scholarly journals A subcellular proteome atlas of the yeast Komagataella phaffii

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Minoska Valli ◽  
Karlheinz Grillitsch ◽  
Clemens Grünwald-Gruber ◽  
Nadine E Tatto ◽  
Bernhard Hrobath ◽  
...  
Keyword(s):  
Lipid Membranes ◽  
Ionization Mass ◽  
Heterologous Proteins ◽  
Regulatory Pathways ◽  
Komagataella Phaffii ◽  
Tandem Mass Tag ◽  
Interactive Map ◽  
Living Organisms ◽  
Cellular Compartments

ABSTRACT The compartmentalization of metabolic and regulatory pathways is a common pattern of living organisms. Eukaryotic cells are subdivided into several organelles enclosed by lipid membranes. Organelle proteomes define their functions. Yeasts, as simple eukaryotic single cell organisms, are valuable models for higher eukaryotes and frequently used for biotechnological applications. While the subcellular distribution of proteins is well studied in Saccharomyces cerevisiae, this is not the case for other yeasts like Komagataella phaffii (syn. Pichia pastoris). Different to most well-studied yeasts, K. phaffii can grow on methanol, which provides specific features for production of heterologous proteins and as a model for peroxisome biology. We isolated microsomes, very early Golgi, early Golgi, plasma membrane, vacuole, cytosol, peroxisomes and mitochondria of K. phaffii from glucose- and methanol-grown cultures, quantified their proteomes by liquid chromatography-electrospray ionization-mass spectrometry of either unlabeled or tandem mass tag-labeled samples. Classification of the proteins by their relative enrichment, allowed the separation of enriched proteins from potential contaminants in all cellular compartments except the peroxisomes. We discuss differences to S. cerevisiae, outline organelle specific findings and the major metabolic pathways and provide an interactive map of the subcellular localization of proteins in K. phaffii.

Redox Reactions in Lipid Membranes as a Model for Primordial Energy-Conserving Systems

1997 ◽  
Vol 161 ◽  
pp. 437-442
Author(s):  
Salvatore Di Bernardo ◽  
Romana Fato ◽  
Giorgio Lenaz
Keyword(s):  
Experimental Evidence ◽  
Lipid Membranes ◽  
Energy Supply ◽  
Redox Reactions ◽  
Living Systems ◽  
Asymmetric Distribution ◽  
Conservation Of Energy ◽  
Asymmetrical Distribution ◽  
Energy Conserving ◽  
Living Organisms

AbstractOne of the peculiar aspects of living systems is the production and conservation of energy. This aspect is provided by specialized organelles, such as the mitochondria and chloroplasts, in developed living organisms. In primordial systems lacking specialized enzymatic complexes the energy supply was probably bound to the generation and maintenance of an asymmetric distribution of charged molecules in compartmentalized systems. On the basis of experimental evidence, we suggest that lipophilic quinones were involved in the generation of this asymmetrical distribution of charges through vectorial redox reactions across lipid membranes.

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.

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.

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>

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