Defining Blood Plasma and Serum Metabolome by GC-MS

Metabolomics uses advanced analytical chemistry methods to analyze metabolites in biological samples. The most intensively studied samples are blood and its liquid components: plasma and serum. Armed with advanced equipment and progressive software solutions, the scientific community has shown that small molecules’ roles in living systems are not limited to traditional “building blocks” or “just fuel” for cellular energy. As a result, the conclusions based on studying the metabolome are finding practical reflection in molecular medicine and a better understanding of fundamental biochemical processes in living systems. This review is not a detailed protocol of metabolomic analysis. However, it should support the reader with information about the achievements in the whole process of metabolic exploration of human plasma and serum using mass spectrometry combined with gas chromatography.

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Capabilities

10.1093/oso/9780199674923.003.0023 ◽

2018 ◽

Author(s):

Paul F. M. J. Verschure

Keyword(s):

Building Blocks ◽

Living Systems ◽

System Level ◽

Cognitive Architectures ◽

Multiple Components ◽

Perception Action

This chapter introduces the “Capabilities” section of the Handbook of Living Machines. Where the previous section considered building blocks, we recognize that components or modules do not automatically make systems. Hence, in the remainder of this handbook, the emphasis is toward the capabilities of living systems and their emulation in artifacts. Capabilities often arise from the integration of multiple components and thus sensitize us to the need to develop a system-level perspective on living machines. Here we summarize and consider the 14 contributions in this section which cover perception, action, cognition, communication, and emotion, and the integration of these through cognitive architectures into systems that can emulate the full gamut of integrated behaviors seen in animals including, potentially, our own capacity for consciousness.

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Comparison of Quantitative Morphology of Layered and Arbitrary Patterns: Contrary to Visual Perception, Binary Arbitrary Patterns Are Layered from a Structural Point of View

Applied Sciences ◽

10.3390/app11146300 ◽

2021 ◽

Vol 11 (14) ◽

pp. 6300

Author(s):

Igor Smolyar ◽

Daniel Smolyar

Keyword(s):

Boolean Function ◽

Layer Structure ◽

Central Element ◽

Morphological Characteristics ◽

Building Blocks ◽

Point Of View ◽

Living Systems ◽

Seismic Profiles ◽

Contour Maps ◽

Anisotropic Layers

Patterns found among both living systems, such as fish scales, bones, and tree rings, and non-living systems, such as terrestrial and extraterrestrial dunes, microstructures of alloys, and geological seismic profiles, are comprised of anisotropic layers of different thicknesses and lengths. These layered patterns form a record of internal and external factors that regulate pattern formation in their various systems, making it potentially possible to recognize events in the formation history of these systems. In our previous work, we developed an empirical model (EM) of anisotropic layered patterns using an N-partite graph, denoted as G(N), and a Boolean function to formalize the layer structure. The concept of isotropic and anisotropic layers was presented and described in terms of the G(N) and Boolean function. The central element of the present work is the justification that arbitrary binary patterns are made up of such layers. It has been shown that within the frame of the proposed model, it is the isotropic and anisotropic layers themselves that are the building blocks of binary layered and arbitrary patterns; pixels play no role. This is why the EM can be used to describe the morphological characteristics of such patterns. We present the parameters disorder of layer structure, disorder of layer size, and pattern complexity to describe the degree of deviation of the structure and size of an arbitrary anisotropic pattern being studied from the structure and size of a layered isotropic analog. Experiments with arbitrary patterns, such as regular geometric figures, convex and concave polygons, contour maps, the shape of island coastlines, river meanders, historic texts, and artistic drawings are presented to illustrate the spectrum of problems that it may be possible to solve by applying the EM. The differences and similarities between the proposed and existing morphological characteristics of patterns has been discussed, as well as the pros and cons of the suggested method.

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Synthesis of sp3-rich scaffolds for molecular libraries through complexity-generating cascade reactions

Organic & Biomolecular Chemistry ◽

10.1039/c6ob00961a ◽

2016 ◽

Vol 14 (21) ◽

pp. 4943-4946 ◽

Cited By ~ 21

Author(s):

T. Flagstad ◽

G. Min ◽

K. Bonnet ◽

R. Morgentin ◽

D. Roche ◽

...

Keyword(s):

Small Molecules ◽

Building Blocks ◽

Cascade Reactions ◽

Efficient Strategy ◽

Molecular Libraries

An efficient strategy for the synthesis of complex small molecules from simple building blocks is presented.

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Rapid approach to complex boronic acids

Science Advances ◽

10.1126/sciadv.aaw4607 ◽

2019 ◽

Vol 5 (7) ◽

pp. eaaw4607 ◽

Cited By ~ 5

Author(s):

Constantinos G. Neochoritis ◽

Shabnam Shaabani ◽

Maryam Ahmadianmoghaddam ◽

Tryfon Zarganes-Tzitzikas ◽

Li Gao ◽

...

Keyword(s):

Small Molecules ◽

Boronic Acid ◽

Multicomponent Reactions ◽

Chemical Space ◽

Building Blocks ◽

Acid Synthesis ◽

Success Rates ◽

Boronic Acid Derivatives ◽

Low Coverage ◽

Target Synthesis

The compatibility of free boronic acid building blocks in multicomponent reactions to readily create large libraries of diverse and complex small molecules was investigated. Traditionally, boronic acid synthesis is sequential, synthetically demanding, and time-consuming, which leads to high target synthesis times and low coverage of the boronic acid chemical space. We have performed the synthesis of large libraries of boronic acid derivatives based on multiple chemistries and building blocks using acoustic dispensing technology. The synthesis was performed on a nanomole scale with high synthesis success rates. The discovery of a protease inhibitor underscores the usefulness of the approach. Our acoustic dispensing–enabled chemistry paves the way to highly accelerated synthesis and miniaturized reaction scouting, allowing access to unprecedented boronic acid libraries.

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Mesenchymal stem cells: building blocks for molecular medicine in the 21st century

Trends in Molecular Medicine ◽

10.1016/s1471-4914(01)02016-0 ◽

2001 ◽

Vol 7 (6) ◽

pp. 259-264 ◽

Cited By ~ 791

Author(s):

Arnold I Caplan ◽

Scott P Bruder

Keyword(s):

Stem Cells ◽

Mesenchymal Stem Cells ◽

21St Century ◽

Building Blocks ◽

Molecular Medicine

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General discussion after session V

Philosophical Transactions of the Royal Society of London. Series A, Mathematical and Physical Sciences ◽

10.1098/rsta.1988.0073 ◽

1988 ◽

Vol 325 (1587) ◽

pp. 611-618 ◽

Cited By ~ 1

Keyword(s):

Origin Of Life ◽

Time Perspective ◽

Applied Mathematics ◽

Building Blocks ◽

Living Systems ◽

Organic Chemical ◽

General Terms ◽

The Earth ◽

The Origin Of Life ◽

Emergence Of Life

N. C. Wickramasinghe ( Department of Applied Mathematics and Astronomy, University College, Cardiff, U. K. ). The question of the origin of life is, of course, one of the most important scientific questions and it is also one of the most difficult. One is inevitably faced here with a situation where there are very few empirical facts of direct relevance and perhaps no facts relating to the actual transition from organic material to material that can even remotely be described as living. The time perspective of events that relate to this problem has already been presented by Dr Chang. Uncertainty still persists as to the actual first moment of the origin or the emergence of life on the Earth. At some time between 3800 and 3300 Ma BP the first microscopic living systems seem to have emerged. There is a definite moment in time corresponding to a sudden appearance of cellular-type living systems. Now, traditionally the evolution of carbonaceous compounds which led to the emergence of life on Earth could be divided into three principal steps and I shall just remind you what those steps are. The first step is the production of chemical building blocks that lead to the origin of the organic molecules necessary as a prerequisite for the evolution of life. Step two can be described in general terms as prebiotic evolution, the arrangement of these chemical units into some kind of sequence of precursor systems that come almost up to life but not quite; and then stage three is the early biological evolution which actually effects the transition from proto-cellular organic-type forms into truly cellular living systems. The transition is from organic chemistry, prebiotic chemistry to biochemistry. Those are the three principal stages that have been defined by traditional workers in the field, the people who, as Dr Chang said, have had the courage to make these queries and attempt to answer them. Ever since the classic experiments where organic materials were synthesized in the laboratory a few decades back, it was thought that the first step, the production of organic chemical units, is important for the origin of life on the Earth, and that this had to take place in some location on the Earth itself.

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Unified synthesis of diverse building blocks for application in the discovery of bioactive small molecules

Tetrahedron ◽

10.1016/j.tet.2019.130513 ◽

2019 ◽

Vol 75 (38) ◽

pp. 130513

Author(s):

Scott Rice ◽

Daniel J. Cox ◽

Stephen P. Marsden ◽

Adam Nelson

Keyword(s):

Small Molecules ◽

Building Blocks

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Regulation of assimilate partitioning in leaves

Functional Plant Biology ◽

10.1071/pp99177 ◽

2000 ◽

Vol 27 (6) ◽

pp. 507 ◽

Cited By ~ 9

Author(s):

Charlotte E. Lewis ◽

Graham Noctor ◽

David Causton ◽

Christine H. Foyer

Keyword(s):

Carbon Fixation ◽

Starch Synthesis ◽

Co2 Concentration ◽

Building Blocks ◽

Energy Budgets ◽

Assimilate Partitioning ◽

Fixed Carbon ◽

Carbon And Nitrogen ◽

Cellular Energy ◽

Photosynthetic Carbon

Concepts of the regulation of assimilate partitioning in leaves frequently consider only the allocation of carbon between sucrose and starch synthesis, storage and export. While carbohydrate metabolism accounts for a large proportion of assimilated carbon, such analyses provide only a restricted view of carbon metabolism and partitioning in leaf cells since photosynthetic carbon fixation provides precursors for all other biosynthetic pathways in the plant. Most of these precursors are required for biosynthesis of amino acids that form the building blocks for many compounds in plants. We have used leaf carbon : nitrogen ratios to calculate the allocation of photosynthetic electrons to the assimilation of nitrogen necessary for amino acid formation, and conclude that this allocation is variable but may be higher than values often quoted in the literature. Respiration is a significant fate of fixed carbon. In addition to supplying biosynthetic precursors, respiration is required for energy production and may also act, in both light and dark, to balance cellular energy budgets. We have used growth CO2 concentration and irradiance to modify source activity in Lolium temulentum in order to explore the interactions between photosynthetic carbon and nitrogen assimilation, assimilate production, respiration and export. It is demonstrated that there is a robust correlation between source activity and foliar respiration rates. Under some conditions concomitant increases in source activity and respiration may be necessary to support faster growth. In other conditions, increases in respiration appear to result from internal homeostatic mechanisms that may be candidate targets for increasing yield.

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Cooperative Strategies and Genome Cybernetics in Formation of Complex Bacterial Patterns

MRS Proceedings ◽

10.1557/proc-367-405 ◽

1994 ◽

Vol 367 ◽

Author(s):

Eshel Ben-Jacob ◽

Ofer Shochet ◽

Inon Cohen ◽

Adam Tenenbaum ◽

Andras CzirÓk ◽

...

Keyword(s):

Pattern Formation ◽

Degrees Of Freedom ◽

Cooperative Behavior ◽

Building Blocks ◽

Growth Conditions ◽

Living Systems ◽

Cooperative Strategies ◽

Additional Level ◽

Bacterial Patterns ◽

The Individual

AbstractWe present a study of interfacial pattern formation during growth of bacterial colonies. Growth of bacterial colonies bears similarities but presents an inherent additional level of complexity in comparison with non-living systems. In the former case, the building blocks themselves are living systems, each with its own autonomous self-interest and internal degrees of freedom. The bacteria have developed sophisticated communication channels, which they utilize when growth conditions are tough. Here we present a non-local communicating walkers model to study the effect of local bacterium-bacterium interaction and communication via chemotaxis signaling. We demonstrate how communication enables the colony to develop complex patterns in response to adverse growth conditions. This self-organization of the colony, which can be achieved only via cooperative behavior of the bacteria, may be viewed as the outcome of an interplay between the micro-level (the individual bacterium) and the macro-level (the colony). Some qualitative features of the complex morphologies can be accounted for by invoking ideas from pattern formation in non-living systems together with a simplified model of chemotactic “feedback”.

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