Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments

Oxygen reducing terminal oxidases differ with respect to their subunit composition, heme groups, operon structure, and affinity for O2. Six families of terminal oxidases are currently recognized, all of which occur in alphaproteobacterial genomes, two of which are also present in mitochondria. Many alphaproteobacteria encode several different terminal oxidases, likely reflecting ecological versatility with respect to oxygen levels. Terminal oxidase evolution likely started with the advent of O2 roughly 2.4 billion years ago and terminal oxidases diversified in the Proterozoic, during which oxygen levels remained low, around the Pasteur point (ca. 2 μM O2). Among the alphaproteobacterial genomes surveyed, those from members of the Rhodospirillaceae reveal the greatest diversity in oxygen reductases. Some harbor all six terminal oxidase types, in addition to many soluble enzymes typical of anaerobic fermentations in mitochondria and hydrogenosomes of eukaryotes. Recent data have it that O2 levels increased to current values (21% v/v or ca. 250 μM) only about 430 million years ago. Ecological adaptation brought forth different lineages of alphaproteobacteria and different lineages of eukaryotes that have undergone evolutionary specialization to high oxygen, low oxygen, and anaerobic habitats. Some have remained facultative anaerobes that are able to generate ATP with or without the help of oxygen and represent physiological links to the ancient proteobacterial lineage at the origin of mitochondria and eukaryotes. Our analysis reveals that the genomes of alphaproteobacteria appear to retain signatures of ancient transitions in aerobic metabolism, findings that are relevant to mitochondrial evolution in eukaryotes as well

Energy metabolism in anaerobic eukaryotes and Earth's late oxygenation

Eukaryotes arose about 1.6 billion years ago, at a time when oxygen levels were still very low on Earth, both in the atmosphere and in the ocean. According to newer geochemical data, oxygen rose to approximately its present atmospheric levels very late in evolution, perhaps as late as the origin of land plants (only about 450 million years ago). It is therefore natural that many lineages of eukaryotes harbor, and use, enzymes for oxygen-independent energy metabolism. This paper provides a concise overview of anaerobic energy metabolism in eukaryotes with a focus on anaerobic energy metabolism in mitochondria. We also address the widespread assumption that oxygen improves the overall energetic state of a cell. While it is true that ATP yield from glucose or amino acids is increased in the presence of oxygen, it is also true that the synthesis of biomass costs thirteen times more energy per cell in the presence of oxygen than in anoxic conditions. This is because in the reaction of cellular biomass with O2, the equilibrium lies very far on the side of CO2. The absence of oxygen offers energetic benefits of the same magnitude as the presence of oxygen. Anaerobic and low oxygen environments are ancient. During evolution, some eukaryotes have specialized to life in permanently oxic environments (life on land), other eukaryotes have remained specialized to low oxygen habitats. We suggest that the Km of mitochondrial cytochrome c oxidase of 0.1–10 μM for O2, which corresponds to about 0.04%–4% (avg. 0.4%) of present atmospheric O2 levels, reflects environmental O2 concentrations that existed at the time that the eukaryotes arose

Parallel Patterns for Agent-based Evolutionary Computing

Computing applications such as metaheuristics-based optimization can greatly benefit from multi-core architectures available on modern supercomputers. In this paper, we describe an easy and efficient way to implement certain population-based algorithms (in the discussed case, multi-agent computing system) on such runtime environments. Our solution is based on an Erlang software library which implements dedicated parallel patterns. We provide technological details on our approach and discuss experimental results

Anaerobic animals from an ancient, anoxic ecological niche

Tiny marine animals that complete their life cycle in the total absence of light and oxygen are reported by Roberto Danovaro and colleagues in this issue of BMC Biology. These fascinating animals are new members of the phylum Loricifera and possess mitochondria that in electron micrographs look very much like hydrogenosomes, the H2-producing mitochondria found among several unicellular eukaryotic lineages. The discovery of metazoan life in a permanently anoxic and sulphidic environment provides a glimpse of what a good part of Earth's past ecology might have been like in 'Canfield oceans', before the rise of deep marine oxygen levels and the appearance of the first large animals in the fossil record roughly 550-600 million years ago. The findings underscore the evolutionary significance of anaerobic deep sea environments and the anaerobic lifestyle among mitochondrion-bearing cells. They also testify that a fuller understanding of eukaryotic and metazoan evolution will come from the study of modern anoxic and hypoxic habitats

Reconstituting the Mammalian Apoptotic Switch in Yeast

Proteins of the Bcl-2 family regulate the permeabilization of the mitochondrial outer membrane that represents a crucial irreversible step in the process of induction of apoptosis in mammalian cells. The family consists of both proapoptotic proteins that facilitate the membrane permeabilization and antiapoptotic proteins that prevent it in the absence of an apoptotic signal. The molecular mechanisms, by which these proteins interact with each other and with the mitochondrial membranes, however, remain under dispute. Although yeast do not have apparent homologues of these apoptotic regulators, yeast cells expressing mammalian members of the Bcl-2 family have proved to be a valuable model system, in which action of these proteins can be effectively studied. This review focuses on modeling the activity of proapoptotic as well as antiapoptotic proteins of the Bcl-2 family in yeast

Animals, anoxic environments, and reasons to go deep

One of the classic questions in the early evolution of eukaryotic life concerns the role of oxygen. Many unicellular eukaryotes are strict anaerobes and many animals have long anoxic phases in their life cycle. But are there also animals that can complete their life cycle without oxygen? In an ongoing debate in BMC Biology, Danovaro and colleagues say “yes” while Bernhard and colleagues say “no”. The debate concerns reports of anoxic metazoans in deep sea anaerobic habitats. In a Correspondence contribution to BMC Biology, Danovaro and colleagues [1] weigh in to defend the view that the loriciferans they reported in 2010 from anoxic sediments beneath the Mediterranean brine were living at the time of collection [2]. That view has recently been challenged by Bernhard et al. [3], who say that the loriciferans in question were not alive, but were dead and merely well preserved. The issue at hand is whether metazoans exist that can complete their entire life cycles without oxygen. This is important, but what is at stake

Ranking the Standards of Living in Districts in Poland between 2003 and 2012 Including Spatial Correlation

W pracy przedstawiono ranking poziomu życia mieszkańców Polski w przekroju powiatów, skonstruowany za pomocą wybranych metod porządkowania liniowego. Analiza miała charakter dynamiczny, badaniem objęto dane z lat 20032012. Wyodrębniono pozycje powiatów w rankingach przekrojowych (dla poszczególnych lat), oceniono także kierunki zmian syntetycznej miary poziomu życia w latach 20032012 dla każdego powiatu. Ważną kwestią podczas tworzenia rankingów jest określenie zakresu przestrzennego prowadzonych badań. Przykładowo, czy badając poziom życia w powiatach województwa podkarpackiego nie należałoby, jako punktu odniesienia, przyjąć także powiatów z innych województw? Wszak w przypadku analizy wielowymiarowej wzajemne relacje obiektów mogą się zmieniać przy rozszerzonym kontekście analizy. Dlatego też w pracy dokonano porównań zgodności rankingów uzyskanych przy analizie zawężonej tylko do jednego województwa z wynikami analiz prowadzonych w szerszym kontekście – wszystkich powiatów w Polsce. Następnie zaproponowano modyfikację metody porządkowania liniowego, w której uwzględnione zostały przestrzenne relacje pomiędzy powiatami. W omówieniu uzyskanych wyników zwrócono uwagę na fakt, iż relacje przestrzenne powinny być określane odrębnie dla każdej zmiennej diagnostycznej. W ten sposób określono kierunki dalszych badań.In this paper, we present the ranking of living standards in Poland in a cross-section of counties as constructed by using selected methods of linear ordering. The analysis was of a dynamic character and the study involved data from the years 2003 to 2012. The positions of the counties in the annual section rankings were distinguished. Additionally, we assessed the trends of the synthetic measure of the standard of living for each country between 20032012. An important issue when creating rankings was determining the spatial extent of the study. For example, when examining the standard of living in the counties of the Podkarpackie province, should not the counties in other provinces be taken into account as a reference point? In the case of multivariate analysis, the interaction of objects can indeed be changed by an extended context analysis. Therefore, in this paper, comparisons made of the rankings compliance obtained in the analysis were narrowed down to a single province with the results of the analyses being carried out in the broader context of all the counties in Poland. As with today’s data processing, it is not important whether the population of a few dozen or a few hundred objects is analysed. The conclusion from the conducted considerations is that one should always strive for the widest possible context for the research. We then propose a modification of the linear ordering method that takes the spatial relationships between the districts into account. Two rankings were presented: one where the neighbourhood matrix between the counties was applied and one where the length of the shared border was considered. In the discussion of the results, we highlighted the fact that spatial relationships should be determined separately for each diagnostic variable. In this way, the directions for further research were determined

RANKING THE STANDARDS OF LIVING IN DISTRICTS IN POLAND BETWEEN 2003 AND 2012 INCLUDING SPATIAL CORRELATION

In this paper, we present the ranking of living standards in Poland in a cross-section of counties as constructed by using selected methods of linear ordering. The analysis was of a dynamic character and the study involved data from the years 2003 to 2012. The positions of the counties in the annual section rankings were distinguished. Additionally, we assessed the trends of the synthetic measure of the standard of living for each country between 2003-2012. An important issue when creating rankings was determining the spatial extent of the study. For example, when examining the standard of living in the counties of the Podkarpackie province, should not the counties in other provinces be taken into account as a reference point? In the case of multivariate analysis, the interaction of objects can indeed be changed by an extended context analysis. Therefore, in this paper, comparisons made of the rankings compliance obtained in the analysis were narrowed down to a single province with the results of the analyses being carried out in the broader context of all the counties in Poland. As with today’s data processing, it is not important whether the population of a few dozen or a few hundred objects is analysed. The conclusion from the conducted considerations is that one should always strive for the widest possible context for the research. We then propose a modification of the linear ordering method that takes the spatial relationships between the districts into account. Two rankings were presented: one where the neighbourhood matrix between the counties was applied and one where the length of the shared border was considered. In the discussion of the results, we highlighted the fact that spatial relationships should be determined separately for each diagnostic variable. In this way, the directions for further research were determined.W pracy przedstawiono ranking poziomu życia mieszkańców Polski w przekroju powiatów, skonstruowany za pomocą wybranych metod porządkowania liniowego. Analiza miała charakter dynamiczny, badaniem objęto dane z lat 2003-2012. Wyodrębniono pozycje powiatów w rankingach przekrojowych (dla poszczególnych lat), oceniono także kierunki zmian syntetycznej miary poziomu życia w latach 2003-2012 dla każdego powiatu. Ważną kwestią podczas tworzenia rankingów jest określenie zakresu przestrzennego prowadzonych badań. Przykładowo, czy badając poziom życia w powiatach województwa podkarpackiego nie należałoby, jako punktu odniesienia, przyjąć także powiatów z innych województw? Wszak w przypadku analizy wielowymiarowej wzajemne relacje obiektów mogą się zmieniać przy rozszerzonym kontekście analizy. Dlatego też w pracy dokonano porównań zgodności rankingów uzyskanych przy analizie zawężonej tylko do jednego województwa z wynikami analiz prowadzonych w szerszym kontekście – wszystkich powiatów w Polsce. Następnie zaproponowano modyfikację metody porządkowania liniowego, w której uwzględnione zostały przestrzenne relacje pomiędzy powiatami. W omówieniu uzyskanych wyników zwrócono uwagę na fakt, iż relacje przestrzenne powinny być określane odrębnie dla każdej zmiennej diagnostycznej.  W ten sposób określono kierunki dalszych badań