Towards a Phylogeny and Definition of Species at the Molecular Level within the Genus Mycobacterium

1990 ◽  
Vol 40 (4) ◽  
pp. 323-330 ◽  
Author(s):  
T. ROGALL ◽  
J. WOLTERS ◽  
T. FLOHR ◽  
E. C. BOTTGER
Keyword(s):  
Molecular Level ◽  
Genus Mycobacterium ◽  
Definition Of

Designing for a green chemistry future

Science ◽  
2020 ◽  
Vol 367 (6476) ◽  
pp. 397-400 ◽  
Author(s):  
Julie B. Zimmerman ◽  
Paul T. Anastas ◽  
Hanno C. Erythropel ◽  
Walter Leitner
Keyword(s):  
Green Chemistry ◽  
Molecular Level ◽  
Positive Impact ◽  
Systems Design ◽  
Global Scale ◽  
Design Stage ◽  
Sustainable Society ◽  
Material Basis ◽  
Chemical Products ◽  
Definition Of

The material basis of a sustainable society will depend on chemical products and processes that are designed following principles that make them conducive to life. Important inherent properties of molecules need to be considered from the earliest stage—the design stage—to address whether compounds and processes are depleting versus renewable, toxic versus benign, and persistent versus readily degradable. Products, feedstocks, and manufacturing processes will need to integrate the principles of green chemistry and green engineering under an expanded definition of performance that includes sustainability considerations. This transformation will require the best of the traditions of science and innovation coupled with new emerging systems thinking and systems design that begins at the molecular level and results in a positive impact on the global scale.

The study of enzyme mechanisms by a combination of cosolvent, low-temperature and high-pressure techniques

1979 ◽  
Vol 12 (4) ◽  
pp. 521-569 ◽  
Author(s):  
Pierre Douzou
Keyword(s):  
High Pressure ◽  
Conformational Changes ◽  
Rate Constants ◽  
Enzyme Catalysis ◽  
Chemical Nature ◽  
Molecular Level ◽  
Essential Feature ◽  
Quantitative Understanding ◽  
Definition Of ◽  
Rapid Data Acquisition

It is generally assumed that the mechanism of enzyme-catalysed reactions would be defined if all the intermediates, complexes and conformational states of each enzyme could be characterized, and the rate-constants for their inter-conversion recorded. In spite of the introduction during the last decades of methods for rapid data acquisition, which permit detection of the number and sequence of intermediates and complexes, measurement of rate-constants, identification of the types of catalysis involved, etc., at best a semi-quantitative understanding of the mechanism of enzyme-catalysis is obtained. The definition of the exact chemical nature of intermediates and complexes is missing because techniques establishing the structures are restricted to the study of transient states which are stable for periods that exceed the half-life of most of typical intermediates. In such conditions, while conformational changes are obviously an essential feature of enzyme activity, the conformational basis of such activity cannot be understood at the molecular level, and enzyme catalysis is still termed a ‘miracle’ compared to the rate-enhancements and specificity of ordinary chemical catalysts.

Artificial Cybernetic Living Individuals Based on SupraMolecular-Level Organization as Dispersed Individuals

2011 ◽  
Vol 17 (1) ◽  
pp. 51-67 ◽  
Author(s):  
Bernard Korzeniewski
Keyword(s):  
Organic Compounds ◽  
Social Insects ◽  
Molecular Level ◽  
Biological Systems ◽  
Chemical Plants ◽  
Fundamental Structure ◽  
Power Stations ◽  
Natural Living ◽  
Characteristic Features ◽  
Definition Of

One of the most characteristic features of spontaneously originating biological systems is that their most fundamental structure and especially functioning is based on molecular-level organization. This property is particularly important when natural living individuals composed of organic compounds of carbon are compared with (hypothetical) artificial living individuals based on metals, plastic, glass, silicon, and so on, whose most basic structural and functional units appear at the supramolecular level. The cybernetic definition of a living individual I proposed previously is used in the present work. I argue that artificial, supramolecular living individuals existing self-dependently in the environment of some distant planet must have the form of dispersed individuals composed of several separate subindividuals that are integrated functionally, but not structurally. These subindividuals would be analogous to such modules of human technical civilization as machines, robots, steelworks, chemical plants, electronic factories, power stations, and mines. Such dispersed individuals would resemble colonies of social insects and moles, which are also composed of separate subindividuals (particular insects and moles) carrying out different specialized functions.

scholarly journals Reconstituting the genus Mycobacterium

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Conor J. Meehan ◽  
Roman A. Barco ◽  
Yong-Hwee E. Loh ◽  
Sari Cogneau ◽  
Leen Rigouts
Keyword(s):  
Amino Acid Identity ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
New Genera ◽  
Opportunistic Pathogens ◽  
Content Type ◽  
Link Type ◽  
Genus Mycobacterium ◽  
Definition Of ◽  
Gene Similarity

The definition of a genus has wide-ranging implications both in terms of binomial species names and also evolutionary relationships. In recent years, the definition of the genus Mycobacterium has been debated due to the proposed split of this genus into five new genera ( Mycolicibacterium , Mycolicibacter , Mycolicibacillus , Mycobacteroides and an emended Mycobacterium ). Since this group of species contains many important obligate and opportunistic pathogens, it is important that any renaming of species does not cause confusion in clinical treatment as outlined by the nomen periculosum rule (56a) of the Prokaryotic Code. In this study, we evaluated the proposed and original genus boundaries for the mycobacteria, to determine if the split into five genera was warranted. By combining multiple approaches for defining genus boundaries (16S rRNA gene similarity, amino acid identity index, average nucleotide identity, alignment fraction and percentage of conserved proteins) we show that the original genus Mycobacterium is strongly supported over the proposed five-way split. Thus, we propose that the original genus label be reapplied to all species within this group, with the proposed five genera potentially used as sub-genus complex names.

scholarly journals Fungal virulence genes as targets for antifungal chemotherapy.

1996 ◽  
Vol 40 (7) ◽  
pp. 1577-1583 ◽  
Author(s):  
J R Perfect
Keyword(s):  
Virulence Genes ◽  
Molecular Level ◽  
Fungal Infections ◽  
Virulence Gene ◽  
Antifungal Drugs ◽  
Fungal Virulence ◽  
Host Interactions ◽  
Antifungal Chemotherapy ◽  
Definition Of ◽  
Simple Definition

Fungal virulence genes have now met the age of molecular pathogenesis. The definition of virulence genes needs to be broad so that it encompasses the focus on molecular antifungal targets and vaccine epitopes. However, in the broad but simple definition of a virulence gene, there will be many complex genetic and host interactions which investigators will need to carefully define. Nevertheless, with the increasing numbers of serious fungal infections produced by old and newly reported organisms, the paucity of present antifungal drugs, and the likelihood of increasing drug resistance, the need for investigations into understanding fungal virulence at the molecular level has never been more important.

scholarly journals Experimental and engineering approaches to intracellular communication

2018 ◽  
Vol 62 (4) ◽  
pp. 515-524 ◽  
Author(s):  
John G. Albeck ◽  
Michael Pargett ◽  
Alexander E. Davies
Keyword(s):  
Information Content ◽  
Data Streams ◽  
Information Transfer ◽  
Molecular Level ◽  
Cellular Behavior ◽  
Theoretical Approaches ◽  
Intracellular Communication ◽  
Intracellular Signal ◽  
Definition Of ◽  
And Control

Communication between and within cells is essential for multicellular life. While intracellular signal transduction pathways are often specified in molecular terms, the information content they transmit remains poorly defined. Here, we review research efforts to merge biological experimentation with concepts of communication that emerge from the engineering disciplines of signal processing and control theory. We discuss the challenges of performing experiments that quantitate information transfer at the molecular level, and we highlight recent studies that have advanced toward a clearer definition of the information content carried by signaling molecules. Across these studies, we emphasize a theme of increasingly well-matched experimental and theoretical approaches to decode the data streams directing cellular behavior.

scholarly journals How the Toxin got its Toxicity

2020 ◽  
Vol 11 ◽  
Author(s):  
Timothy N. W. Jackson ◽  
Ivan Koludarov
Keyword(s):  
Gene Product ◽  
Evolutionary History ◽  
Molecular Level ◽  
Ecological Traits ◽  
Active Molecule ◽  
Dynamic Form ◽  
History Of ◽  
Pluralistic Approach ◽  
Definition Of ◽  
And Function

Venom systems are functional and ecological traits, typically used by one organism to subdue or deter another. A predominant subset of their constituent molecules—“toxins”—share this ecological function and are therefore molecules that mediate interactions between organisms. Such molecules have been referred to as “exochemicals.” There has been debate within the field of toxinology concerning the evolutionary pathways leading to the “recruitment” of a gene product for a toxic role within venom. We review these discussions and the evidence interpreted in support of alternate pathways, along with many of the most popular models describing the origin of novel molecular functions in general. We note that such functions may arise with or without gene duplication occurring and are often the consequence of a gene product encountering a novel “environment,” i.e., a range of novel partners for molecular interaction. After stressing the distinction between “activity” and “function,” we describe in detail the results of a recent study which reconstructed the evolutionary history of a multigene family that has been recruited as a toxin and argue that these results indicate that a pluralistic approach to understanding the origin of novel functions is advantageous. This leads us to recommend that an expansive approach be taken to the definition of “neofunctionalization”—simply the origins of a novel molecular function by any process—and “recruitment”—the “weaponization” of a molecule via the acquisition of a toxic function in venom, by any process. Recruitment does not occur at the molecular level or even at the level of gene expression, but only when a confluence of factors results in the ecological deployment of a physiologically active molecule as a toxin. Subsequent to recruitment, the evolutionary regime of a gene family may shift into a more dynamic form of “birth-and-death.” Thus, recruitment leads to a form of “downwards causation,” in which a change at the ecological level at which whole organisms interact leads to a change in patterns of evolution at the genomic level.

scholarly journals Reconstituting the genus Mycobacterium

2021 ◽  
Author(s):  
Conor J Meehan ◽  
Roman A. Barco ◽  
Yong-Hwee E Loh ◽  
Sari Cogneau ◽  
Leen Rigouts
Keyword(s):  
Amino Acid Identity ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
New Genera ◽  
Opportunistic Pathogens ◽  
Acid Identity ◽  
Genus Mycobacterium ◽  
Definition Of ◽  
Gene Similarity

AbstractThe definition of a genus has wide ranging implications both in terms of binomial species names and also evolutionary relationships. In recent years, the definition of the genus Mycobacterium has been debated due to the proposed split of this genus into five new genera (Mycolicibacterium, Mycolicibacter, Mycolicibacillus, Mycobacteroides and an emended Mycobacterium). Since this group of species contains many important obligate and opportunistic pathogens, it is important that any renaming of species is does not cause confusion in clinical treatment as outlined by the nomen periculosum rule (56a) of the Prokaryotic Code.In this study, we evaluated the proposed and original genus boundaries for the mycobacteria, to determine if the split into five genera was warranted. By combining multiple approaches for defining genus boundaries (16S rRNA gene similarity, amino acid identity index, average nucleotide identity, alignment fraction and percentage of conserved proteins) we show that the original genus Mycobacterium is strongly supported over the proposed five-way split. Thus, we propose that the original genus label be reapplied to all species within this group, with the proposed five genera used as sub-genus complex names.

Towards an antigenic map of human thyroglobulin: identification of ten epitope-bearing sequences within the primary structure of thyroglobulin

1989 ◽  
Vol 122 (1) ◽  
pp. 169-176 ◽  
Author(s):  
Q. Dong ◽  
M. Ludgate ◽  
G. Vassart
Keyword(s):  
Autoimmune Thyroid Disease ◽  
Molecular Level ◽  
Human Thyroid ◽  
Rabbit Antibody ◽  
Thyroglobulin Antibodies ◽  
Autoimmune Thyroid ◽  
Terminal Amino ◽  
Carboxyl Terminal ◽  
Definition Of ◽  
Very High

ABSTRACT The aim of this study was to define, at the molecular level, epitopes of thyroglobulin recognized by heterologous antibodies and autoantisera. One hundred thousand clones from a λgt11 human thyroid cDNA library were screened using a rabbit antibody to human thyroglobulin at a 1:2000 dilution. Twenty clones were plaque-purified to homogeneity, and characterization and sequencing of their cDNA inserts showed that they represented four distinct regions of the thyroglobulin molecule, one of them being the 22 carboxyl-terminal amino acids. Rescreening of the library with the same rabbit antibody to human thyroglobulin absorbed with peptides encoded by the carboxyl-terminal clone, led to the definition of six further epitope-bearing fragments of thyroglobulin. The ten regions that we have identified were recognized by ten further rabbit antibodies to human thyroglobulin, showing that they are representative of the repertoire of heterologous epitopes. In contrast, none of the ten heteroepitope-bearing fragments was recognized by sera from ten patients with autoimmune thyroid disease with various titres of thyroglobulin antibodies. Screening of 2 × 106 clones from the library using a pool of ten autoantisera (individual sera diluted to 1:1000), and of 1 × 106 clones using a single autoantiserum of very high antithyroglobulin titre (diluted 1:400) resulted in no thyroglobulin clones being isolated. The significance of these results to the immune process is discussed. Journal of Endocrinology (1989) 122, 169–176

Cambridge Genome Meeting, June 22–24, 1981

Paleobiology ◽  
1981 ◽  
Vol 7 (3) ◽  
pp. 308-310
Author(s):  
Thomas J. M. Schopf
Keyword(s):  
Mutation Rate ◽  
Molecular Level ◽  
Broad Definition ◽  
Definition Of

Almost at the end of his chapter on Mutation, G. G. Simpson in 1953 in The Major Features of Evolution noted that “There is also increasing evidence that mutation rate is itself, to some degree, a genetically controlled character.” If for mutation one uses the broad definition of the origin of new hereditary types, then the glimmerings to which Simpson referred now have become a documented fact at the molecular level.

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