On a Safe Conclusion Concerning the Origin of the Eskimo, which Can Be Drawn from the Designation of Certain Objects in Their Language

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Shape mode analysis exposes movement patterns in biology: flagella and flatworms as case studies

We illustrate shape mode analysis as a simple, yet powerful technique to concisely describe complex biological shapes and their dynamics. We characterize undulatory bending waves of beating flagella and reconstruct a limit cycle of flagellar oscillations, paying particular attention to the periodicity of angular data. As a second example, we analyze non-convex boundary outlines of gliding flatworms, which allows us to expose stereotypic body postures that can be related to two different locomotion mechanisms. Further, shape mode analysis based on principal component analysis allows to discriminate different flatworm species, despite large motion-associated shape variability. Thus, complex shape dynamics is characterized by a small number of shape scores that change in time. We present this method using descriptive examples, explaining abstract mathematics in a graphic way.Comment: 20 pages, 6 figures, accepted for publication in PLoS On

Stem cells and fluid flow drive cyst formation in an invertebrate excretory organ.

Cystic kidney diseases (CKDs) affect millions of people worldwide. The defining pathological features are fluid-filled cysts developing from nephric tubules due to defective flow sensing, cell proliferation and differentiation. The underlying molecular mechanisms, however, remain poorly understood, and the derived excretory systems of established invertebrate models (Caenorhabditis elegans and Drosophila melanogaster) are unsuitable to model CKDs. Systematic structure/function comparisons revealed that the combination of ultrafiltration and flow-associated filtrate modification that is central to CKD etiology is remarkably conserved between the planarian excretory system and the vertebrate nephron. Consistently, both RNA-mediated genetic interference (RNAi) of planarian orthologues of human CKD genes and inhibition of tubule flow led to tubular cystogenesis that share many features with vertebrate CKDs, suggesting deep mechanistic conservation. Our results demonstrate a common evolutionary origin of animal excretory systems and establish planarians as a novel and experimentally accessible invertebrate model for the study of human kidney pathologies

Kolmogorov condition near hyperbolic singularities of integrable Hamiltonian systems

In this paper we show that, if an integrable Hamiltonian system admits a nondegenerate hyperbolic singularity then it will satisfy the Kolmogorov condegeneracy condition near that singularity (under a mild additional condition, which is trivial if the singularity contains a fixed point)Comment: revised version, 11p, accepted for publication in a sepecial volume in Regular and Chaotic Dynamics in honor of Richard Cushma

‘Antiflammins’: Two nonapeptide fragments of uteroglobin and lipocortin I have no phospholipase A2 -inhibitory and anti-inflammatory activity

AbstractThe ‘antiflammin’ nonapeptides P1 and P2 [(1988) Nature 335, 726-730] were synthesized and tested for inhibition of phospholipase A2 and release of prostaglandin E2, and leukotriene C4 in stimulated cells in vitro, and in vivo for anti-inflammatory activity in rats with carrageenan-induced paw oedema. Porcine pancreatic phospholipase A2, was not inhibited at concentrations of 0.5–50 μM. Prostaglandin E2, and leukotriene C4 release by mouse macrophages stimulated with zymosan or ATP was not affected up to a concentration of 10 μm, nor was prostaglandin release by interleukin 1β-stimulated mesangial cells and angiotensin II-stimulated smooth muscle cells. Both peptides exhibited no anti-inflammatory activity in carrageenan-induced rat paw oedema after topical (250 μg/paw) or systemic administration (1 or 4 mgkg s.c.). These results do not support the claim of potent phospholipase A2-inhibitory and anti-imflammatory activity of the ‘antiflammins’ P1 and P2 [1]

S-adenosyl-L-methionine: (S)-scoulerine 9-O-methyltransferase, a highly stereo- and regio-specific enzyme in tetrahydroprotoberberine biosynthesis

Suspension cultures of Berberis species are useful sources for the detection and isolation of a new enzyme which transfers the methyl group from S-adenosyl-L-methionine specifically to the 9-position of the (S)-enantiomer of scoulerine, producing (S)-tetrahydrocolumbamine. The enzyme was enriched 27-fold; it is not particle bound, has a pH optimum of 8.9, a molecular weight of 63 000 and shows a high degree of substrate specificity

A Cantor set of tori with monodromy near a focus-focus singularity

We write down an asymptotic expression for action coordinates in an integrable Hamiltonian system with a focus-focus equilibrium. From the singularity in the actions we deduce that the Arnol'd determinant grows infinitely large near the pinched torus. Moreover, we prove that it is possible to globally parametrise the Liouville tori by their frequencies. If one perturbs this integrable system, then the KAM tori form a Whitney smooth family: they can be smoothly interpolated by a torus bundle that is diffeomorphic to the bundle of Liouville tori of the unperturbed integrable system. As is well-known, this bundle of Liouville tori is not trivial. Our result implies that the KAM tori have monodromy. In semi-classical quantum mechanics, quantisation rules select sequences of KAM tori that correspond to quantum levels. Hence a global labeling of quantum levels by two quantum numbers is not possible.Comment: 11 pages, 2 figure

Kinetic Characterization and X-ray Structure of a Mutant of Haloalkane Dehalogenase with Higher Catalytic Activity and Modified Substrate Range

Conversion of halogenated aliphatics by haloalkane dehalogenase proceeds via the formation of a covalent alkyl-enzyme intermediate which is subsequently hydrolyzed by water. In the wild type enzyme, the slowest step for both 1,2-dichloroethane and 1,2-dibromoethane conversion is a unimolecular enzyme isomerization preceding rapid halide dissociation. Phenylalanine 172 is located in a helix-loop-helix structure that covers the active site cavity of the enzyme, interacts with the Clβ of 1,2-dichloroethane during catalysis, and could be involved in stabilization of this helix-loop-helix region of the cap domain of the enzyme. To obtain more information about the role of this residue in dehalogenase function, we performed a mutational analysis of position 172 and studied the kinetics and X-ray structure of the Phe172Trp enzyme. The Phe172Trp mutant had a 10-fold higher kcat/Km for 1-chlorohexane and a 2-fold higher kcat for 1,2-dibromoethane than the wild-type enzyme. The X-ray structure of the Phe172Trp enzyme showed a local conformational change in the helix-loop-helix region that covers the active site. This could explain the elevated activity for 1-chlorohexane of the Phe172Trp enzyme, since it allows this large substrate to bind more easily in the active site cavity. Pre-steady-state kinetic analysis showed that the increase in kcat found for 1,2-dibromoethane conversion could be attributed to an increase in the rate of an enzyme isomerization step that preceeds halide release. The observed conformational difference between the helix-loop-helix structures of the wild-type enzyme and the faster mutant suggests that the isomerization required for halide release could be a conformational change that takes place in this region of the cap domain of the dehalogenase. It is proposed that Phe172 is involved in stabilization of the helix-loop-helix structure that covers the active site of the enzyme and creates a rigid hydrophobic cavity for small apolar halogenated alkanes.