“The” genetic code?

The DNA‐based code for protein through messenger and transfer RNA is widely regarded as the code of life. But genomes are littered with other kinds of coding elements as well, and all of them probably came after a supercode for the tRNA system itself.     

“Right” or “wrong”? insights into the ecology of sidedness in european flounder,Platichthys flesus

Sidedness polymorphism in flatfish has been linked to ecological selection between morphs. However, the alternate hypothesis that morphological differences between right‐ and left‐sided forms may be due to errors during development, as a consequence of disturbed homeostasis, which still remains largely unexplored. Here, we examined the case of Platichthys flesus (flounder), a polymorphic flatfish exhibiting large and clinal variation in the frequency of the left‐sided morph, which is the reversed condition in this generally right‐sided species. An integrated approach consisting of the analyses of shape variation, stomach contents, and skeletal anomalies was used. Morphological differences were observed between morphs, which are in agreement with previous findings in a congeneric species (Platichthys stellatus). In parallel, significant differences in feeding choices were detected, suggesting a coherent association between subtle morphological differences between morphs and their use of trophic resources. Skeletal anomalies and meristic counts did not corroborate the hypothesis that morphometric divergence in reversed individuals may be caused or reinforced by developmental instability. J. Morphol. 2012. © 2011 Wiley Periodicals, Inc.     

Are the Kow Swamp hominids “archaic”?

Initial reports of hominids recovered at Kow Swamp, in the Murray Valley of Victoria indicated that, on the basis of cranial analyses, there was a "survival of Homo erectus features in Australia until as recently as 10,000 years ago (Thorne and Macumber, 1972, p. 316). This claim was later refuted by others, who suggested that artificial cranial deformation may have been responsible for at least some of the distinctive and "primitive" traits seen in the Kow Swamp individuals. Previous research by this worker and others has indicated that taxonomic traits at both specific and subspecific levels are present in hominine femora. Therefore, it may be possible to evaluate the "primitiveness" of the Kow Swamp sample on the basis of their femoral anatomy. Morphometric analyses were undertaken, using as controls femora of Romano British, Tasmanian, and other Murray Valley populations. On the basis of bivariate and multivariate analyses it was found that, at least in this single element of the postcranium, no primitive features were present. The Kow Swamp sample, in fact, shows a very close morphometric relationship with all included Homo sapiens controls and is significantly distinct from Homo erectus.     

Does hydrogen peroxide exist “free” in biological systems?

Hydrogen peroxide (H₂O₂) can diffuse far from the site of production to intracellular locations where biological effects may be greater. The diffusion range is extended by H₂O₂ carriers formed spontaneously by hydrogen bonding with monomeric and polymeric compounds, including amino and dicarboxylic acids, peptides, proteins, nucleic acid bases, and nucleosides. Hydrogen peroxide adducts (HPAs) are readily synthesized, e.g., crystalline histidine (His)-H₂O₂ adducts. An equilibrium exists between an adduct-forming compound and H₂O₂. The detection and relative stabilities of HPAs are measured by the degree of decomposition of H₂O₂ as influenced by test compounds in buffered solution competing with glucose or fructose for H₂O₂. The HPAs delay decomposition of H₂O₂ up to several hundredfold. The overall charge on an HPA, i.e., its ability to penetrate cell membranes, influences the cytotoxic and clastogenic effects of H₂O₂. Growth inhibition of Salmonella typhimurium LT₂ by H₂O₂ is enhanced by neutral HPAs but decreased by anionic HPAs. Addition of catalase 1, 10, or 30 min after inoculation of S. typhimurium LT₂ reduces or nearly eliminates partial growth inhibition by H₂O₂, but a neutral HPA, expecially his-H₂O₂, transported H₂O₂ into the cells within 1 min, and in about 10 min completely inhibited growth. The stability of HPAs decreases with increasing pH or increasing temperature, while added Fe(II) in the presence and absence of EDTA accelerates H₂O₂ and HPA decomposition. Calculations indicate H₂O₂ hydrogen bonds with nucleic acid-base pairs with no apparent bond strain and energy stabilization comparable to normal hydrogen bonding.     

Parrot claylick distribution in South America: do patterns of “where” help answer the question “why”?

Geophagy is well known among some Neotropical parrots. The clay apparently adsorbs dietary toxins and/or provides supplemental nutrients. We used location data and 23 environmental layers to develop a predictive model of claylick distribution using Maxent software. We related species characteristics to claylick use and examined how parrot assemblages using claylicks changed with distance from the centre of claylick distribution. Fifty‐two parrot claylicks were reported from an area of ca 4 million km² but over 50% were restricted to a 35 000 km² region of southeast Peru and northern Bolivia. Claylicks were strongly associated with moist forest on younger (<65 millions of yr) geological formations and exposed river banks. The predictive model of claylick distribution matched our reported range well, with precipitation of warmest quarter, land cover, temperature seasonality, and distance from the ocean being most important predictors of claylick presence. Twenty‐six of the region's 46 parrot species visited claylicks. Species differed greatly in their lick use, but body size, dietary breadth, abundance and other traits were poor predictors of lick use. We are confident that our survey identified the distribution of major parrot claylicks in South America, although less conspicuous parrot geophagy may occur elsewhere. We suggest that claylick distribution reflects both underlying geology (allowing claylick formation in only some regions) and the physiological need for geophagy among parrots in different parts of the continent. Data on the latter are inconclusive, but we argue that parrot claylick distribution supports the contention that geophagy is related more to sodium deficiencies than to protection from dietary toxins.     

Does the “C3 effect” offset the Δ2 effect,as regards the solution flexibility of aldoses?

The solution flexibility of carbohydrates influences a variety of molecular recognition and regulatory processes. For aldoses and other monosaccharides, this flexibility is dictated by the orientations of the various hydroxyl (OH) groups present, which influences conformer and anomer ratios, interactions among these OH groups, and interactions between them and the surrounding solvent. Depending on the number and position of axial OH groups, a variety of structures can coexist in solutions at equilibrium. In 1950, as part of his pioneering studies on the shape of pyranoside rings, Reeves described the Δ2 effect, the greater destabilization of the pyranose ring conformation when the OH group on carbon 2 (C₂) is in the axial position. It was later proposed by Angyal that the Δ2 effect could be cancelled by the presence of an axial OH on C₃, termed here the “C₃ effect.” Employing size‐exclusion chromatography, an entropically‐controlled separation technique, we have investigated whether or not the C₃ and Δ2 effects indeed do compensate for one another with respect to their influence on the solution flexibility of select aldohexoses and aldopentoses. As will be seen, while qualitatively and semiquantitatively this mutual cancellation of effects does occur in aldohexoses, it does not appear to do so in aldopentoses. An explanation for the latter appears to lie in the variety of anomers and conformers present in equilibrium solutions of those aldopentoses studied and in the relative entropic contribution of individual conformers or anomers to the total solution flexibility. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 703–711, 2014.     

Was heißt “lebendig”?

“Life” means “being alive” of special entities, which we call “organisms”. From a physical point of view, living entities are open systems, which exchange matter as well as energy with their surroundings. Against disruptive influences permanently present, they maintain actively and autonomously a steady state far from the thermodynamic equilibrium. This dynamic state of living beings represents a functional order, an internal “organization”. That means that the involved processes one and all must be correlated in such a way that they in sum prevent the breakdown of the living state. Organization implies functionality, which in turn requires structural relationships, and structures require information for their specification. Information in turn presupposes a source, which is constituted in living systems by the nucleic acids. Organisms are unique in having a capacity to use information, which is stored in the nucleic acid and yields the basis for their specific internal organization in its perpetuation: Living beings, and only they, show a self‐maintained organization.     

Survivin study: An update of “What is the next wave?”

Studies on survivin over the past 2-3 years have shown that survivin possesses multiple subcellular localizations and is a multifunctional molecule involved in many aspects of cellular processes and/or behaviors. The subcellular localization and function of the survivin splice variants, however, have not yet been well elucidated. We have, therefore, provided additional observations on several survivin splice variants for further exploration. This review article will update the role of survivin, and its splice variants in the mitosis/cell cycle, apoptosis, tumorigenesis, chemoprevention, drug/radiation resistance, and cancer therapeutics.     

Is REP a measure of “objective support”?

Grant and Kluge have recently stated that Bremer support and their own REP (“relative explanatory power”), are the only objective measures of group support. This paper discusses their claim, showing that their philosophical arguments have no basis, and that their own numerical examples actually serve to illustrate shortcomings of REP.     

Does the morphology of the ear of the Chinese bamboo rat (Rhizomys sinensis) show “Subterranean” characteristics?

In spite of the growing interest in rodents with subterranean activity in general and the spalacids (Spalacidae) in particular, little is known about the biology of most members of this clade, such as the Chinese bamboo rat (Rhizomys sinensis). Here, we analyzed the ear morphology of R. sinensis with respect to hearing specialization for subterranean or aboveground modes of communication. It is well‐known that ecology and style of life of a particular species can be reflected in morphology of its ear, its hearing and vocalization, so we expect that such information could provide us insight into its style of life and its sensory environment. The ratio between the eardrum and stapedial footplate areas, which influences the efficiency of middle ear sound transmission, suggests low hearing sensitivity, as is typical for subterranean species. The cochlea had 3.25 coils and resembled species with good low frequency hearing typical for subterranean mammals. The length of the basilar membrane was 18.9 ± 0.8 mm and its width slowly increased towards the cochlear apex from 60 to 85 μm. The mean density of outer hair cells was 344 ± 22 and of inner hair cells 114 ± 7.3 per 1 mm length of the organ of Corti, and increased apically. These values (except for relatively low hair cell density) usually characterize ears specialized for low frequency hearing. There was no evidence for an acoustic fovea. Apart of low hair cell density which is common in aboveground animals, this species has also relatively large auricles, suggesting the importance of sound localization during surface activity. The ear of the Chinese bamboo rat thus contains features typical for both aboveground and subterranean mammals and suggests that this spalacid has fossorial habits combined with regular aboveground activity. J. Morphol. 277:575–584, 2016. © 2016 Wiley Periodicals, Inc.