Systems of Classification of Living Organisms: Great Steps in Chemical and Biological Evolution

2014 ◽  
pp. 1-12
Author(s):  
Jean-Michel Kornprobst
Keyword(s):  
Biological Evolution ◽  
Living Organisms

Natural history of ABC systems: not only transporters

2011 ◽  
Vol 50 ◽  
pp. 19-42 ◽  
Author(s):  
Elie Dassa
Keyword(s):  
Common Ancestor ◽  
Three Dimensional ◽  
Last Common Ancestor ◽  
Abc Proteins ◽  
Hypothetical Scenario ◽  
History Of ◽  
Phylogenetic Perspective ◽  
Living Organisms

In recent years, our understanding of the functioning of ABC (ATP-binding cassette) systems has been boosted by the combination of biochemical and structural approaches. However, the origin and the distribution of ABC proteins among living organisms are difficult to understand in a phylogenetic perspective, because it is hard to discriminate orthology and paralogy, due to the existence of horizontal gene transfer. In this chapter, I present an update of the classification of ABC systems and discuss a hypothetical scenario of their evolution. The hypothetical presence of ABC ATPases in the last common ancestor of modern organisms is discussed, as well as the additional possibility that ABC systems might have been transmitted to eukaryotes, after the two endosymbiosis events that led to the constitution of eukaryotic organelles. I update the functional information of selected ABC systems and introduce new families of ABC proteins that have been included recently into this vast superfamily, thanks to the availability of high-resolution three-dimensional structures.

Evolutionary History of Plant Lipolytic Enzymes

2018 ◽  
pp. 155-178
Keyword(s):  
Higher Plants ◽  
Evolutionary Relationship ◽  
Biological Evolution ◽  
Sequence Motifs ◽  
Multiple Sequence ◽  
Lipolytic Enzymes ◽  
Conserved Sequence ◽  
Potential Applications ◽  
History Of ◽  
Living Organisms

The discovery of enzymes with lipolytic activities in all kingdoms of life from prokaryote to eukaryote species raises the possibility of the presence of an evolutionary relationship history of these proteins among many species of various living organisms. The chapter suggests a strategy based on the phylogenetic distribution and homology conservation in plant lipolytic enzymes for possible depiction of their biological evolution. Extensive databases and online resources for lipidomics and related areas are useful tools to analyze the different lipolytic enzymes in the three major super kingdoms of life, including higher plants kingdom and confined organisms such as algae that have recently gained much interest due to their promising potential applications in lipids hydrolysis and biosynthesis. Multiple sequence alignments of the identified lipolytic enzymes from databases could serve to the identification of globally conserved residues as well as conserved sequence motifs. Estimation of evolutionary distance between the various identified lipolytic enzymes could also be carried out to better understand the pattern of evolution.

Paleolimnology in Deep Time: The Evolution of Lacustrine Ecosystems

2003 ◽  
Author(s):  
Andrew S. Cohen
Keyword(s):  
Fossil Record ◽  
World Ocean ◽  
Biological Evolution ◽  
Body Distribution ◽  
Freshwater Organisms ◽  
History Of ◽  
Living Organisms ◽  
Lake Basins ◽  
Lake Beds

Most lakes are geologically ephemeral; even the longest-lived individual lakes persist only for tens of millions of years. However there is a continuity to lake systems that transcends the geologically short history of individual lake basins. This continuity comes from the long-term biological evolution of life in freshwater, and fittingly, forms the final subject of this treatment of paleolimnology. Like the oceans, lakes have provided habitats for living organisms for most of the earth’s history. Yet the patterns of aquatic ecosystem evolution in rivers and lakes have differed dramatically from those of the oceans. In large part this can be traced to the fundamentally ephemeral nature of most continental aquatic habitats and the ‘‘disconnectedness’’ in both time and space that exists between individual lakes and rivers compared with the world ocean. This pattern of temporal and spatial patchiness in water body distribution on the continents has shaped the evolution of lacustrine species and communities. Some understanding of this history can be gleaned from the study of modern ecology and molecular genetics of living freshwater organisms. But to understand long-term trends in lacustrine biodiversity and their relationship to the history of the lacustrine environment we must turn to the pre- Quaternary fossil record. Understanding this history, the timing and tempo of major species diversification and extinction events, and the evolution of key ecological innovations is critical for correctly interpreting ancient lake deposits. The fossil record of pre-Quaternary lakes is more difficult to interpret than that of more recent lake basins. Robust phylogenies are largely unavailable for clades of ancient lacustrine fossils, hindering our ability to test hypotheses of evolutionary ecology, although that situation hopefully will improve in coming years. Many major clades of fossil lacustrine organisms are extinct, and ecologies must be inferred from their depositional context. Even for organisms that have close-living relatives, our certainty in making inferences about habitat and relationship with other species weakens as we go back in time. Also the record we have to work with deteriorates with age, the result of (a) a declining volume of lake beds available for study with increasing age, (b) difficulties associated with processing lithified lake beds for their fossil content, and (c) an increasing likelihood of destruction by diagenesis with increasing age.

The classification of pollutants and their pathways in the atmosphere

1979 ◽  
Vol 290 (1376) ◽  
pp. 469-476 ◽  
Keyword(s):  
Boundary Layer ◽  
Human Life ◽  
Biogeochemical Cycles ◽  
Climatic Conditions ◽  
Atmospheric Pollutants ◽  
Relative Importance ◽  
Natural Sources ◽  
Living Organisms ◽  
Broad Classification

Atmospheric pollutants may damage, directly or indirectly, human life and health, other living organisms and complete ecosystems, human artefacts, and climatic conditions. The development of appropriate policies and methods for control of pollution requires, inter alia , an assessment of the routes taken by pollutants or their precursors through the atmosphere. Consideration of these routes leads to a broad classification on a local, regional or global basis associated mainly, but not exclusively, with the terrestrial boundary layer, with the troposphere and with the stratosphere respectively. This may require in some cases the perspective of total biogeochemical cycles, and in any event of the relative importance of man-made and natural sources of materials to be regarded as pollutants.

scholarly journals Recognition of Pharmacological Bi-Heterocyclic Compounds by Using Terahertz Time Domain Spectroscopy and Chemometrics

Sensors ◽  
2019 ◽  
Vol 19 (15) ◽  
pp. 3349 ◽  
Author(s):  
Maciej Roman Nowak ◽  
Rafał Zdunek ◽  
Edward Pliński ◽  
Piotr Świątek ◽  
Małgorzata Strzelecka ◽  
...  
Keyword(s):  
Heterocyclic Compounds ◽  
Chemical Compounds ◽  
Functional System ◽  
Support Vector ◽  
Optimal Parameters ◽  
Terahertz Time Domain Spectroscopy ◽  
Kernel Support Vector Machine ◽  
Inflammatory Drugs ◽  
Living Organisms

In this study, we presented the concept and implementation of a fully functional system for the recognition of bi-heterocyclic compounds. We have conducted research into the application of machine learning methods to correctly recognize compounds based on THz spectra, and we have described the process of selecting optimal parameters for the kernel support vector machine (KSVM) with an additional `unknown’ class. The chemical compounds used in the study contain a target molecule, used in pharmacy to combat inflammatory states formed in living organisms. Ready-made medical products with similar properties are commonly referred to as non-steroidal anti-inflammatory drugs (NSAIDs) once authorised on the pharmaceutical market. It was crucial to clearly determine whether the tested sample is a chemical compound known to researchers or is a completely new structure which should be additionally tested using other spectrometric methods. Our approach allows us to achieve 100% accuracy of the classification of the tested chemical compounds in the time of several milliseconds counted for 30 samples of the test set. It fits perfectly into the concept of rapid recognition of bi-heterocyclic compounds without the need to analyse the percentage composition of compound components, assuming that the sample is classified in a known group. The method allows us to minimize testing costs and significant reduction of the time of analysis.

scholarly journals Statistical mechanics and hydrodynamics of bacterial suspensions

2009 ◽  
Vol 106 (37) ◽  
pp. 15567-15572 ◽  
Author(s):  
Aparna Baskaran ◽  
M. Cristina Marchetti
Keyword(s):  
Physical Model ◽  
Large Scale ◽  
Hydrodynamic Interactions ◽  
Nonequilibrium Phenomena ◽  
Active Particles ◽  
Cilia And Flagella ◽  
Living Organisms ◽  
The Individual ◽  
Scale Behavior

Unicellular living organisms, such as bacteria and algae, propel themselves through a medium via cyclic strokes involving the motion of cilia and flagella. Dense populations of such “active particles” or “swimmers” exhibit a rich collective behavior at large scales. Starting with a minimal physical model of a stroke-averaged swimmer in a fluid, we derive a continuum description of a suspension of active organisms that incorporates fluid-mediated, long-range hydrodynamic interactions among the swimmers. Our work demonstrates that hydrodynamic interactions provide a simple, generic origin for several nonequilibrium phenomena predicted or observed in the literature. The continuum model derived here does not depend on the microscopic physical model of the individual swimmer. The details of the large-scale physics do, however, differ for “shakers” (particles that are active but not self-propelled, such as melanocytes) and “movers” (self-propelled particles), “pushers” (most bacteria) and “pullers” (algae like Chlamydomonas). Our work provides a classification of the large-scale behavior of all these systems.

Dynamics of membrane processes

1968 ◽  
Vol 1 (2) ◽  
pp. 127-175 ◽  
Author(s):  
A. Katchalsky ◽  
R. Spangler
Keyword(s):  
Biological Evolution ◽  
Second Law Of Thermodynamics ◽  
Second Law ◽  
Membrane Processes ◽  
Biological Phenomena ◽  
Living Organisms ◽  
The Universe ◽  
Intrinsic Contradiction

I. I. In his illuminating book onThe Nature of Thermodynamics, Bridgeman (1941) points out an intrinsic contradiction between the concepts of physical and biological evolution. In his words: ‘The view that the universe is running down into a condition where its entropy and the amount of disorder are as great as possible has had a profound effect on the views of many biologists on the nature of biological phenomena. It springs to the eye, however, that the tendency of living organisms is to organize their surroundings—that is to “produce” order where formerly there was disorder. Life then appears in some way to oppose the otherwise universal drive to disorder. Does it mean that living organisms do, or may violate the second law of thermodynamics?…’

Science and creativity

2020 ◽  
Author(s):  
Flavia Bruno
Keyword(s):  
Chemical Reactions ◽  
Scientific Conference ◽  
Scientific Terminology ◽  
Educational Standard ◽  
The Earth ◽  
Hands On ◽  
Earth Structures ◽  
Lithospheric Plates ◽  
Living Organisms

<p>I teach Natural Sciences in a Liceo Artistico, a type of secondary school in Italy. It is designed to give students the skills to progress to any university, but specifically devoted to art related topics.<br>During my career I have been following the national educational standard of the Ministero dell’Istruzione, dell’Università e della Ricerca of my Country.<br>During the years students are involved in meaningful hands-on activities   such as the study of the rocks in the country, preparation of easy chemical reactions and observations through a microscope of vegetal and animal organisms. These last ones are very interesting in a Liceo Artistico where many topics focus on the study of the morphology.<br>The theory confirms what the students learn during the practical activities, furthermore it is important to acquire a correct scientific terminology as well as to be able to express scientific issues.<br>I teach during the year the following main topics:<br>Science of Earth: the Solar System, the two motions of the Earth, structures of the Earth surface (rivers, lakes, glaciers, oceans and seas), the Earth’s Spheres, the movement of lithospheric plates.<br>Biology: the characteristics and functions of living organisms especially the cells and the biodiversity. The Evolution, Mendel’s genetic laws, organism-environment relationship in order to valorize and to maintain the biodiversity. Chemistry: state of matter, classification of matter, the Mendeleev’s Periodic Table, the main chemical reactions, atomics models, chemical bonds, chemical nomenclature.<br>The extra-curricular course proposal of my school (POFT-Piano dell’Offerta Formativa Triennale) includes my project whose title is “Science and creativity”. The achievement is to create a link between scientific subjects and the art ones in order to approach knowledge which appear distant but have really many points to share.<br>Every year some classrooms study different topics such as the Nanoparticles, Biomimetic and this year the Adaptations of the animals.<br>After a scientific conference, plastic models and graphic drawings will be realised by the students, who starting from the scientific reality, can express their creativity.<br>During the years I organize some educational visits for example to the Botanic Garden as well as to the countryside; in this way the students have opportunities to create an e-book with texts and photographs.<br>For instance two years ago my classroom created an e-book with botanical cards and the following year another one with the title “Rocce a Milano” where students took pictures and texts about this topic.<br>Many classrooms and teachers are involved in this project for example Plastic and Drawing teachers, as well as Multimedia teachers. I manage to gather the interested teachers and to realize the projects.<br>With our productions we participate in competitions and we are sometimes selected.</p>

The rich but confusing terminology of biological nomenclature: a first step towards a comprehensive glossary

Bionomina ◽  
2011 ◽  
Vol 3 (1) ◽  
pp. 63-70
Author(s):  
Alain DUBOIS
Keyword(s):  
Scientific Discipline ◽  
Human Needs ◽  
Higher Taxa ◽  
Unique System ◽  
Basic Need ◽  
The Rich ◽  
Living Organisms ◽  
Protect Study

Biology deals with billions of living organisms, which display a great diversity but also share many characters, being the result of an evolution. Designating these organisms in a universal and unambiguous way is a basic need for communication, not only among taxonomists or even biologists, but with society as a whole. It is indispensable to have a unique system for distinguishing and naming the organisms that may be used for alimentary, agronomical, veterinary or medical purposes or for any other human needs, that may be responsible for diseases, pollutions, biotic invasions, that we may wish to protect, study or admire, etc. For all these purposes, we need a scientific discipline, taxonomy, dealing not only with the classification of living organisms into millions of classificatory units, the taxa, but also with the designation and indexation of these taxa (nomenclature). Biological nomenclature has to care for the scientific naming of millions of taxa (species and higher taxa like genera or families), the inventory of which is still very far from being finished.

Classification Synopsis and Classification of Living Organisms Sybil P. Parker

BioScience ◽  
1984 ◽  
Vol 34 (5) ◽  
pp. 330-330
Author(s):  
George Hechtel
Keyword(s):  
Living Organisms
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