Losing the last feather: feather loss as an antipredator adaptation in birds

Birds often lose feathers during predation attempts, and thisability has evolved as a means of escape. Because predatorsare more likely to grab feathers on the rump and the back thanon the ventral side of an escaping bird, we predicted that theformer feathers would have evolved to be relatively looselyattached as an antipredator strategy in species that frequentlydie from predation. We estimated the force required to removefeathers from the rump, back, and breast by pulling featherswith a spring balance from a range of European bird speciesin an attempt to investigate ecological factors associated withease of feather loss during predation attempts. The force requiredto loosen a feather from the rump was less than that requiredto loosen a feather from back, which in turn was less than thatrequired to loosen a feather from the breast. The relative forceneeded to loosen rump feathers compared with feathers from theback and the breast was smaller for prey species preferred bythe most common predator of small passerine birds, the sparrowhawkAccipiter nisus. Likewise, the relative force was also smallerin species with a high frequency of complete tail loss amongfree-living birds, which we used as an index of the frequencyof failed predation attempts. The relative force required toremove feathers from the rump was smaller in species with ahigh frequency of fear screams, another measure of the relativeimportance of predation as a cause of death. Feather loss requiredparticularly little force among solitarily breeding bird speciesthat suffer the highest degree of predation. Antipredator defensein terms of force required to remove feathers from the rumpwas larger in species with a strong antiparasite defense interms of T-cell–mediated immune response. These findingsare consistent with the hypothesis that different defenses areantagonistic and that they are traded off against each other.     

A Mechanism of Energy Dissipation in Cyanobacteria

When grown under a variety of stress conditions, cyanobacteria express the isiA gene, which encodes the IsiA pigment-protein complex. Overexpression of the isiA gene under iron-depletion stress conditions leads to the formation of large IsiA aggregates, which display remarkably short fluorescence lifetimes and thus a strong capacity to dissipate energy. In this work we investigate the underlying molecular mechanism responsible for chlorophyll fluorescence quenching. Femtosecond transient absorption spectroscopy allowed us to follow the process of energy dissipation in real time. The light energy harvested by chlorophyll pigments migrated within the system and eventually reaches a quenching site where the energy is transferred to a carotenoid-excited state, which dissipates it by decaying to the ground state. We compare these findings with those obtained for the main light-harvesting complex in green plants (light-harvesting complex II) and artificial light-harvesting antennas, and conclude that all of these systems show the same mechanism of energy dissipation, i.e., one or more carotenoids act as energy dissipators by accepting energy via low-lying singlet-excited S₁ states and dissipating it as heat.     

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

Background  

Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabilities of organisms and interpreting experimental data. As the number of such reconstructions and analysis methods increases, there is a greater need for data uniformity and ease of distribution and use.     

Aerobic biomineralization of alpha-hexachlorocyclohexane in contaminated soil

The factors identified to be important for the aerobic biodegradation of alpha-hexachlorocyclohexane (alpha-HCH) in a soil slurry are temperature, auxiliary carbon source, substrate concentration, and soil inhomogeneities. Temperatures in the range of 20 to 30 degrees C were determined to be most favorable for biodegradation of alpha-HCH. No alpha-HCH biodegradation was detected at temperatures below 4 degrees C and above 40 degrees C. The addition of auxiliary organic carbon compounds showed repressive effects on alpha-HCH biomineralization. Increased oxygen partial pressures reduced the repressive effects of added auxiliary organic carbon compounds. A linear relationship between alpha-HCH concentration and its conversion rate was found in a Lineweaver-Burk plot. Inhomogeneities such as clumping of alpha-HCH significantly affected its biodegradation. Inhomogeneity as an influence on biodegradation has not drawn sufficient attention in the past, even though it certainly has affected both laboratory studies and the application of biotechnological methods to clean up contaminated sites. On the basis of metabolites detected during degradation experiments, the initial steps of aerobic alpha-HCH bioconversion in a soil slurry are proposed.     

Demographic incidence rates

Demographers commonly interpret incidence rates (for first marriages, say, or for births of a given order), cumulated over age for a closed cohort, as prevalences of corresponding demographic statuses. Since one is hard put to find an explicit justification for this interpretation in the literature, this note offers a mathematical proof that it is correct if and only if there is nondifferential mortality, as well as an extension to incidences for events which can happen more than once to an individual. Mortality incidence rates are discussed as well, and some of the evidence that cumulative incidence rates may get absurd values when computed from period data is reviewed.     

Lateral diffusion of gramicidin S,M-13 coat protein and glycophorin in bilayers of saturated phospholipids: Mean field and Monte Carlo studies

We have developed a general model that relates the lateral diffusion coefficient of one isolated large intrinsic molecule (mol. wt. ?1000) in a phosphatidylcholine bilayer to the static lipid hydrocarbon chain order. We have studied how protein lateral diffusion can depend upon protein-lipid interactions but have not investigated possible non-specific contributions from gel-state lattice defects. The model has been used in Monte Carlo simulations or in mean-field approximations to study the lateral diffusion coefficients of Gramicidin S, the M-13 coat protein and glycophorin in dimyristoyl- and dipalmitoylphosphatidylcholine (DMPC and DPPC) bilayers as functions of temperature. Our calculated lateral diffusion coefficients for Gramicidin S and the M-13 coat protein are in good agreement with what has been observed and suggest that Gramicidin S is in a dimeric form in DMPC bilayers. In the case of glycophorin we find that the ‘ice breaker’ effect can be understood as a consequence of perturbation of the lipid polar region around the protein. In order to understand this effect is is necessary that the protein hydrophilic section perturb the polar regions of at least approx. 24 lipid molecules, in good agreement with the numbers of 29–30 measured using ³¹P-NMR. Because of lipid-lipid interactions this effect extends itself out to four or five lipid layers away from the protein so that the hydrocarbon chains of between approx. 74 and approx. 108 lipid molecules are more disordered in the gel phase, so contributing less to the transition enthalpy, in agreement with the numbers of 80–100 deduced from differential scanning calorimetry (DSC). An understanding of the abrupt change in the diffusion coefficient at a temperature below the main bilayer transition temperature requires an additional mechanism. We propose that this change may be a consequence of a ‘coupling-uncoupling’ transition involving the protein hydrophilic section and the lipid polar regions, which may be triggered by the lipid bilayer pretransition. Our calculation of the average number of gauche bonds per lipid chain as a function of temperature and distance away from an isolated polypeptide or integral protein shows the extent of statically disordered lipid around such molecules. The range of this disorder depends upon temperature, particularly near the main transition.     

Sur la notion de l'identité en biologie

Summary While refuting the standpoint taken byCharles Richet (that the identical phenomena do not occur in nature at all) and simultaneously setting aside the contrary view ofEmil Meyerson (that the very essence of our scientific thinking and method of deductions consists of the process of logical identification, proceeding from the complex and heterogeneous to the simple and homogenous, more and more diminishing particles), the author argues that in biology the perfectly identical creatures, features or phenomena must occur, so to say by virtue of mathematical necessity, if the inheritance of features through the course of sexual propagation, governed by the laws ofMendel, is proceeding according to the rules ofNewton's binomial. Then the expanded series of the latter brings us the expression of some sort of biological multiplication, which — in their successive terms — leads to the origin of natural groups of so called binomions (the notion introduced by the author in his previous papers, 1942 aetc., which he is referring to), each of which being composed of identical individuals, appearing in the exactly definite frequencies, issuing from the very procedure of multiplication of the factors, partaking in those series in any given term.Again, the possibility of ascertaining the eventual, if any, individualising differencies (deviations) in the identical so originated beings is explained by the author as being actually due to the gradual deepening of our diagnosing analysis, by the use of which the more and more minute units, material or energetic ones, are introduced.Finally, referring to the few, mostly incidentally chosen, examples taken from astronomy, chemistry, embryology, anthropology, sociology, logic and philosophy, the author calls the attention to the fact that the modern science shows a general tendency towards the foundation of its conclusions on the interaction of factors and on the use of the general principle of complexity (ofMalfitano andHonnelaitre) as an obligatory course of very scientific methodology.

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Zusammenfassung Gegenüber den Ansichten vonCharles Richet (dass es in der Natur überhaupt keine identische Gebilde geben könne), sowie auch die gegensätzliche, die von E.Meyerson (dass unseres Denkvermögen und methodologische Schlussziehung eben nur einen einzig möglichen Prozess der ständigen Identifizierung, die vom Komplexen und Heterogenen zum Elementaren und Homogenen in den Strukturen der immer mehr und mehr sich verkleinernden Partikeln fortschreitet, darstellen sollen), bei Seite lassend, hebt der Verfasser hervor, dass gerade auf dem Gebiete der Biologie vollständig identische Gebilde, Merkmale oder Erscheinungen, so zu sagen mit mathematischer Notwendigkeit, auftreten müssen, falls die Verterbung der Merkmale, die sich auf dem Wege der geschlechtlichen Fortpflanzung abspielt und derMendel-Gesetzen unterworfen ist, auf das Verfahren desNewton'schen Binoms zurückzuführen ist. Die entwickelte Reihe dieses letzteren — in deren Gliedern vertreten — stellt dann ein zusammengesetztes Beispiel einer eigenartigen biologischen Multiplizierung dar, die die Entstehung der natürlichen homogenen Gruppen von sogenannten Binomionen (— der Begriff in früheren Arbeiten des Verfassers, 1942 a, eingeführt —) verursacht.Jede einzelne derselben setz sich bekanntlich aus vollständig identischen Individuen zusammen, die in durch die binomische Regel festgesetzten, genau bestimmten Häufigkeiten auftreten und lauter aus dem Verfahren der Multiplizierung der teilnehmenden Elementen (als Factoren oder Multiplikatoren gedeutet) in allen gegebenen Gliedern jeder beliebigen Reihe herrühren können.Die eventuelle Entstehung etwaiger kleinsten individuellen Differenzen (Variationen) in auf solche Weise entstandenen vollständig identischen Gebilden ist als Folge der allmählichen Vertiefung unseres Erkenntnissverfahrens, bzw. diagnostischer Analyse zu deuten, in welcher mit immer kleiner und kleiner werdenden — materiellen oder energetischen — Einheiten gearbeitet wird.Zum Schluss, sich auf wenige hauptsächlich beiläufig ausgewählte Beispiele aus den Gebieten der Astronomie, der Chemie, der Embryologie, der Anthropologie, der Soziologie, der Logik und der Philosophie stützend, sucht der Verfasser zu beweisen, dass in der modernen Wissenschaft überhaupt eine allgemeine Tendenz herrscht die Schlüsse auf die Wechselwirkung der Factoren, bzw. auf den Prinzip der Komplexität (lautMalfitano undHonnelaitre), als einer grundsetzlichen Eigenschaft jeder wissenschaftlichen Methode, zurückzuführen.

     

Exchange of phosphatidylcholine between small unilamellar liposomes and human plasma high-density lipoprotein involves exclusively the phospholipid in the outer monolayer of the liposomal membrane

By making use of the capacity of phospholipase A₂ to degrade selectively the phospholipid in the outer half of the lipid bilayer of small unilamellar phospholipid/cholesterol vesicles without affecting the retention of a vesicle-encapsulated solute, we demonstrated that the exchange of phosphatidylcholine between such vesicles and human high density lipoprotein involves exclusively the phosphatidylcholine present in the outer monolayer of the vesicle membrane.