Cyanobacteria(?) in iron banded formations of the Kursk magnetic anomaly

Fossilized cyanobacteria(?) represented by trichomes enclosed in common sheaths were detected in early Proterozoic iron banded formations of the Kursk magnetic anomaly (limonite–martite ores of the Lebedinsky mine and iron banded formations of the Korobkovskoye deposit). These fossils morphologically similar to current representatives of the genus Microcoleus were buried in situ.     

Formation of hydroxyl radicals from hydrogen peroxide in the presence of iron. Is haemoglobin a biological Fenton reagent?

The ability of oxyhaemoglobin and methaemoglobin to generate hydroxyl radicals (OH.) from H2O2 has been investigated using deoxyribose and phenylalanine as 'detector molecules' for OH.. An excess of H2O2 degrades methaemoglobin, releasing iron ions that react with H2O2 to form a species that appears to be OH.. Oxyhaemoglobin reacts with low concentrations of H2O2 to form a 'reactive species' that degrades deoxyribose but does not hydroxylate phenylalanine. This 'reactive species' is less amenable to scavenging by certain scavengers (salicylate, phenylalanine, arginine) than is OH., but it appears more reactive than OH. is to others (Hepes, urea). The ability of haemoglobin to generate not only this 'reactive species', but also OH. in the presence of H2O2 may account for the damaging effects of free haemoglobin in the brain, the eye, and at sites of inflammation.     

Possible origin of life between mica sheets: does life imitate mica?

The mica hypothesis for the origin of life proposes that life originated between the sheets of muscovite mica. This paper elaborates on two ways that life resembles what might have originated between mica sheets. First, enzymes: The configurations and dynamics of enzymes, with their substrates, cofactors, and sometimes transition metal ions, often resemble mica sheets, with their open-and-shut motions, acting on small molecules between them, sometimes assisted by transition metal ions. Second, organisms: Mica world had the potential to be a community or ecosystem of prebiotic organisms in a way unlike other models for the origin of life.     

Eogenesis — The origin of animal forms

Zusammenfassung Alle Formen von Leben entstanden aus der primitiven Zelle, betrachtet eher als eine Art denn als ein Individuum, welches die Fähigkeit für ununterbrochene Selbst-Teilung besass. Fortgesetzte Vermehrung der Zellen mag eins von drei verschiedenen Verfahren folgen: 1. Die zwei Zellen von jeder Teilung hervorgehend, mögen sich vollständig von einander trennen; diese Linie der Entwicklung der primitiven Zelle rief die Protozoa hervor. 2. Während die Zellen sich teilen, mögen sie mehr oder weniger unregelmässig zusammen hängen. Diese Linie rief die Porifera (Schwämme) hervor. 3. Die sich teilenden Zellen mögen regelmässig zusammenhängen, eine Blastula und eine Gastrula bildend. Die Gastrula ist fähig eine unbestimmte Anzahl von Variationen hervorzubringen, und durch diese Variationen in der Gastrula entstanden alle Tier-Typen ausser der Protozoa und der Porifera.Diese Linien der Entwicklung von der einzelnen Zelle stellen alle die physischen und geometrischen entfaltungsfähigen Möglichkeiten, denkbar im Falle von Zellen, dar, die die Kraft besitzen sich durch Selbst-Teilung zu vermehren. Da diese entfaltungsfähigen Linien einfach mechanische Antworten auf die geometrischen und physischen Eigentümlichkeiten sind, eigen der Vermehrung der sich selbst teilenden Zellen, so gibt es keine Rechtfertigung für die Annahme einer bestimmten Ordnung in ihrem Vorkommen. Es ist logischer anzunehmen, dass die primitive Zelle gleich nach ihrem Erscheinen sich nach jeder möglichen Richtung gleichzeitig entwickelte, kurz, dass alle die Haupttypen des Tierlebens gleichzeitig erschienen.Es gibt keinen Beweis gegen diese Annahme, welche in Übereinstimmung mit dem geologischen Hintergrund des Lebens ist, wie wir es verstehen; mit der Fossilien-Urkunde, wie illustriert durch Fossilien von genau vergleichbaren Umgebungen; und mit der angenommenen Nötigkeit für ein System von Kontrolle und Ausgleich zwischen den verschiedenen Typen von Leben.

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Résumé Toutes les formes de la vie proviennent d'une cellule primitive unique, considérée comme espèce plutôt que comme individu, possédant le pouvoir de se multiplier par bi-partition répétée. La propagation continue de cellules peut avoir lieu de trois façons différentes: 1. Les deux cellules, après la division, peuvent se séparer complètement l'une de l'autre; cette forme de propagation de la cellule primitive a donné lieu aux Protozoaires. 2. Les cellules, en se divisant, peuvent rester liées plus ou moins irrégulièrement; cette forme de propagation caractérise les Porifères (spongiées). 3. Les cellules, en se divisant, peuvent rester liées selon un arrangement régulier, en formant une blastula et une gastrula; la gastrula peut être formée selon un infinité de modalités, et c'est à ces différences de la formation de la gastrula que sont dues toutes les espèces animales exceptés les Protozoaires et les spongiées.Ces formes de propagation de la cellule unique représentent la somme des possibilités d'arrangement permises par les lois de la géométrie et de la physique. Du moment que ces procédés de propagation sont soumis à un arrangement mécanique gouverné par des lois physiques et géométriques, il n'y a pas lieu d'admettre qu'il y ait, dans leur succession, d'ordre déterminé. Il est plus logique de supposer qu'aussitôt parue la cellule primitive se soit propager simutanément dans toutes les directions concevables, en d'autres mots que toutes les phyla animales se soient différenciées au même moment.Aucune preuve ne démont cette hypothèse qui, d'ailleurs, concorde avec les prémises géologiques de la vie telles que nous les comprenons, avec les vestiges fossilisés de couches géologiques strictément comparable, et avec la théorie qui admet l'établissement de l'équilibre entre les différentes espèces animales au moyen d'un contrôle et de limitations mutuelles.

     

Engineering aspects of biological ion channels—from biosensors to computational models for permeation

Molecular sequencing has helped resolve the phylogenetic relationships amongst the diverse groups of algal, fungal-like and protist organisms that constitute the Chromalveolate “superkingdom” clade. It is thought that the whole clade evolved from a photosynthetic ancestor and that there have been at least three independent plastid losses during their evolutionary history. The fungal-like oomycetes and hyphochytrids, together with the marine flagellates Pirsonia and Developayella, form part of the clade defined by Cavalier-Smith and Chao (2006) as the phylum “Pseudofungi”, which is a sister to the photosynthetic chromistan algae (phylum Ochrophyta). Within the oomycetes, a number of predominantly marine holocarpic genera appear to diverge before the main “saprolegnian” and “peronosporalean” lines, into which all oomycetes had been traditionally placed. It is now clear that oomycetes have their evolutionary roots in the sea. The earliest diverging oomycete genera so far documented, Eurychasma and Haptoglossa, are both obligate parasites that show a high degree of complexity and sophistication in their host parasite interactions and infection structures. Key morphological and cytological features of the oomycetes will be reviewed in the context of our revised understanding of their likely phylogeny. Recent genomic studies have revealed a number of intriguing similarities in host–pathogen interactions between the oomycetes with their distant apicocomplexan cousins. Therefore, the earlier view that oomycetes evolved from the largely saprotrophic “saprolegnian line” is not supported and current evidence shows these organisms evolved from simple holocarpic marine parasites. Both the hyphal-like pattern of growth and the acquisition of oogamous sexual reproduction probably developed largely after the migration of these organisms from the sea to land.     

Possible nonanthropogenic origin of two methanogenic isolates from oil‐producing wells in the san miguelito field,ventura county,California

Two novel strains of rod‐shaped methanogens were isolated from oil‐producing wells of high temperature and moderate salinity in the San Miguelito field. The strains grow at 65°C in media containing 6% NaCl, form large aggregates of cell materials in liquid culture, and produce methane from H₂ and CO₂ only. The geochemistry and microbiology of the oil reservoir and surrounding areas support the view that not all methanogens isolated from oil wells are results of colonization during or after human exploration, and that methanogens can exist in situ under thermal, haline conditions.     

Critical limitations in biological production of chemicals: process or genetic solutions?

Abstract: Production of bulk chemicals by biological processes is presently limited by failure of contemporary biological and bioreactor technology to deliver high product concentrations in high space-time yields in fluids of sufficiently low water content for subsequent down-stream processing operations. Limitations in the bioreactor portion of the process can arise due to failure to process sufficient substrate, substrate inhibition, inadequate rates or yields, and product inhibition. Various process approaches for addressing many of these limitations have been demonstrated or conceptualized. Less developed but potentially effective are genetic strategies addressing these process limitations. Ideally, the most effective combination of genetic and process approaches should be integrated in a synergistic fashion to maximize the economic potential of biological production of chemicals.     

An origin of DNA replication from streptomycete phage ΦU1

A DNA fragment from phage ΦU1 containing an origin of DNA replication was identified. This fragment, designatedori, was able to support the maintenance inStreptomyces lividans of a plasmid lacking a functional Gram-positiveori. The sequence of the minimalori fragment was determined and analyzed. The minimal fragment conferring replication origin function contained a number of direct and inverted repeats. The absence of an open reading frame in thisori fragment indicates that host factors alone were sufficient to initiate replication atori.     

Antibiotic-resistant Escherichia coli in karstic systems: a biological indicator of the origin of fecal contamination?

Occurrences of antibiotic-resistant Escherichia coli in two springs of a karstic system (NW France) providing drinking water were determined to study the role of aquifers in the dissemination of the resistance genes. Water samples were collected during wet and dry periods and after a heavy rainfall event to investigate E. coli density, antibiotic resistance patterns, and occurrences of class 1, 2, and 3 integrons. By observing patterns of the resistant isolates (i.e. number and type of resistances) and their occurrences, we were able to define two resistant subpopulations, introduced in the aquifer via surface water: (1) R1-2, characterized by one or two resistance(s), essentially to chloramphenicol and/or tetracycline (96.5%), was always found during the heavy rainfall event; (2) R3-10, characterized by three or more resistances, mostly resistant to tetracycline (94.1%) and beta-lactams (86%), was found transiently. Class 1 and 2 integrons were detected, mostly in the R3-10 subpopulation for class 1 integrons. The characteristics of these two subpopulations strongly suggest that the contamination originates from pasture runoff for the R1-2 subpopulation and from wastewater treatment plant effluents for the R3-10 subpopulation. These two subpopulations of E. coli could be used as biological indicators to determine the origin of groundwater contamination.     

Fluorescent oligo and poly-thiophenes and their utilization for recording biological events of diverse origin—when organic chemistry meets biology

The technique of using luminescent oligo-thiophenes and luminescent conjugated poly-thiophenes to monitor biological processes has gained increased interest from scientists within different research areas, ranging from organic chemistry and photo-physics to biology since its introduction. The technique is generally straightforward and requires only standard equipment, and the result is available within minutes from sample preparation. In this review, the syntheses of oligo and polythiophenes developed over the last decades are discussed. Furthermore, the utilization of these molecular agents for exploring biological events, e.g., DNA hybridization or protein misfolding events, are covered.     

Phylogenetic origin of Beckmannia （Poaceae） inferred from molecular evidence

The phylogenetic origin of Beckmannia remains unknown. The genus has been placed within the Chlorideae, Aveneae （Agrostideae）, Poeae, or treated as an isolate lineage, Beckmanniinae. In the present study, we used nuclear internal transcribed spacer （ITS） and chloroplast trnL-F sequences to examine the phylogenetic relationship between Beckmannia and those genera that have assumed to be related. On the basis of the results of our studies, the following conclusions could be drawn： （i） Beckmannia and Alopecurus are sister groups with high support; and （ii） Beckmannia and Alopecurus are nested in the Poeae clade with high support. The results of our analysis suggest that Beckmannia should be placed in Poeae.     

Microbial hydantoinases – industrial enzymes from the origin of life?

Hydantoinases are valuable enzymes for the production of optically pure d- and l-amino acids. They catalyse the reversible hydrolytic ring cleavage of hydantoin or 5′-monosubstituted hydantoins and are therefore classified in the EC nomenclature as cyclic amidases (EC 3.5.2.). In the EC nomenclature, four different hydantoin-cleaving enzymes are described: dihydropyrimidinase (3.5.2.2), allantoinase (EC 3.5.2.5), carboxymethylhydantoinase (EC 3.5.2.4), and N-methylhydantoinase (EC 3.5.2.14). Beside these, other hydantoinases with known metabolic functions, such as imidase and carboxyethylhydantoinase and enzymes with unknown metabolic function, are described in the literature and have not yet been classified. An important question is whether the distinct hydantoinases, which are frequently classified as l-, d-, and non-selective hydantoinases depending on their substrate specificity and stereoselectivity, are related to each other. In order to investigate the evolutionary relationship, amino acid sequence data can be used for a phylogenetic analysis. Although most of these enzymes only share limited sequence homology (identity<15%) and therefore are only distantly related, it can be shown (i) that most of them are members of a broad set of amidases with similarities to ureases and build a protein superfamily, whereas ATP-dependent hydantoinases are not related, (ii) that the urease-related amidases have evolved divergently from a common ancestor and (iii) that they share a metal-binding motif consisting of conserved histidine residues. The difference in enantioselectivity used for the classification of hydantoinases on the basis of their biotechnological value does not reflect their evolutionary relationship, which is to a more diverse group of enzymes than was assumed earlier. This protein superfamily probably has its origin in the prebiotic conditions of the primitive earth. Received: 24 August 1998 / Received revision: 9 November 1998 / Accepted: 21 November 1998     

Botanical origin of honey from south of Calde´n district (Argentina)

We performed palynological analysis of 75 honey samples from the south of Caldén district, which is the part of the phytogeographical province del Espinal. Prosopis caldenia , "caldén" (Fabaceae) is the dominant arboreal species in this region. 79 pollen types that belong to 36 plant families were identified. Honeydew elements are absent or present in negligible amounts. Native flora is intensely utilized. Main nectar sources that characterize monofloral honey samples, are these natives Condalia microphylla (Rhamnaceae), Prosopis sp. and Vicia sp. (Fabaceae), Larrea divaricata (Zygophyllaceae) and Brassicaceae, which are foreign to the area. The pollen from these plants along with the pollen of Trichocline sp. (Asteraceae) and Prosopidastrum globosum (Fabaceae), Schinus fasciculatus (Anacardiaceae), Astereae and Lycium sp.(Solanaceae), characterize honey from Caldén.     

The Aversive Effect of Electromagnetic Radiation on Foraging Bats—A Possible Means of Discouraging Bats from Approaching Wind Turbines

Large numbers of bats are killed by collisions with wind turbines and there is at present no accepted method of reducing or preventing this mortality. Following our demonstration that bat activity is reduced in the vicinity of large air traffic control and weather radars, we tested the hypothesis that an electromagnetic signal from a small portable radar can act as a deterrent to foraging bats. From June to September 2007 bat activity was compared at 20 foraging sites in northeast Scotland during experimental trials (radar switched on) and control trials (no radar signal). Starting 45 minutes after sunset, bat activity was recorded for a period of 30 minutes during each trial and the order of trials were alternated between nights. From July to September 2008 aerial insects at 16 of these sites were sampled using two miniature light-suction traps. At each site one of the traps was exposed to a radar signal and the other functioned as a control. Bat activity and foraging effort per unit time were significantly reduced during experimental trials when the radar antenna was fixed to produce a unidirectional signal therefore maximising exposure of foraging bats to the radar beam. However, although bat activity was significantly reduced during such trials, the radar had no significant effect on the abundance of insects captured by the traps.     

The other kind of biological NMR—Studies of enzyme-substrate interactions

NMR spectroscopy has proved to be a valuable tool in the study of the interactions between enzymes and their substrates. The kinds of structural and dynamic information which can be obtained are illustrated by studies of three enzymes involved in drug metabolism. Cytochromes P₄₅₀ play a crucial role in metabolism of a wide range of exogenous chemicals. NMR has been used to measure distances from the haem iron of the cytochrome to protons of the bound substrate, leading to detailed structural models for the enzyme-substrate complexes. The other two enzymes, chloramphenicol acetyltransferase and β-lactamase, are responsible for bacterial resistance to specific antibiotics. In chloramphenicol acetyltransferase, NMR has been used to determine the conformation of coenzyme A bound to the enzyme, while in the case of β-lactamase the pK of a specific lysine residue at the active site has been determined, providing valuable information on the catalytic mechanism. Special issue dedicated to Dr. Herman Bachelard.     

Iwao’s patchiness regression through the origin: biological importance and efficiency of sampling applications

Iwao’s mean crowding-mean density relation can be treated both as a linear function describing the biological characteristics of a species at a population level, or a regression model fitted to empirical data (Iwao’s patchiness regression). In this latter form its parameters are commonly used to construct sampling plans for insect pests, which are characteristically patchily distributed or overdispersed. It is shown in this paper that modifying both the linear function and statistical model to force the intercept or lower functional limit through the origin results in more intuitive biological interpretation of parameters and better sampling economy. Firstly, forcing the function through the origin has the effect of ensuring that zero crowding occurs when zero individuals occupy a patch. Secondly, it ensures that negative values of the intercept, which do not yield an intuitive biological interpretation, will not arise. It is shown analytically that sequential sampling plans based on regression through the origin should be more efficient compared to plans based on conventional regression. For two overdispersed data sets, through-origin based plans collected a significantly lower sample size during validation than plans based on conventional regression, but the improvement in sampling efficiency was not large enough to be of practical benefit. No difference in sample size was observed when through-origin and conventional regression based plans were validated using underdispersed data. A field researcher wishing to adopt a through-origin form of Iwao’s regression for the biological reasons outlined above can therefore be confident that their sampling strategies will not be affected by doing so.     

On the origin of SARS-CoV-2——The blind watchmaker argument

正In the comparison with SARS-CoVof 2003, SARS-CoV-2 is extremely well adapted to the human populations and its adaptive shift from the animal host to humans must have been even more extensive. By the blind watchmaker argument, such an adaptive shift can only happen prior to the onset of the current pandemic and with the aid of step-by-step selection.