Laterality of Eye Use by Bottlenose (Tursiops truncatus) and Rough-toothed (Steno bredanensis) Dolphins While Viewing Predictable and Unpredictable Stimuli

Laterality of eye use has been increasingly studied in cetaceans. Research supports that many cetacean species keep prey on the right side while feeding and preferentially view unfamiliar objects with the right eye. In contrast, the left eye has been used more by calves while in close proximity to their mothers. Despite some discrepancies across and within species, laterality of eye use generally indicates functional specialization of brain hemispheres in cetaceans. The present study aimed to examine laterality of eye use in bottlenose dolphins (Tursiops truncatus) and rough-toothed dolphins (Steno bredanensis) under managed care. Subjects were video-recorded through an underwater window while viewing two different stimuli, one predictable and static and the other unpredictable and moving. Bottlenose dolphins displayed an overall right-eye preference, especially while viewing the unpredictable, moving stimulus. Rough-toothed dolphins did not display eye preference while viewing stimuli. No significant correlations between degree of laterality and behavioral interest in the stimuli were found. Only for bottlenose dolphins were the degree of laterality and curiosity ratings correlated. This study extends research on cetacean lateralization to a species not extensively examined and to stimuli that varied in movement and degree of predictability. Further research is needed to make conclusions regarding lateralization in cetaceans

Precursor ion scanning for detection and structural characterization of heterogeneous glycopeptide mixtures

AbstractThe structure of N-linked glycans is determined by a complex, anabolic, intracellular pathway but the exact role of individual glycans is not always clear. Characterization of carbohydrates attached to glycoproteins is essential to aid understanding of this complex area of biology. Specific mass spectral detection of glycopeptides from protein digests may be achieved by on-line HPLC-MS, with selected ion monitoring (SIM) for diagnostic product ions generated by cone voltage fragmentation, or by precursor ion scanning for terminal saccharide product ions, which can yield the same information more rapidly. When glycosylation is heterogeneous, however, these approaches can result in spectra that are complex and poorly resolved. We have developed methodology, based around precursor ion scanning for ions of high m/z, that allows site specific detection and structural characterization of glycans at high sensitivity and resolution. These methods have been developed using the standard glycoprotein, fetuin, and subsequently applied to the analysis of the N-linked glycans attached to the scrapie-associated prion protein, PrPSc. These glycans are highly heterogeneous and over 30 structures have been identified and characterized site specifically. Product ion spectra have been obtained on many glycopeptides confirming structure assignments. The glycans are highly fucosylated and carry Lewis X or sialyl Lewis X epitopes and the structures are in-line with previous results. [Abbreviations: Hex–Hexose, C6H12O6 carbohydrates, including mannnose and galactose; HexNAc—N-acetylhexosamine, C8H15NO6 carbohydrates, including N-acetylglucosamine and N-acetylgalactosamine; GlcNAc—N-acetylglucosamine; GalNAc—N-acetylgalactosamine; Fuc–Fucose; NeuAC—N-acetylneuraminic acid or sialic acid; TSE—Transmissible Spongiform Encephalopathy.

Do Pinnipeds Have Personality? Broad Dimensions and Contextual Consistency of Behavior in Harbor Seals (Phoca vitulina) and California Sea Lions (Zalophus californianus)

Personality has now been studied in species as diverse as chimpanzees and cuttlefish, but marine mammals remain vastly underrepresented in this area. A broad range of traits have been assessed only once in each of bottlenose dolphins and California sea lions, while consistent individual differences in a few specific behaviors have been identified in grey seals. Furthermore, the context component of definitions of personality is not often assessed, despite evidence that animals may show individual patterns of behavioral consistency across contexts. The current study therefore aimed to use behavioral coding to assess underlying personality factors and consistency across contexts in two marine mammal species: California sea lions and harbor seals. In both species, two personality factors were extracted using exploratory factor analysis. Both were broadly similar across species; the first, Boldness, resembled human Extraversion, and to some extent Openness, with sea lions exhibiting a greater social component. The second factor was labeled Routine Activity, and may contain some Conscientiousness-like traits. Species-specific patterns were also identified for interactive behaviors across two contexts. However, there was substantial individual variation in the frequency of these behaviors, as well as some animals who did not conform to group-level trends. This study therefore provides novel evidence for broad personality factors and both groupand individual-level patterns of contextual consistency in two pinniped species

Laterality of Eye Use by Bottlenose (Tursiops truncatus) and Rough-toothed (Steno bredanensis) Dolphins While Viewing Predictable and Unpredictable Stimuli

Laterality of eye use has been increasingly studied in cetaceans. Research supports that many cetacean species keep prey on the right side while feeding and preferentially view unfamiliar objects with the right eye. In contrast, the left eye has been used more by calves while in close proximity to their mothers. Despite some discrepancies across and within species, laterality of eye use generally indicates functional specialization of brain hemispheres in cetaceans. The present study aimed to examine laterality of eye use in bottlenose dolphins (Tursiops truncatus) and rough-toothed dolphins (Steno bredanensis) under managed care. Subjects were video-recorded through an underwater window while viewing two different stimuli, one predictable and static and the other unpredictable and moving. Bottlenose dolphins displayed an overall right-eye preference, especially while viewing the unpredictable, moving stimulus. Rough-toothed dolphins did not display eye preference while viewing stimuli. No significant correlations between degree of laterality and behavioral interest in the stimuli were found. Only for bottlenose dolphins were the degree of laterality and curiosity ratings correlated. This study extends research on cetacean lateralization to a species not extensively examined and to stimuli that varied in movement and degree of predictability. Further research is needed to make conclusions regarding lateralization in cetaceans

DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism

Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. Firstly, a twist-induced denaturation bubble must diffuse so that its midpoint is near the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must be large enough to allow one of the arms to form a small number of hairpin bonds. Once the first arm is partially formed, the second arm can rapidly grow to a similar size. Because bubbles can twist back on themselves, they need considerably fewer bases to resolve torsional stress than the final cruciform state does. The initially stabilised cruciform therefore continues to grow, which typically proceeds synchronously, reminiscent of the S-type mechanism of cruciform formation. By using umbrella sampling techniques we calculate, for different temperatures and superhelical densities, the free energy as a function of the number of bonds in each cruciform along the correlated but non-synchronous nucleation pathways we observed in direct simulations.Comment: 12 pages main paper + 11 pages supplementary dat

Environmentally co-occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context-dependent fitness effects

Plasmids are important mobile elements that can facilitate genetic exchange and local adaptation within microbial communities. We compared the sequences of four co-occurring pQBR-family environmental mercury resistance plasmids and measured their effects on competitive fitness of a Pseudomonas fluorescens SBW25 host, which was isolated at the same field site. Fitness effects of carriage differed between plasmids and were strongly context dependent, varying with medium, plasmid status of competitor and levels of environmental mercury. The plasmids also varied widely in their rates of conjugation and segregational loss. We found that few of the plasmid-borne accessory genes could be ascribed functions, although we identified a putative chemotaxis operon, a type IV pilus-encoding cluster, and a region encoding putative arylsulfatase enzymes, which were conserved across geographically distant isolates. One plasmid, pQBR55, conferred the ability to catabolise sucrose. Transposons, including the mercury resistance Tn5042, appeared to have been acquired by the different pQBR plasmids by recombination, indicating an important role for horizontal gene transfer in the recent evolution of pQBR plasmids. Our findings demonstrate extensive genetic and phenotypic diversity amongst co-occurring members of a plasmid community and suggest a role for environmental heterogeneity in the maintenance of plasmid diversity

First record of promops davisoni (Thomas, 1921) (chiroptera, molossidae) from Chile and a description of its echolocation calls

[Primer registro de promops davisoni (Thomas, 1921) (chiroptera, molossidae) en Chile, y des-cripción de sus llamadas de ecolocación]Few studies have been conducted on the bat fauna of the Arica and Parinacota region, northern Chile. The genus Promops (Gervais, 1855) is a poorly known group of molossid bats, with three species widely distributed in Central and South America. We report for the first time the species Promops davisoni in Chile. Identification was based on echolocation calls obtained at the Azapa and Lluta valleys and compared to reference calls from Tacna, Peru. We report the species as far as 127 km south of the previous published southernmost record in Pampa Alta, Peru. In addition we obtained an individual found at the Anzota caves, near the city of Arica. The species is found on the coast and in the fluvial valleys of Northern Chile, with altitudes ranging from sea level to 822 m a.s.l. We propose that the distribution of P. davisoni may extend further south, to the locality of Tana in the Tarapacá region, based on the capacity of the species to cross distances of over 100 km over large desert areas. With this species, we increase the known bat fauna of Chile to 14 species, and the bat fauna of the Arica and Parinacota region to nine species. © SAREM, 2018.Peer reviewe

The effect of organelle discovery upon sub-cellular protein localisation.

Prediction of protein sub-cellular localisation by employing quantitative mass spectrometry experiments is an expanding field. Several methods have led to the assignment of proteins to specific subcellular localisations by partial separation of organelles across a fractionation scheme coupled with computational analysis. Methods developed to analyse organelle data have largely employed supervised machine learning algorithms to map unannotated abundance profiles to known protein–organelle associations. Such approaches are likely to make association errors if organelle-related groupings present in experimental output are not included in data used to create a protein–organelle classifier. Currently, there is no automated way to detect organelle-specific clusters within such datasets. In order to address the above issues we adapted a phenotype discovery algorithm, originally created to filter image-based output for RNAi screens, to identify putative subcellular groupings in organelle proteomics experiments. We were able to mine datasets to a deeper level and extract interesting phenotype clusters for more comprehensive evaluation in an unbiased fashion upon application of this approach. Organelle-related protein clusters were identified beyond those sufficiently annotated for use as training data. Furthermore, we propose avenues for the incorporation of observations made into general practice for the classification of protein–organelle membership from quantitative MS experiments. Biological significance Protein sub-cellular localisation plays an important role in molecular interactions, signalling and transport mechanisms. The prediction of protein localisation by quantitative mass-spectrometry (MS) proteomics is a growing field and an important endeavour in improving protein annotation. Several such approaches use gradient-based separation of cellular organelle content to measure relative protein abundance across distinct gradient fractions. The distribution profiles are commonly mapped in silico to known protein–organelle associations via supervised machine learning algorithms, to create classifiers that associate unannotated proteins to specific organelles. These strategies are prone to error, however, if organelle-related groupings present in experimental output are not represented, for example owing to the lack of existing annotation, when creating the protein–organelle mapping. Here, the application of a phenotype discovery approach to LOPIT gradient-based MS data identifies candidate organelle phenotypes for further evaluation in an unbiased fashion. Software implementation and usage guidelines are provided for application to wider protein–organelle association experiments. In the wider context, semi-supervised organelle discovery is discussed as a paradigm with which to generate new protein annotations from MS-based organelle proteomics experiments. This article is part of a Special Issue entitled: New Horizons and Applications for Proteomics [EuPA 2012]

Non-Equilibrium Reaction Rates in the Macroscopic Chemistry Method for DSMC Calculations

The Direct Simulation Monte Carlo (DSMC) method is used to simulate the flow of rarefied gases. In the Macroscopic Chemistry Method (MCM) for DSMC, chemical reaction rates calculated from local macroscopic flow properties are enforced in each cell. Unlike the standard total collision energy (TCE) chemistry model for DSMC, the new method is not restricted to an Arrhenius form of the reaction rate coefficient, nor is it restricted to a collision cross-section which yields a simple power-law viscosity. For reaction rates of interest in aerospace applications, chemically reacting collisions are generally infrequent events and, as such, local equilibrium conditions are established before a significant number of chemical reactions occur. Hence, the reaction rates which have been used in MCM have been calculated from the reaction rate data which are expected to be correct only for conditions of thermal equilibrium. Here we consider artificially high reaction rates so that the fraction of reacting collisions is not small and propose a simple method of estimating the rates of chemical reactions which can be used in the Macroscopic Chemistry Method in both equilibrium and non-equilibrium conditions. Two tests are presented: (1) The dissociation rates under conditions of thermal non-equilibrium are determined from a zero-dimensional Monte-Carlo sampling procedure which simulates ‘intra-modal’ non-equilibrium; that is, equilibrium distributions in each of the translational, rotational and vibrational modes but with different temperatures for each mode; (2) The 2-D hypersonic flow of molecular oxygen over a vertical plate at Mach 30 is calculated. In both cases the new method produces results in close agreement with those given by the standard TCE model in the same highly nonequilibrium conditions. We conclude that the general method of estimating the non-equilibrium reaction rate is a simple means by which information contained within non-equilibrium distribution functions predicted by the DSMC method can be included in the Macroscopic Chemistry Method

Correction: Hokynar, K. et al. Chlamydia-Like Organisms (CLOs) in Finnish Ixodes ricinus Ticks and Human Skin. Microorganisms 2016, 4, 28

The authors wish to make the following modification to this paper [...