less effort has been put into profiling the end products of gene expression, metabolites. To date, analytical approaches have been aimed primarily at the accurate quantification of a number of pre-defined target metabolites, or at producing fingerprints of metabolic changes without individually determining metabolite identities. Neither of these approaches allows the formation of an in-depth understanding of the biochemical behaviour within metabolic networks. Yet, by carefully choosing protocols for sample preparation and analytical techniques, a number of chemically different classes of compounds can be quantified simultaneously to enable such understanding. In this review, the terms describing various metabolite-oriented approaches are given, and the differences among these approaches are outlined. Metabolite target analysis, metabolite profiling, metabolomics, and metabolic fingerprinting are considered. For each approach, a number of examples are given, and potential applications are discussed.

scholarly journals Characterization and Quantification of Selenoprotein P: Challenges to Mass Spectrometry

2021 ◽  
Vol 22 (12) ◽  
pp. 6283
Author(s):  
Jérémy Lamarche ◽  
Luisa Ronga ◽  
Joanna Szpunar ◽  
Ryszard Lobinski
Keyword(s):  
Mass Spectrometry ◽  
State Of The Art ◽  
Animal Health ◽  
Primary Standard ◽  
Selenoprotein P ◽  
Primary Standards ◽  
Analytical Approaches ◽  
Careful Investigation ◽  
Accurate Quantification

Selenoprotein P (SELENOP) is an emerging marker of the nutritional status of selenium and of various diseases, however, its chemical characteristics still need to be investigated and methods for its accurate quantitation improved. SELENOP is unique among selenoproteins, as it contains multiple genetically encoded SeCys residues, whereas all the other characterized selenoproteins contain just one. SELENOP occurs in the form of multiple isoforms, truncated species and post-translationally modified variants which are relatively poorly characterized. The accurate quantification of SELENOP is contingent on the availability of specific primary standards and reference methods. Before recombinant SELENOP becomes available to be used as a primary standard, careful investigation of the characteristics of the SELENOP measured by electrospray MS and strict control of the recoveries at the various steps of the analytical procedures are strongly recommended. This review critically discusses the state-of-the-art of analytical approaches to the characterization and quantification of SELENOP. While immunoassays remain the standard for the determination of human and animal health status, because of their speed and simplicity, mass spectrometry techniques offer many attractive and complementary features that are highlighted and critically evaluated.

scholarly journals General Analytical Schemes for the Characterization of Pectin-Based Edible Gelled Systems

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Maryam Haghighi ◽  
Karamatollah Rezaei
Keyword(s):  
Image Analysis ◽  
Three Dimensional ◽  
Analytical Techniques ◽  
Physicochemical Analysis ◽  
Visual Observation ◽  
Scientific Data ◽  
Rheological Measurement ◽  
Rheological Measurements ◽  
Analytical Approaches

Pectin-based gelled systems have gained increasing attention for the design of newly developed food products. For this reason, the characterization of such formulas is a necessity in order to present scientific data and to introduce an appropriate finished product to the industry. Various analytical techniques are available for the evaluation of the systems formulated on the basis of pectin and the designed gel. In this paper, general analytical approaches for the characterization of pectin-based gelled systems were categorized into several subsections including physicochemical analysis, visual observation, textural/rheological measurement, microstructural image characterization, and psychorheological evaluation. Three-dimensional trials to assess correlations among microstructure, texture, and taste were also discussed. Practical examples of advanced objective techniques including experimental setups for small and large deformation rheological measurements and microstructural image analysis were presented in more details.

scholarly journals Sulprostone-Induced Gastric Dysrhythmia in the Ferret: Conventional and Advanced Analytical Approaches

2021 ◽  
Vol 11 ◽  
Author(s):  
Zengbing Lu ◽  
Yu Zhou ◽  
Longlong Tu ◽  
Sze Wa Chan ◽  
Man P. Ngan ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Body Temperature ◽  
Core Body Temperature ◽  
Analytical Techniques ◽  
Dominant Frequency ◽  
Fluctuation Analysis ◽  
Prostaglandin E ◽  
Myoelectric Activity ◽  
Core Body ◽  
Analytical Approaches

Nausea and emesis resulting from disease or drug treatment may be associated with disrupted gastric myoelectric activity (GMA). Conventional analytical techniques can determine the relative degrees of brady-, normo-, and tachygastric power, but lose information relative to the basic slow wave shape. The aim of the present study was to investigate the application of advanced analytical techniques in the analysis of disrupted GMA recorded after administration of sulprostone, a prostaglandin E3/1 agonist, in ferrets. Ferrets were implanted with radiotelemetry devices to record GMA, blood pressure, heart rate (HR) and core body temperature 1 week before the administration of sulprostone (30 μg/kg) or vehicle (saline, 0.5 mL/kg). GMA was initially analyzed using fast Fourier transformations (FFTs) and a conventional power partitioning. Detrended fluctuation analysis (DFA) was also applied to the GMA recordings to reveal information relative to the fluctuation of signals around local trends. Sample entropy (SampEn) analysis was used for examining the regularity of signals. Conventional signal processing techniques revealed that sulprostone increased the dominant frequency (DF) of slow waves, with an increase in the percentage power of the tachygastric range and a decrease in the percentage power of the normogastric range. DFA revealed that sulprostone decreased the fluctuation function, indicative of a loss of the variability of GMA fluctuations around local trends. Sulprostone increased SampEn values, indicating a loss of regularity in the GMA data. Behaviorally, sulprostone induced emesis and caused defecation. It also increased blood pressure and elevated HR, with an associated decrease in HR variability (HRV). Further analysis of HRV revealed a decrease in both low-frequency (LF) and high-frequency (HF) components, with an overall increase in the LF/HF ratio. Sulprostone did not affect core body temperature. In conclusion, DFA and SampEn permit a detailed analysis of GMA, which is necessary to understand the action of sulprostone to modulate gastric function. The action to decrease HRV and increase the LF/HF ratio may be consistent with a shift toward sympathetic nervous system dominance, commonly seen during nausea.

Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets

2012 ◽  
pp. 774-791
Author(s):  
Takeyuki Tamura ◽  
Kazuhiro Takemoto ◽  
Tatsuya Akutsu
Keyword(s):  
Integer Programming ◽  
Metabolic Network ◽  
Drug Targets ◽  
Metabolic Networks ◽  
Boolean Model ◽  
Pentose Phosphate ◽  
Minimum Size ◽  
E Coli ◽  
Potential Applications ◽  
Vertex Set

In this paper, the authors consider the problem of, given a metabolic network, a set of source compounds and a set of target compounds, finding a minimum size reaction cut, where a Boolean model is used as a model of metabolic networks. The problem has potential applications to measurement of structural robustness of metabolic networks and detection of drug targets. They develop an integer programming-based method for this optimization problem. In order to cope with cycles and reversible reactions, they further develop a novel integer programming (IP) formalization method using a feedback vertex set (FVS). When applied to an E. coli metabolic network consisting of Glycolysis/Glyconeogenesis, Citrate cycle and Pentose phosphate pathway obtained from KEGG database, the FVS-based method can find an optimal set of reactions to be inactivated much faster than a naive IP-based method and several times faster than a flux balance-based method. The authors also confirm that our proposed method works even for large networks and discuss the biological meaning of our results.

scholarly journals High-throughput phenotyping in cotton: a review

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Irish Lorraine B. PABUAYON ◽  
Yazhou SUN ◽  
Wenxuan GUO ◽  
Glen L. RITCHIE
Keyword(s):  
High Throughput ◽  
Cropping Systems ◽  
Three Dimensional ◽  
Growth Yield ◽  
Analytical Techniques ◽  
Phenotypic Traits ◽  
Technological Advances ◽  
Recent Developments ◽  
Potential Applications ◽  
High Throughput Phenotyping

Abstract Recent technological advances in cotton (Gossypium hirsutum L.) phenotyping have offered tools to improve the efficiency of data collection and analysis. High-throughput phenotyping (HTP) is a non-destructive and rapid approach of monitoring and measuring multiple phenotypic traits related to the growth, yield, and adaptation to biotic or abiotic stress. Researchers have conducted extensive experiments on HTP and developed techniques including spectral, fluorescence, thermal, and three-dimensional imaging to measure the morphological, physiological, and pathological resistance traits of cotton. In addition, ground-based and aerial-based platforms were also developed to aid in the implementation of these HTP systems. This review paper highlights the techniques and recent developments for HTP in cotton, reviews the potential applications according to morphological and physiological traits of cotton, and compares the advantages and limitations of these HTP systems when used in cotton cropping systems. Overall, the use of HTP has generated many opportunities to accurately and efficiently measure and analyze diverse traits of cotton. However, because of its relative novelty, HTP has some limitations that constrains the ability to take full advantage of what it can offer. These challenges need to be addressed to increase the accuracy and utility of HTP, which can be done by integrating analytical techniques for big data and continuous advances in imaging.

About this title - Application of Analytical Techniques to Petroleum Systems

10.1144/sp484 ◽  
2020 ◽  
Vol 484 (1) ◽  
pp. NP-NP
Author(s):  
Patrick J. Dowey ◽  
Mark Osborne ◽  
Herbert Volk
Keyword(s):  
Oil And Gas ◽  
Organic Geochemistry ◽  
Analytical Techniques ◽  
Petroleum Exploration ◽  
Electricity Production ◽  
Sediment Provenance ◽  
Chemical Production ◽  
Petroleum Systems ◽  
Wide Range ◽  
Analytical Approaches

Cutting-edge techniques have always been utilized in petroleum exploration and production to reduce costs and improve efficiencies. The demand for petroleum in the form of oil and gas is expected to increase for electricity production, transport and chemical production, largely driven by an increase in energy consumption in the developing world. Innovations in analytical methods will continue to play a key role in the industry moving forwards as society shifts towards lower carbon energy systems and more advantaged oil and gas resources are targeted. This volume brings together new analytical approaches and describes how they can be applied to the study of petroleum systems. The papers within this volume cover a wide range of topics and case studies, in the fields of fluid and isotope geochemistry, organic geochemistry, imaging and sediment provenance. The work illustrates how the current, state-of-the-art technology can be effectively utilised to address ongoing challenges in petroleum geoscience.

scholarly journals Engineering microbial chemical factories using metabolic models

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Debolina Sarkar ◽  
Costas D. Maranas
Keyword(s):  
Metabolic Engineering ◽  
Metabolic Networks ◽  
Reaction Rates ◽  
Control Engineering ◽  
Current Perspective ◽  
Simple Molecules ◽  
Living Organisms ◽  
Metabolic Network Modeling ◽  
And Control ◽  
Analytical Approaches

Abstract Living organisms in analogy with chemical factories use simple molecules such as sugars to produce a variety of compounds which are necessary for sustaining life and some of which are also commercially valuable. The metabolisms of simple (such as bacteria) and higher organisms (such as plants) alike can be exploited to convert low value inputs into high value outputs. Unlike conventional chemical factories, microbial production chassis are not necessarily tuned for a single product overproduction. Despite the same end goal, metabolic and industrial engineers rely on different techniques for achieving productivity goals. Metabolic engineers cannot affect reaction rates by manipulating pressure and temperature, instead they have at their disposal a range of enzymes and transcriptional and translational processes to optimize accordingly. In this review, we first highlight how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed in systems and control engineering. Specifically, how algorithmic concepts derived in operations research can help explain the structure and organization of metabolic networks. Finally, we consider the future directions and challenges faced by the field of metabolic network modeling and the possible contributions of concepts drawn from the classical fields of chemical and control engineering. The aim of the review is to offer a current perspective of metabolic engineering and all that it entails without requiring specialized knowledge of bioinformatics or systems biology.

Proteomics: current techniques and potential applications to lung disease

2004 ◽  
Vol 287 (1) ◽  
pp. L1-L23 ◽  
Author(s):  
Jan Hirsch ◽  
Kirk C. Hansen ◽  
Alma L. Burlingame ◽  
Michael A. Matthay
Keyword(s):  
Posttranslational Modifications ◽  
Protein Separation ◽  
Protein Identification ◽  
Cell Types ◽  
Protein Profiling ◽  
Complex Samples ◽  
Potential Value ◽  
Potential Applications ◽  
Tissue Specimens ◽  
Different Cell Types

Proteomics aims to study the whole protein content of a biological sample in one set of experiments. Such an approach has the potential value to acquire an understanding of the complex responses of an organism to a stimulus. The large vascular and air space surface area of the lung expose it to a multitude of stimuli that can trigger a variety of responses by many different cell types. This complexity makes the lung a promising, but also challenging, target for proteomics. Important steps made in the last decade have increased the potential value of the results of proteomics studies for the clinical scientist. Advances in protein separation and staining techniques have improved protein identification to include the least abundant proteins. The evolution in mass spectrometry has led to the identification of a large part of the proteins of interest rather than just describing changes in patterns of protein spots. Protein profiling techniques allow the rapid comparison of complex samples and the direct investigation of tissue specimens. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. These methodologies have made the application of proteomics on the study of specific diseases or biological processes under clinically relevant conditions possible. The quantity of data that is acquired with these new techniques places new challenges on data processing and analysis. This article provides a brief review of the most promising proteomics methods and some of their applications to pulmonary research.

Overview of the current status of sediment chemical analysis: trends in analytical techniques

2010 ◽  
Vol 18 (NA) ◽  
pp. 37-59 ◽  
Author(s):  
Don-Roger Parkinson ◽  
Julian M. Dust
Keyword(s):  
Chemical Analysis ◽  
Organic Contaminants ◽  
Analytical Techniques ◽  
Integrated Approach ◽  
Extraction Methods ◽  
Current Status ◽  
Anthropogenic Pollutants ◽  
The Status ◽  
Analytical Approaches ◽  
Inorganic And Organic

This article reviews selected techniques and current trends in the analysis of contaminants in sediments since the year 2000. Because of the variety of anthropogenic target analytes encountered in sediments, the monograph is separated into inorganic and organic subsections. Practical aspects, including advances in: analysis of standards, biological methods, instrumental methods, modeling aspects, sample preparation and extraction methods, and speciation techniques are discussed. The sediment matrices are complex and require an integrated approach encompassing sampling, preparation, extraction, and analysis steps to reach the detection levels required. Often hyphenated techniques are employed to utilize the multi-resolving and isolation powers of the combined instrumentation. The review mainly focuses on the ability of developing techniques and their approaches and applications not only to solve new problems but also to push detection limits on historically well known inorganic and organic contaminants, while highlighting emerging persistent organic pollutants. The impetus of such research is to obtain a more factual understanding of an ecosystem and overall condition of its habitant in the context of sediments that may act as reservoirs for anthropogenic pollutants. The review is not comprehensive but rather provides an overview of the status of sediment chemical analysis and focuses on the trends in analytical approaches towards analytes of anthropogenic contaminants in sediments.

With the Right Map, Survey Key Driver Analysis Can Help Get Organizations to the Right Destination

2017 ◽  
Vol 10 (2) ◽  
pp. 290-298
Author(s):  
Charles A. Scherbaum ◽  
Justin Black ◽  
Sara P. Weiner
Keyword(s):  
Data Analysis ◽  
Best Practices ◽  
Survey Data ◽  
Analytical Techniques ◽  
Opinion Survey ◽  
Key Driver ◽  
Driver Analysis ◽  
Employee Opinion Survey ◽  
The Right ◽  
Analytical Approaches

Cucina, Walmsley, Gast, Martin, and Curtin (2017) raise an important issue in evaluating whether our current approaches for key driver analysis on employee opinion survey data are indeed best practices. As has been argued elsewhere (Putka & Oswald, 2016; Scherbaum, Putka, Naidoo, & Youssefnia, 2010), there is and can be misalignment between current and best practices. We agree with Cucina et al. that our field should engage in larger discussion of these issues. That discussion is critical, as industrial and organizational (I-O) psychologists are competing with those outside our field who have either little knowledge of best practices in data analysis (but who have been empowered by technology that automates the analysis) or little knowledge of psychology (but a great deal of knowledge in big data analytical techniques). I-O psychologists are in the vanguard of survey data analysis (Ducey et al., 2015), and we have a responsibility to maintain the standards of our field as well as to wield our influence to guide other practitioners outside our field on sound theoretical and analytical approaches.

Sign in / Sign up

Export Citation Format

Share Document