The effect of pyrophosphate, tripolyphosphate and ATP on the rate of the Fenton reaction

It has been recently reported that pyrophosphate, tri-polyphosphate, ATP and analogous ligands considerably decrease the yield of hydroxyl radicals by the Fenton reaction under conditions where [H₂O₂] > > [Fe(II)L_n]. It was suggested that this effect is due to the slowing down of the Fenton reaction by these ligands. This suggestion seemed surprising as polyphosphate ligands stabilize Fe(III). Indeed, a kinetic study points out that these ligands accelerate the rate of the Fenton reaction by several orders of magnitude. Thus it is suggested that the effect of the ligands on the yield of the hydroxyl radicals is due to the stabilization of the Fe(III) complexes which slows down, or inhibits, their reduction by the radicals formed in the system and thus decreases the overall yield of hydroxyl radicals.     

Early Stages of the Evolution of Life: a Cybernetic Approach

Early stages of the evolution of life are considered in terms of control theory. A model is proposed for the transport of substances in a protocell possessing the property of robustness with regard to changes in the environmental concentration of a substance.     

Bacterial and Chemical Iron Oxide Deposition in a Shallow Bay on Palaea Kameni,Santorini, Greece: Microscopy,Electron Probe Microanalysis,and Photometry of in situ Experiments

The present study was aimed at determining whether microorganisms mediate iron oxide deposition in a shallow bay (Iron Bay) on the still volcanically active island of Palaea Kameni, Santorini, Greece, north of Crete in the Aegean Sea. The results of in situ experiments showed that iron oxide deposition in this marine environment occurs at an exceptionally high rate. It was also found that deposition in the central part of the bay proceeded within specific vertical zones in the water column, showing that the bay may be regarded as a stratified system. Using light and scanning electron microscopic methods, including electron probe microanalysis, it was shown that deposition (binding and oxidation) of Fe(II) was mediated by bacteriological processes, which differed in intensity depending on their specific location in the bay. The most intensive iron oxidations and depositions were found in the hot volcanic springs at the toe of the bay, where rates more than 60 times those found in freshwater iron-oxidizing environments were measured. Bacteria that excreted extracellular slime (EPS), which apparently catalysed the process and itself became encrusted with tiny globules of hydrated iron(III) oxide, were responsible for this extremly high rate of iron deposition. The same process of oxidation catalysed by bacterial EPS was also responsible for iron oxide deposition in the main oxidation zone in the central part of the bay. Thus, precipitation of Fe(II) in Iron Bay is not, as was previously assumed, a purely chemical, Eh- and pH-dependent process, but results from the interaction of water chemistry with a high level of bacterial activity, especially surface reactions on bacterial excretion products.     

Question 7: The Vesicle World: The Emergence of Cellular Life can be Related to Properties Specific to Vesicles

The question “What was the minimum number of genes necessary in the early cell” is rephrased as “Is it feasible to assume that early cells had no genes?” It is shown that a kind of primitive life process could exist on the basis only of properties specific to vesicles, and that it would have the potential to evolve into more complex cell-like processes.     

Science and the Concept of Evolution: From the Big Bang to the Origin and Evolution of Life

The common thread of evolution runs through all science disciplines, and the concept of evolution enables students to better understand the nature of the universe and our origins. “Science and the Concept of Evolution” is one of two interdisciplinary science Core courses taken by Dowling College undergraduates as part of their General Education requirements. The course examines basic principles and methods of science by following the concept of evolution from the big bang to the origin and evolution of life. Case studies of leading scientists illustrate how their ideas developed and contributed to the evolution of our understanding of the world. Evidences for physical, chemical, and biological evolution are explored, and students learn to view the evolution of matter and of ideas as a natural process of change over space and time.     

Learning to Eat Vegetables in Early Life: The Role of Timing,Age and Individual Eating Traits

Vegetable intake is generally low among children, who appear to be especially fussy during the pre-school years. Repeated exposure is known to enhance intake of a novel vegetable in early life but individual differences in response to familiarisation have emerged from recent studies. In order to understand the factors which predict different responses to repeated exposure, data from the same experiment conducted in three groups of children from three countries (n = 332) aged 4–38 m (18.9±9.9 m) were combined and modelled. During the intervention period each child was given between 5 and 10 exposures to a novel vegetable (artichoke puree) in one of three versions (basic, sweet or added energy). Intake of basic artichoke puree was measured both before and after the exposure period. Overall, younger children consumed more artichoke than older children. Four distinct patterns of eating behaviour during the exposure period were defined. Most children were “learners” (40%) who increased intake over time. 21% consumed more than 75% of what was offered each time and were labelled “plate-clearers”. 16% were considered “non-eaters” eating less than 10 g by the 5^th exposure and the remainder were classified as “others” (23%) since their pattern was highly variable. Age was a significant predictor of eating pattern, with older pre-school children more likely to be non-eaters. Plate-clearers had higher enjoyment of food and lower satiety responsiveness than non-eaters who scored highest on food fussiness. Children in the added energy condition showed the smallest change in intake over time, compared to those in the basic or sweetened artichoke condition. Clearly whilst repeated exposure familiarises children with a novel food, alternative strategies that focus on encouraging initial tastes of the target food might be needed for the fussier and older pre-school children.     

The Recent Evolution of a Maternally-Inherited Endosymbiont of Ticks Led to the Emergence of the Q Fever Pathogen,Coxiella burnetii

Q fever is a highly infectious disease with a worldwide distribution. Its causative agent, the intracellular bacterium Coxiella burnetii, infects a variety of vertebrate species, including humans. Its evolutionary origin remains almost entirely unknown and uncertainty persists regarding the identity and lifestyle of its ancestors. A few tick species were recently found to harbor maternally-inherited Coxiella-like organisms engaged in symbiotic interactions, but their relationships to the Q fever pathogen remain unclear. Here, we extensively sampled ticks, identifying new and atypical Coxiella strains from 40 of 58 examined species, and used this data to infer the evolutionary processes leading to the emergence of C. burnetii. Phylogenetic analyses of multi-locus typing and whole-genome sequencing data revealed that Coxiella-like organisms represent an ancient and monophyletic group allied to ticks. Remarkably, all known C. burnetii strains originate within this group and are the descendants of a Coxiella-like progenitor hosted by ticks. Using both colony-reared and field-collected gravid females, we further establish the presence of highly efficient maternal transmission of these Coxiella-like organisms in four examined tick species, a pattern coherent with an endosymbiotic lifestyle. Our laboratory culture assays also showed that these Coxiella-like organisms were not amenable to culture in the vertebrate cell environment, suggesting different metabolic requirements compared to C. burnetii. Altogether, this corpus of data demonstrates that C. burnetii recently evolved from an inherited symbiont of ticks which succeeded in infecting vertebrate cells, likely by the acquisition of novel virulence factors.     

The two forms of the S2 state multiline signal in Photosystem II: effect of methanol and ethanol

The characteristic Mn hyperfine ‘multiline’ signal exhibited in the S₂ state of the oxygen-evolving complex (OEC) complex of Photosystem II (PSII) has been shown to be heterogeneous in character. In this study, we have explored the effects that influence the proportions of the two forms of the S₂ state multiline signal present in any sample. The narrow form of the signal is lost upon storage (weeks) at 77 K, whereas the broad form remains. In particular, we explore the roles of ethanol and methanol as well as effects of the second turnover of the enzyme on storage of the sample at 77 K. We find that in samples containing methanol, the narrow form may predominate upon the first flash, but the broad form predominates on the fifth flash and also in samples containing ethanol.     

Germination of Monocolpate Angiosperm Pollen: Evolution of the Actin Cytoskeleton and Wall during Hydration, Activation and Tube Emergence

The monocolpate pollen grain of Narcissus pseudonarcissus L.has two preferred sites for tube emergence, one at each endof the colpus. While the cellulosic microfibnls of the innerlayer of the intine are disposed circumferentially in the centreof the grain, the microfibrils in these terminal sites are shorterand randomly oriented Soon after the beginning of hydration,inclusions of the vegetative cell begin movement, firstly ina rotatory manner, and then in a pattern focused on one or bothgermination sites, where the intine bulges as hydration progresses.These changes are associated with the evolution of the actincytoskeleton. Actin is present in the unactivated grain in theform of fusiform bodies. During hydration these dissociate toform finer fibrils, initially randomly disposed. Then, correlatedwith the change of the pattern of movement in the vegetativecell, the actin fibril system becomes polarized towards thegermination sites, where shorter fibrils accumulate. Callose,absent from the ungerminated grain, is deposited within thecellulosic wall in these locations, forming a shallow dome whicheventually develops into an annulus subtending the inner calloselining of the emerging tube. The transition to cylindrical growthis associated firstly with the development of zonation in thecytoplasm of the vegetative cell, with the tip occupied by apopulation of wall precursor bodies (P-particles) and a denseaggregate of short actin fibrils; and then with the establishmentof the ‘inverse fountain’ pattern of movement characteristicof the apical part of the extending tube. Narcissus pseudonarcissus L, pollen activation, pollen germination, actin cytoskeleton, tip-growth system, pollen-tube wall development     

Reprint of PSII Manganese Cluster: Protonation of W2, O5, O4 and His337 in the S1 state explored by combined quantum chemical and electrostatic energy computations

Photosystem II (PSII) is a membrane-bound protein complex that oxidizes water to produce energized protons, which are used to built up a proton gradient across the thylakoidal membrane in the leafs of plants. This light-driven reaction is catalyzed by withdrawing electrons from the Mn₄CaO₅-cluster (Mn-cluster) in four discrete oxidation steps [S₁ − (S₄ / S₀)] characterized in the Kok-cycle. In order to understand in detail the proton release events and the subsequent translocation of such energized protons, the protonation pattern of the Mn-cluster need to be elucidated. The new high-resolution PSII crystal structure from Umena, Kawakami, Shen, and Kamiya is an excellent basis to make progress in solving this problem. Following our previous work on oxidation and protonation states of the Mn-cluster, in this work, quantum chemical/electrostatic calculations were performed in order to estimate the pKa of different protons of relevant groups and atoms of the Mn-cluster such as W2, O4, O5 and His337. In broad agreement with previous experimental and theoretical work, our data suggest that W2 and His337 are likely to be in hydroxyl and neutral form, respectively, O5 and O4 to be unprotonated. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy.     

The Case of Paul Kammerer: Evolution and Experimentation in the Early 20th Century

To some, a misguided Lamarckian and a fraud, to others a martyr in the fight against Darwinism, the Viennese zoologist Paul Kammerer (1880–1926) remains one of the most controversial scientists of the early 20th century. Here his work is reconsidered in light of turn-of-the-century problems in evolutionary theory and experimental methodology, as seen from Kammerer’s perspective in Vienna. Kammerer emerges not as an opponent of Darwinism, but as one would-be modernizer of the 19th-century theory, which had included a role for the inheritance of acquired characteristics. Kammerer attempted a synthesis of Darwinism with genetics and the chromosome theory, while retaining the modifying effects of the environment as the main source of favorable variation, and he developed his program of experimentation to support it. Kammerer never had a regular university position, but worked at a private experimental laboratory, with sidelines as a teacher and a popular writer and lecturer. On the lecture circuit he held forth on the significance of his science for understanding and furthering cultural evolution and he satisfied his passion for the arts and performance. In his dual career as researcher and popularizer, he did not always follow academic convention. In the contentious and rapidly changing fields of heredity and evolution, some of his stances and practices, as well as his outsider status and part-Jewish background, aroused suspicion and set the stage for the scandal that ended his career and prompted his suicide.     

Massive Thermal Acceleration of the Emergence of Primordial Chemistry,the Incidence of Spontaneous Mutation,and the Evolution of Enzymes

Kelvin considered it unlikely that sufficient time had elapsed on the earth for life to have reached its present level of complexity. In the warm surroundings in which life first appeared, however, elevated temperatures would have reduced the kinetic barriers to reaction. Recent experiments disclose the profound extent to which very slow reactions are accelerated by elevated temperatures, collapsing the time that would have been required for early events in primordial chemistry before the advent of enzymes. If a primitive enzyme, like model catalysts and most modern enzymes, accelerated a reaction by lowering its enthalpy of activation, then the rate enhancement that it produced would have increased automatically as the environment cooled, quite apart from any improvements in catalytic activity that arose from mutation and natural selection. The chemical events responsible for spontaneous mutation are also highly sensitive to temperature, furnishing an independent mechanism for accelerating evolution.     

PSII manganese cluster: Protonation of W2, O5, O4 and His337 in the S1 state explored by combined quantum chemical and electrostatic energy computations

Photosystem II (PSII) is a membrane-bound protein complex that oxidizes water to produce energized protons, which are used to built up a proton gradient across the thylakoidal membrane in the leafs of plants. This light-driven reaction is catalyzed by withdrawing electrons from the Mn₄CaO₅-cluster (Mn-cluster) in four discrete oxidation steps [S₁ − (S₄ / S₀)] characterized in the Kok-cycle. In order to understand in detail the proton release events and the subsequent translocation of such energized protons, the protonation pattern of the Mn-cluster need to be elucidated. The new high-resolution PSII crystal structure from Umena, Kawakami, Shen, and Kamiya is an excellent basis to make progress in solving this problem. Following our previous work on oxidation and protonation states of the Mn-cluster, in this work, quantum chemical/electrostatic calculations were performed in order to estimate the pKa of different protons of relevant groups and atoms of the Mn-cluster such as W2, O4, O5 and His337. In broad agreement with previous experimental and theoretical work, our data suggest that W2 and His337 are likely to be in hydroxyl and neutral form, respectively, O5 and O4 to be unprotonated. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy.     

Styles of Reasoning in Early to mid-Victorian Life Research: Analysis:Synthesis and Palaetiology

To better understand the work of pre-Darwinian British life researchers in their own right, this paper discusses two different styles of reasoning. On the one hand there was analysis:synthesis, where an organism was disintegrated into its constituent parts and then reintegrated into a whole; on the other hand there was palaetiology, the historicist depiction of the progressive specialization of an organism. This paper shows how each style allowed for development, but showed it as moving in opposite directions. In analysis:synthesis, development proceeded centripetally, through the fusion of parts. Meanwhile in palaetiology, development moved centrifugally, through the ramifying specialization of an initially simple substance. I first examine a community of analytically oriented British life researchers, exemplified by Richard Owen, and certain technical questions they considered important. These involved the neurosciences, embryology, and reproduction and regeneration. The paper then looks at a new generation of British palaetiologists, exemplified by W.B. Carpenter and T.H. Huxley, who succeeded at portraying analysts’ questions as irrelevant. The link between styles of reasoning and physical sites is also explored. Analysts favored museums, which facilitated the examination and display of unchanging marine organisms while providing a power base for analysts. I suggest that palaetiologists were helped by vivaria, which included marine aquaria and Wardian cases. As they became popular in the early 1850s, vivaria provided palaetiologists with a different kind of living and changing evidence. Forms of evidence, how they were preserved and examined, and career options all reinforced each other: social and epistemic factors thus merged.