scholarly journals Tracing the Ancestry of Operons in Bacteria

2017 ◽  
Author(s):  
Huy N Nguyen ◽  
Ashish Jain ◽  
Oliver Eulenstein ◽  
Iddo Friedberg
Keyword(s):  
Complex Systems ◽  
Protein Structures ◽  
Software Tool ◽  
Molecular Complexes ◽  
Ancestral Gene ◽  
Gene Block ◽  
Molecular Systems ◽  
Polycistronic Mrna ◽  
Operon Evolution ◽  
The Individual

Complexity is a fundamental attribute of life. Complex systems are made of parts that together perform functions that a single component, or subsets containing individual components, cannot. Examples of complex molecular systems include protein structures such as the F1Fo-ATPase, the ribosome, or the flagellar motor: each one of these structures requires most or all of its components to function properly. Given the ubiquity of complex systems in the biosphere, understanding the evolution of complexity is central to biology. At the molecular level, operons are a classic example of a complex system. An operon's genes are co-transcribed under the control of a single promoter to a polycistronic mRNA molecule, and the operon's gene products often form molecular complexes or metabolic pathways. With the large number of complete bacterial genomes available, we now have the opportunity to explore the evolution of these complex entities, by identifying possible intermediate states of operons. In this work, we developed a maximum parsimony algorithm to reconstruct ancestral operon states, and show a simple vertical evolution model of how operons may evolve from the individual component genes. We describe several ancestral states that are plausible functional intermediate forms leading to the full operon. We also offer Reconstruction of Ancestral Gene blocks Using Events or ROAGUE as a software tool for those interested in exploring gene block and operon evolution.

scholarly journals Tracing the ancestry of operons in bacteria

2019 ◽  
Vol 35 (17) ◽  
pp. 2998-3004 ◽  
Author(s):  
Huy N Nguyen ◽  
Ashish Jain ◽  
Oliver Eulenstein ◽  
Iddo Friedberg
Keyword(s):  
Complex Systems ◽  
Protein Structures ◽  
Software Tool ◽  
Molecular Complexes ◽  
Supplementary Information ◽  
Ancestral Gene ◽  
Gene Block ◽  
Molecular Systems ◽  
Polycistronic Mrna ◽  
The Individual

Abstract Motivation Complexity is a fundamental attribute of life. Complex systems are made of parts that together perform functions that a single component, or subsets of components, cannot. Examples of complex molecular systems include protein structures such as the F1Fo-ATPase, the ribosome, or the flagellar motor: each one of these structures requires most or all of its components to function properly. Given the ubiquity of complex systems in the biosphere, understanding the evolution of complexity is central to biology. At the molecular level, operons are classic examples of a complex system. An operon’s genes are co-transcribed under the control of a single promoter to a polycistronic mRNA molecule, and the operon’s gene products often form molecular complexes or metabolic pathways. With the large number of complete bacterial genomes available, we now have the opportunity to explore the evolution of these complex entities, by identifying possible intermediate states of operons. Results In this work, we developed a maximum parsimony algorithm to reconstruct ancestral operon states, and show a simple vertical evolution model of how operons may evolve from the individual component genes. We describe several ancestral states that are plausible functional intermediate forms leading to the full operon. We also offer Reconstruction of Ancestral Gene blocks Using Events or ROAGUE as a software tool for those interested in exploring gene block and operon evolution. Availability and implementation The software accompanying this paper is available under GPLv3 license on: https://github.com/nguyenngochuy91/Ancestral-Blocks-Reconstruction. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Controlling the length of porphyrin supramolecular polymers via coupled equilibria and dilution-induced supramolecular polymerization

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Elisabeth Weyandt ◽  
Luigi Leanza ◽  
Riccardo Capelli ◽  
Giovanni M. Pavan ◽  
Ghislaine Vantomme ◽  
...  
Keyword(s):  
Complex Systems ◽  
Self Assembly ◽  
Chiral Discrimination ◽  
Coarse Grained ◽  
Supramolecular Polymers ◽  
Supramolecular System ◽  
Precise Control ◽  
Aggregate Morphology ◽  
The Individual ◽  
Supramolecular Polymerization

AbstractMulti-component systems often display convoluted behavior, pathway complexity and coupled equilibria. In recent years, several ways to control complex systems by manipulating the subtle balances of interaction energies between the individual components have been explored and thereby shifting the equilibrium between different aggregate states. Here we show the enantioselective chain-capping and dilution-induced supramolecular polymerization with a Zn2+-porphyrin-based supramolecular system when going from long, highly cooperative supramolecular polymers to short, disordered aggregates by adding a monotopic Mn3+-porphyrin monomer. When mixing the zinc and manganese centered monomers, the Mn3+-porphyrins act as chain-cappers for Zn2+-porphyrin supramolecular polymers, effectively hindering growth of the copolymer and reducing the length. Upon dilution, the interaction between chain-capper and monomers weakens as the equilibria shift and long supramolecular polymers form again. This dynamic modulation of aggregate morphology and length is achieved through enantioselectivity in the aggregation pathways and concentration-sensitive equilibria. All-atom and coarse-grained molecular simulations provide further insights into the mixing of the species and their exchange dynamics. Our combined experimental and theoretical approach allows for precise control of molecular self-assembly and chiral discrimination in complex systems.

scholarly journals Confronting Functional Complexity Failures: The Case of a Runway Excursion in Munich

2019 ◽  
Vol 63 (1) ◽  
pp. 116-120
Author(s):  
Robert Mauro ◽  
Lance Sherry
Keyword(s):  
Complex Systems ◽  
Emergent Behavior ◽  
Operating Region ◽  
Geographically Distributed ◽  
Functional Complexity ◽  
The Individual ◽  
Emergent Behaviors ◽  
Normal Accidents

Complex systems often produce unanticipated emergent behavior as a result of the interactions between behaviorally complex sub-systems or agents. The sub-systems may be human or artificial. They may be co-located or geographically distributed and operate autonomously. Although the individual sub-systems may be tested and certified for high levels of reliability (e.g. 10-7), interactions between the sub-systems may occur so that emergent behaviors allow the system to migrate into an unsafe operating region. This may occur even when all of the sub-systems are behaving nominally and no equipment has failed. This phenomenon is called a “functional complexity failure.” In this paper, we present an analysis of a functional complexity failure that resulted in a runway excursion and discuss the options for detecting and mitigating the conditions for these “normal accidents” before the accident occurs.

scholarly journals Closed-loop conductance scanning tunneling spectroscopy: demonstrating the equivalence to the open-loop alternative

2015 ◽  
Vol 6 ◽  
pp. 1116-1124 ◽  
Author(s):  
Chris Hellenthal ◽  
Kai Sotthewes ◽  
Martin H Siekman ◽  
E Stefan Kooij ◽  
Harold J W Zandvliet
Keyword(s):  
Closed Loop ◽  
Scanning Tunneling Spectroscopy ◽  
Tunneling Spectroscopy ◽  
Open Loop ◽  
Scanning Tunneling ◽  
Image Charge ◽  
Tunneling Barrier ◽  
Molecular Systems ◽  
Individual Contributions ◽  
The Individual

We demonstrate the validity of using closed-loop z(V) conductance scanning tunneling spectroscopy (STS) measurements for the determination of the effective tunneling barrier by comparing them to more conventional open-loop I(z) measurements. Through the development of a numerical model, the individual contributions to the effective tunneling barrier present in these experiments, such as the work function and the presence of an image charge, are determined quantitatively. This opens up the possibility of determining tunneling barriers of both vacuum and molecular systems in an alternative and more detailed manner.

A Reorientation of Niche Theory in Human Ecology

1986 ◽  
Vol 29 (2) ◽  
pp. 259-283 ◽  
Author(s):  
Cynthia A. Broussard ◽  
Gerald L. Young
Keyword(s):  
Social Sciences ◽  
Complex Systems ◽  
Human Ecology ◽  
Social Forces ◽  
Niche Theory ◽  
Species Problem ◽  
Social Scientists ◽  
The Past ◽  
The Individual ◽  
The Relationship

Symptomatic of social forces is the character of the relationship between the individual and society; study of that relationship is central to sociology, a part-whole problem shared with other social sciences. A number of sociological concepts have been developed at least in part to examine this relationship. In the past couple of decades, sociologists and other social scientists have borrowed from niche theory in biological ecology, applying niche in a number of ways. In this article, the Hutchinsonian revolution in niche theory is stressed to establish that adaptations of niche into sociological human ecology are based on misleading analogies and are derived from a failure to recognize the implications of changes in niche theory. The difficulties issue in part from “the species problem” and from unclear differentiation between niche and more established sociological concepts, particularly role and status. These differences are specified and clarified prior to a radical reorientation of niche in human ecology. The reorientation resolves the species problem, updates and reinforces ties with biological ecology, and enlarges the potential for study of the linkages between individual and society and between micro and macro in complex systems.

Analysis of hydraulic systems on the basis of the decomposition method

2015 ◽  
Vol 8 (2) ◽  
pp. 34-37 ◽  
Author(s):  
Сазонова ◽  
Svetlana Sazonova
Keyword(s):  
Complex Systems ◽  
Boundary Conditions ◽  
Decomposition Method ◽  
Internal Communication ◽  
Target Product ◽  
Hydraulic Systems ◽  
Decomposition Approach ◽  
The Status ◽  
The Individual ◽  
System Nodes

Hydraulic systems belong to the category of complex systems, between the individual elements of the histories and subsystems exist internal communication, precluding the possibility of an Autonomous fashion from cancellation. The scale of such systems and their development trends lead to the inevitable decomposition approach. Research is not always to be the whole system, and some of its fragments, which border taking into account the accepted scheme of allocation of the target product to consumers submit a set of system nodes. In this case, the nodes acquire the status of power units, because through them there is an exchange of energy between IP investigated fragment of the system and the metasystem. Examines the emerging conflict between the need for a complementary decomposition and inner interconnection of all elements. He is overcome by the imposition of conditions one of znanosti, including boundary conditions.

scholarly journals Detection of Spatial Correlations in Protein Structures and Molecular Complexes

Structure ◽  
2012 ◽  
Vol 20 (4) ◽  
pp. 718-728 ◽  
Author(s):  
Manfred J. Sippl ◽  
Markus Wiederstein
Keyword(s):  
Protein Structures ◽  
Molecular Complexes ◽  
Spatial Correlations

THERMODYNAMICS OF THE MOLECULAR COMPLEXES WITH CHAINS OF HYDROGEN BONDS

1992 ◽  
Vol 06 (02) ◽  
pp. 85-91 ◽  
Author(s):  
I.V. STASYUK ◽  
A.L. IVANKIV
Keyword(s):  
Hydrogen Bonds ◽  
Molecular Complexes ◽  
High Energy ◽  
Spin Model ◽  
Strong Correlations ◽  
Reduced Basis ◽  
Molecular Systems ◽  
Ionic Groups ◽  
Energy Proton ◽  
Initial Basis

A pseudo-spin reduced basis model for the description of the linear hydrogen-bonds molecular systems with strong correlations between protons on the neighbouring bonds is proposed. The proton states corresponding to the high-energy proton configurations near the heavy ionic groups are excluded from the initial basis. Some aspects of thermodynamics and energy spectrum for the proton subsystem of the molecular complexes are considered in the framework of reduced basis model. It is shown that for the complexes with large but finite number of hydrogen bonds N, the polarizability is proportional to N2, the specific heat is proportional to N−1 and the spectrum includes both zone and localized proton states. At the same time it is shown that correct thermodynamic limit is obtained as N→∞ on the base of pseudo-spin model with initial basis. As a result the limits of application of reduced basis model are determined.

scholarly journals Point-of-contact Interactive Record Linkage (PIRL): A software tool to prospectively link demographic surveillance and health facility data

2018 ◽  
Vol 1 ◽  
pp. 8 ◽  
Author(s):  
Christopher T. Rentsch ◽  
Chodziwadziwa Whiteson Kabudula ◽  
Jason Catlett ◽  
David Beckles ◽  
Richard Machemba ◽  
...  
Keyword(s):  
Health Facility ◽  
Record Linkage ◽  
Software Tool ◽  
Patient Specific ◽  
Local Health ◽  
Linkage Algorithm ◽  
Rural Tanzania ◽  
Local Health Facility ◽  
Extraneous Information ◽  
The Individual

Linking a health and demographic surveillance system (HDSS) to data from a health facility that serves the HDSS population generates a research infrastructure for directly observed data on access to and utilization of health facility services. Many HDSS sites, however, are in areas that lack unique national identifiers or suffer from data quality issues, such as incomplete records, spelling errors, and name and residence changes, all of which complicate record linkage approaches when applied retrospectively. We developed Point-of-contact Interactive Record Linkage (PIRL) software that is used to prospectively link health records from a local health facility to an HDSS in rural Tanzania. This prospective approach to record linkage is carried out in the presence of the individual whose records are being linked, which has the advantage that any uncertainty surrounding their identity can be resolved during a brief interaction, whereby extraneous information (e.g., household membership) can be referred to as an additional criterion to adjudicate between multiple potential matches. Our software uses a probabilistic record linkage algorithm based on the Fellegi-Sunter model to search and rank potential matches in the HDSS data source. Key advantages of this software are its ability to perform multiple searches for the same individual and save patient-specific notes that are retrieved during subsequent clinic visits. A search on the HDSS database (n=110,000) takes less than 15 seconds to complete. Excluding time spent obtaining written consent, the median duration of time we spend with each patient is six minutes. In this setting, a purely automated retrospective approach to record linkage would have only correctly identified about half of the true matches and resulted in high linkage errors; therefore highlighting immediate benefit of conducting interactive record linkage using the PIRL software.

Polymorphism of cow colostrum proteinase inhibitor

1981 ◽  
Vol 46 (3) ◽  
pp. 807-816 ◽  
Author(s):  
Věra Jonáková ◽  
Dana Čechová ◽  
Otakar Mach
Keyword(s):  
Amino Acid ◽  
Primary Structure ◽  
Proteinase Inhibitor ◽  
Protein Structures ◽  
Amino Acid Residues ◽  
Net Charge ◽  
C Terminus ◽  
Isoelectric Points ◽  
The Individual ◽  
Protein Moiety

Cow colostrum contains three isoinhibitors A, B, and C, which are glycoproteins. In this study isoinhibitor A was isolated and characterized and the structure of its protein moiety compared with the known protein structures of isoinhibitors B and C. It was found that the primary structure of isoinhibitor A is identical with the primary structure of isoinhibitor B except that the C-terminus of its molecule is shorter by five amino acid residues. Four discrete chromatographic forms (I-IV) with different isoelectric points (pI 3.8 - I, 4.0 - II, 4.3 - III, and 4.5 - IV) were isolated by chromatography on SE-Sephadex, Form I is identical with isoinhibitor A. Forms II, III, and IV are represented by mixtures of isoinhibitors A, B, and C with a heterogeneous carbohydrate moiety which affects the total net charge of the individual inhibitor forms.

Sign in / Sign up

Export Citation Format

Share Document