Aquamoleculomics: A Thermodynamic Cornerstone of Systems Biology

2021 ◽  
Author(s):  
Zilin Nie ◽  
Yanming Nie
Keyword(s):  
Systems Biology ◽  
Thermodynamic Characteristics ◽  
Living System ◽  
Structure And Function ◽  
Biological Processes ◽  
Modern Biology ◽  
Cell Tissue ◽  
Novel Concept ◽  
And Function ◽  
Current Systems

Systems biology has been established for more than a decade in the post-genomic era. With the help of the computational and mathematical tools, systems biology reconstitutes the entire scenario of the cell, tissue and even organism from the pieces data generated in the past decades. However, the modern biology is mainly focusing on the structure and function of the biomolecule, cell, tissue or organ, which are far from the essence of the life because of missing thermodynamic information. It is doubtable that the current systems biology-based omics is no-how to fully understand the dynamic courses of the structure, function and information in life. For this reason, we promote a novel concept of aquamoleculomics, in which the biological structure and function as well as thermodynamic characteristics and bioinformation of the aquamolecule complexes are included in this theoretical model of systems biology. Water is mother of life, matter and matrix of organism. Indeed, the fundamental roles of H2O molecules in biological processes might be dramatically underestimated. Extremely speaking, H2O networks in the living system might be engaged in all the biological processes including building all the biological structures, the residential places of the motherhood molecules as the honeycombs of honeybees.

Fractal analysis in biology and medicine

2020 ◽  
pp. 85-92
Keyword(s):  
Fractal Analysis ◽  
A Priori ◽  
Research Work ◽  
Structure And Function ◽  
Review Article ◽  
Living Systems ◽  
Modern Biology ◽  
Additional Information ◽  
Important Additional Information ◽  
And Function

The review article discusses the possibilities of using fractal mathematical analysis to solve scientific and applied problems of modern biology and medicine. The authors show that only such an approach, related to the section of nonlinear mechanics, allows quantifying the chaotic component of the structure and function of living systems, that is a priori important additional information and expands, in particular, the possibilities of diagnostics, differential diagnosis and prediction of the course of physiological and pathological processes. A number of examples demonstrate the specific advantages of using fractal analysis for these purposes. The conclusion can be made that the expanded use of fractal analysis methods in the research work of medical and biological specialists is promising.

scholarly journals The contribution of voltage clamp fluorometry to the understanding of channel and transporter mechanisms

2019 ◽  
Vol 151 (10) ◽  
pp. 1163-1172 ◽  
Author(s):  
John Cowgill ◽  
Baron Chanda
Keyword(s):  
Voltage Clamp ◽  
Conformational Changes ◽  
Physiological State ◽  
Structure And Function ◽  
Modern Biology ◽  
The Past ◽  
Mechanistic Insight ◽  
Atomistic Models ◽  
Multiple Conformations ◽  
And Function

Key advances in single particle cryo-EM methods in the past decade have ushered in a resolution revolution in modern biology. The structures of many ion channels and transporters that were previously recalcitrant to crystallography have now been solved. Yet, despite having atomistic models of many complexes, some in multiple conformations, it has been challenging to glean mechanistic insight from these structures. To some extent this reflects our inability to unambiguously assign a given structure to a particular physiological state. One approach that may allow us to bridge this gap between structure and function is voltage clamp fluorometry (VCF). Using this technique, dynamic conformational changes can be measured while simultaneously monitoring the functional state of the channel or transporter. Many of the important papers that have used VCF to probe the gating mechanisms of channels and transporters have been published in the Journal of General Physiology. In this review, we provide an overview of the development of VCF and discuss some of the key problems that have been addressed using this approach. We end with a brief discussion of the outlook for this technique in the era of high-resolution structures.

scholarly journals Glycans for the greater good

2021 ◽  
Author(s):  
Jessica Lloyd
Keyword(s):  
Climate Change ◽  
Infectious Disease ◽  
Point Of Care ◽  
Structure And Function ◽  
Biological Processes ◽  
Biological Impact ◽  
Heterogeneous Nature ◽  
Health And Disease ◽  
Greater Good ◽  
And Function

Carbohydrates are ubiquitous in nature and present across all kingdoms of life – bacteria, fungi, viruses, yeast, plants, animals and humans. They are essential to many biological processes. However, due to their complexity and heterogeneous nature they are often neglected, sometimes referred to as the ‘dark matter’ of biology. Nevertheless, due to their extensive biological impact on health and disease, glycans and the field of glycobiology have become increasingly popular in recent years, giving rise to glycan-based drug development and therapeutics. Forecasting of communicable diseases predicts that we will see an increase in pandemics of humans and livestock due to global loss of biodiversity from changes to land use, intensification of agriculture, climate change and disruption of ecosystems. As such, the development of point-of-care devices to detect pathogens is vital to prevent the transmission of infectious disease, as we have seen with the COVID-19 pandemic. So, can glycans be exploited to detect COVID-19 and other infectious diseases? And is this technology sensitive and accurate? Here, I discuss the structure and function of glycans, the current glycan-based therapeutics and how glycan binding can be exploited for detection of infectious disease, like COVID-19.

scholarly journals Sex and the cardiovascular system: the intriguing tale of how women and men regulate cardiovascular function differently

2007 ◽  
Vol 31 (1) ◽  
pp. 17-22 ◽  
Author(s):  
Virginia H. Huxley
Keyword(s):  
Cardiovascular System ◽  
Cardiovascular Function ◽  
Living System ◽  
Structure And Function ◽  
Men And Women ◽  
Diagnostic Instruments ◽  
Appropriate Treatment ◽  
Organ Systems ◽  
Males And Females ◽  
And Function

The ability to recognize and appreciate from a reproductive standpoint that males and females possess different attributes has been long standing. Only more recently have we begun to look more deeply into both the similarities and differences between men and women, as well as between boys and girls, with respect to the structure and function of other organ systems. This article focuses on the cardiovascular system, with examples of sex differences in the control of coronary function, blood pressure, and volume. Recognizing the differences between the sexes with respect to cardiovascular function facilitates understanding of the mechanisms whereby homeostasis can be achieved using different contributions or components of the living system. Furthermore, recognition of the differences as well as the similarities permits the design of appropriate diagnostic instruments, recognition of sex-specific pathophysiology, and implementation of appropriate treatment of cardiovascular disease in men and women.

A Laboratory Exercise to Explore Sustained Gravitational-Force Tolerance by Insects

2015 ◽  
Vol 77 (9) ◽  
pp. 707-709
Author(s):  
W. Wyatt Hoback ◽  
Adrianne Pursley ◽  
Kerri Farnsworth-Hoback ◽  
Leon G. Higley
Keyword(s):  
Gravitational Force ◽  
Structure And Function ◽  
Background Information ◽  
Biological Processes ◽  
Scientific Process ◽  
Laboratory Exercise ◽  
Physical Forces ◽  
And Function

This exercise examines the correlation between gravitational-force (g-force) tolerance and the sizes of organisms, emphasizing differences between vertebrates and invertebrates, particularly the effects of size and scale on biological processes. Students form a hypothesis based on background information and then test it by spinning subjects in a centrifuge. Class results can be graphed, analyzed, and compared to human tolerance. The activity engages students in scientific process while investigating the effects of physical forces on structure and function.

scholarly journals Comparative Analysis of Super-enhancers Across Mammals Reveals Their High Function Conservation

2020 ◽  
Author(s):  
Yanling Peng ◽  
Yubo Zhang
Keyword(s):  
Cell Types ◽  
Regulatory Elements ◽  
Biological Processes ◽  
Orthologous Sequence ◽  
Orthologous Genes ◽  
Promoter Regions ◽  
Cell Tissue ◽  
Intergenic Regions ◽  
Regulation Function ◽  
And Function

Abstract BackgroundSuper-enhancers (SEs) are key positive regulatory elements in defining cells/tissues identity in mammals, yet their similarities and differences of sequence and function across mammals have been poor studied. To allow sequence and function comparison across mammalian SEs, we employ H3K27ac ChIP-seq data to six cell types/tissues across human, pig, and mouse, which represent different lineages of mammals in the evolutionary tree.ResultsOverall, a median of 848 human SEs, 888 pig SEs and 503 mouse SEs are identified across cells/tissues. These SEs are largely distributed in promoter regions for human (91.9% in median) and mouse (63.4% in median), while mostly in distal intergenic regions for pig (66.1% in median). Extremely higher unique orthologous SEs frequency (91.6%~92.1%) has been detected for the same cell/tissue across species. Consistently, their overlapping rates are very low for the same cell/tissue across species (0.1%~0.5%). For the SE-associated orthologous genes, they also show high unique frequency for species (63.3%~83.9%) and low overlapping rates (0.8%~1.3%) at inter-species comparison. However, orthologous SEs function comparisons across species have shown similar biological processes related to cells/tissues identity in the top 15 significant enriched terms for the same cell/tissue. Meanwhile, common core transcription factors that determine cells/tissues identity are determined for the same cell/tissue across mammals.ConclusionsThis study highlights the differences of SEs genomic distribution across mammals. It reveals low orthologous sequence overlapping but high function conservation of SEs across mammals. It would improve our understanding of regulation function cis-regulatory elements in mammals.

scholarly journals Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology

2006 ◽  
Vol 17 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Kurt W. Kohn ◽  
Mirit I. Aladjem ◽  
John N. Weinstein ◽  
Yves Pommier
Keyword(s):  
Computer Simulation ◽  
Systems Biology ◽  
Molecular Interactions ◽  
Molecular Interaction ◽  
Structure And Function ◽  
Graphical Notations ◽  
Interaction Map ◽  
And Function ◽  
Network Diagrams

A standard for bioregulatory network diagrams is urgently needed in the same way that circuit diagrams are needed in electronics. Several graphical notations have been proposed, but none has become standard. We have prepared many detailed bioregulatory network diagrams using the molecular interaction map (MIM) notation, and we now feel confident that it is suitable as a standard. Here, we describe the MIM notation formally and discuss its merits relative to alternative proposals. We show by simple examples how to denote all of the molecular interactions commonly found in bioregulatory networks. There are two forms of MIM diagrams. “Heuristic” MIMs present the repertoire of interactions possible for molecules that are colocalized in time and place. “Explicit” MIMs define particular models (derived from heuristic MIMs) for computer simulation. We show also how pathways or processes can be highlighted on a canonical heuristic MIM. Drawing a MIM diagram, adhering to the rules of notation, imposes a logical discipline that sharpens one's understanding of the structure and function of a network.

From protoplasmic theory to cellular systems biology: a 150-year reflection

2010 ◽  
Vol 298 (6) ◽  
pp. C1280-C1290 ◽  
Author(s):  
G. Rickey Welch ◽  
James S. Clegg
Keyword(s):  
Systems Biology ◽  
Cell Biology ◽  
Cell Structure ◽  
Structure And Function ◽  
Cellular Systems ◽  
Controversial Issues ◽  
Cell Theory ◽  
History Of ◽  
And Function

Present-day cellular systems biology is producing data on an unprecedented scale. This field has generated a renewed interest in the holistic, “system” character of cell structure-and-function. Underlying the data deluge, however, there is a clear and present need for a historical foundation. The origin of the “system” view of the cell dates to the birth of the protoplasm concept. The 150-year history of the role of “protoplasm” in cell biology is traced. It is found that the “protoplasmic theory,” not the “cell theory,” was the key 19th-century construct that drove the study of the structure-and-function of living cells and set the course for the development of modern cell biology. The evolution of the “protoplasm” picture into the 20th century is examined by looking at controversial issues along the way and culminating in the current views on the role of cytological organization in cellular activities. The relevance of the “protoplasmic theory” to 21st-century cellular systems biology is considered.

scholarly journals Polyamines Mediate Folding of Primordial Hyper-Acidic Helical Proteins

2020 ◽  
Author(s):  
Dragana Despotović ◽  
Liam M. Longo ◽  
Einav Aharon ◽  
Amit Kahana ◽  
Tali Scherf ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Structure And Function ◽  
Biological Processes ◽  
Phosphodiester Backbone ◽  
Chemical Chaperones ◽  
Disordered Protein ◽  
Early Proteins ◽  
Amine Groups ◽  
Helical Proteins ◽  
And Function

AbstractPolyamines are known to mediate diverse biological processes, and specifically to bind and stabilize compact conformations of nucleic acids, acting as chemical chaperones that promote folding by offsetting the repulsive negative charges of the phosphodiester backbone. However, whether and how polyamines modulate the structure and function of proteins remains unclear. Further, early proteins are thought to have been highly acidic, like nucleic acids, due to a scarcity of basic amino acids in the prebiotic context. Perhaps polyamines, the abiotic synthesis of which is simple, could have served as chemical chaperones for such primordial proteins? We replaced all lysines of an ancestral 60-residue helix-bundle protein to glutamate, resulting in a disordered protein with 21 glutamates in total. Polyamines efficiently induce folding of this hyper-acidic protein at sub-millimolar concentrations, and their potency scaled with the number of amine groups. Compared to cations, polyamines were several orders of magnitude more potent than Na+, while Mg2+ and Ca2+ had an effect similar to a di-amine, inducing folding at approximately seawater concentrations. We propose that (i) polyamines and dications may have had a role in promoting folding of early proteins devoid of basic residues, and that (ii) coil-helix transitions could be the basis of polyamine regulation in contemporary proteins.

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