Signatures of positive selection in the mitochondrial genome of neotropical freshwater stingrays provide clues about the transition from saltwater to freshwater environment.

Neotropical freshwater stingrays (subfamily Potamotrygoninae) are carnivorous bottom feeder batoids widely distributed in most river basins of South America. They represent the unique extant group of elasmobranchs that evolved to live exclusively in freshwater environments. These species are exploited either by commercial fisheries (e.g., for food or ornamental industry) or by indigenous communities allocated along with their natural range. Restrictive life history characteristics coupled with habitat degradation make Potamotrygoninae species highly vulnerable to human impacts and highlight the necessity of studies to inform basic biological aspects, from ecology to genetics, to guide their conservation and clarify the molecular basis of adaptation to the freshwater environment. We used available and newly assembled Potamotrygon spp. mitogenomes to perform a comparative investigation of their molecular evolution. A phylogenetic estimation using the mitogenome of Potamotrygon falkneri and other Elasmobranchii supports monophyly for Potamotrygonidae and indicates a close relationship to Dasyatidae. A synteny analysis comprising 3 Potamotrygon and other 51 batoids revealed a highly conserved mitogenomic context. We detected various amino acid sites under positive selection exclusively in Potamotrygon spp., within the sequences of ND4, ND5, ND6, and COXII genes. Positively selected mutational events in key genes of energetic metabolism may be related to the physiological adaptation of Potamotrygon spp. during the ancient incursion into freshwater. This broad comparative mitogenomic study provides novel insights into the evolutionary history of neotropical freshwater stingrays and their relatives and stands out as a valuable resource to aid in current and future research on elasmobranch molecular evolution.

Theoretical investigation of layered zeolites with MWW topology: MCM-22P vs. MCM-56.

The inter-layer interactions and the possible arrangements of MWW-type layers were investigated computationally at the non-local density functional theory level. Powder XRD patterns were simulated for structures obtained computationally and compared with experimental data. The MCM-22P material corresponds to the layers bound with relatively strong hydrogen bonds between surface silanol groups that is an energetically preferred structure in the presence of a structure directing agent (hexamethyleneimine). The powder XRD pattern of MCM-56 is best matched for relatively disordered (in the ab plane) MWW layers that are partially condensed. The appearance of the powder XRD pattern in the 2θ range of 7.5-10° depends on the extent of interlayer condensation. The combination of density functional investigation of interactions between MWW layers together with simulation of powder XRD patterns brings atomistic insight into the inter-layer arrangement and better understanding of the effects responsible for the differences between various layered materials of the MWW family.

The nature of cationic adsorption sites in alkaline zeolites--single, dual and multiple cation sites.

Gas adsorption on zeolites constitutes the base of many technological applications of these versatile porous materials. Quite often, especially when dealing with small molecules, individual extra-framework (exchangeable) cations are considered to be the adsorption site on which molecules coming from a gas phase form the corresponding adsorption complex. Nonetheless, while that can be the case in some instances, recent research work that combines variable temperature infrared spectroscopy with periodic DFT calculations showed that some types of adsorption sites involve two or more cations, which constitute dual and multiple cation sites, respectively. Adsorption complexes formed on these cationic adsorption sites differ in both structure and stability from those formed on a single cation alone. Examples concerning CO, CO(2) and H(2) adsorption on alkali and alkaline-earth metal exchanged zeolites are reviewed, with the double purpose of clarifying concepts and highlighting their relevance to practical use of zeolites in such fields as gas separation and purification, gas storage and heterogeneous catalysis.

A re-evaluation of auditory filter shape in delphinid odontocetes: evidence of constant-bandwidth filters.

The auditory filter shape of delphinid odontocetes was previously considered to be typically mammalian constant-quality in which filter bandwidths increase proportionally with frequency. Recent studies with porpoises demonstrate constant-bandwidth portions of the auditory filter. The critical ratios for a bottlenose dolphin were measured between 40 and 120 kHz by behaviorally determining the subject's ability to detect pure tones in the presence of white noise. Critical ratios as a function of frequency were constant, indicating the auditory filter acts as a constant-bandwidth system in this frequency range. Re-analysis of past studies supports these findings, and suggests the delphinid auditory system is best characterized as a constant-Q system below 40 kHz and a constant-bandwidth-like system between 40 kHz and 120 kHz before returning to a constant Q pattern at the highest frequencies.

Decreased echolocation performance following high-frequency hearing loss in the false killer whale (Pseudorca crassidens).

Toothed whales and dolphins possess a hypertrophied auditory system that allows for the production and hearing of ultrasonic signals. Although the fossil record provides information on the evolution of the auditory structures found in extant odontocetes, it cannot provide information on the evolutionary pressures leading to the hypertrophied auditory system. Investigating the effect of hearing loss may provide evidence for the reason for the development of high-frequency hearing in echolocating animals by demonstrating how high-frequency hearing assists in the functioning echolocation system. The discrimination abilities of a false killer whale (Pseudorca crassidens) were measured prior to and after documented high-frequency hearing loss. In 1992, the subject had good hearing and could hear at frequencies up to 100 kHz. In 2008, the subject had lost hearing at frequencies above 40 kHz. First in 1992, and then again in 2008, the subject performed an identical echolocation task, discriminating between machined hollow aluminum cylinder targets of differing wall thickness. Performances were recorded for individual target differences and compared between both experimental years. Performances on individual targets dropped between 1992 and 2008, with a maximum performance reduction of 36.1%. These data indicate that, with a loss in high-frequency hearing, there was a concomitant reduction in echolocation discrimination ability, and suggest that the development of a hypertrophied auditory system capable of hearing at ultrasonic frequencies evolved in response to pressures for fine-scale echolocation discrimination.

Audiogram of a formerly stranded long-finned pilot whale (Globicephala melas) measured using auditory evoked potentials.

Long-finned pilot whales are highly social odontocetes found in temperate and subpolar regions. This species is particularly known for its interaction with fisheries as well as its mass strandings. Recent tagging work has provided some information about pilot whales in the wild but, even though they have been successfully kept in captivity, little is known about their sensory capabilities. This study investigates the hearing abilities of a rehabilitated 2 year old male long-finned pilot whale. A complete audiogram was collected using auditory evoked potential techniques that included measurements of nine frequencies from 4 to 100 kHz presented as sinusoidally amplitude-modulated tones. The results indicated that the region of best hearing was between 11.2 and 50 kHz and the subject had relatively poor high frequency hearing compared with other odontocete species. This study emphasizes the importance of collecting basic hearing measurements from new species, understanding diagnostic life histories as well as continuously increasing the sample size of audiometry measurements within and between odontocete species as animals become available.

Periodic DFT investigation of the effect of aluminium content on the properties of the acid zeolite H-FER.

Periodic DFT calculations were performed on H-FER models having Si/Al ratios of 71 : 1, 35 : 1 and 8 : 1, in order to investigate the effect of aluminium content on the properties of the zeolite Brønsted acid sites. Relative stability of these sites was found to be dependent on Si/Al ratio, which is the main factor dictating the relative concentration of Brønsted acid sites having different types of local configuration, to the point that some types of acid site are formed only when the aluminium content of the zeolite is relatively high. The number of AlO(4) tetrahedra sharing an oxygen with the SiO(4) tetrahedron involved in the Brønsted acid site determines the Si-O(H)-Al angle, O-H stretching frequency and deprotonation energy (and hence acid strength). For Brønsted acid protons not involved in intra-zeolite H-bonding, a correlation was found between Si-O(H)-Al angle and O-H stretching frequency.

Computational and FTIR spectroscopic studies on carbon monoxide and dinitrogen adsorption on a high-silica H-FER zeolite.

Adsorption (at a low temperature) of carbon monoxide and dinitrogen on a high-silica ferrierite-type zeolite (H-FER, Si : Al = 27.5 : 1) was investigated by means of variable temperature infrared spectroscopy and theoretical calculations at the periodic DFT level. This combined experimental and computational approach led to detailed characterization of several types of hydrogen-bonded OHCO and OHN(2) complexes, formed by interaction between the adsorbed molecules and the Brønsted acid OH groups of the zeolite. CO or N(2), forming linear complexes with OH groups pointing towards a sufficiently ample void space, show the largest adsorption enthalpy which was found to be in the (approximate) range of -25 to -29 kJ mol(-1) for CO and -15 to -19 kJ mol(-1) for N(2). Less stable OHCO or OHN(2) complexes can be formed when either the Brønsted acid OH group is involved in intra-zeolite hydrogen bonding or when the free space available is too small to allow formation of linear complexes without previous re-location of the proton of the OH group involved. The details of experimental IR spectra in the O-H, C-O, and N-N stretching regions could be interpreted on the basis of good agreement between experimental and calculated results.

Interaction of acetonitrile with Na-zeolites: adsorption modes and vibrational dynamics in the zeolite channels and cavities.

The interaction of acetonitrile with the extra-framework Na(+) cations in zeolites, namely Na-LTA and Na-FER, was investigated. The relative stabilities of possible types of adsorption complexes were calculated at the periodic DFT level. Individual effects on the complex stability and on the vibrational dynamics of adsorbed acetonitrile were qualitatively analysed on various cluster models. The acetonitrile primarily interacts with the Na(+) cation (via the N end), and the complex stability is modulated by the interaction of the methyl group with the framework oxygen atoms, which has a partial hydrogen-bond character. In line with the results of recent analyses of CO interactions with metal-exchanged zeolites [D. Nachtigallová, O. Bludský, C. O. Areán, R. Bulanek and P. Nachtigall, Phys. Chem. Chem. Phys., 2006, 8, 4849], two types of effects should be taken into consideration for acetonitrile complexes in Na-zeolites: (i) the effects from the bottom, reflecting the accessibility and coordination of the primary metal cation, to which the acetonitrile molecule is bonded via the N atom; and (ii) the effects from the top, including H-bond formation (stabilising effect) or repulsion due to the secondary metal cation. The effect from the bottom results in a blue shift of nu(CN) while the effect from the top (H-bond formation) results in a red shift in both nu(CN) and nu(CH).

Shipboard measurements of the hearing of the white-beaked dolphin Lagenorhynchus albirostris.

This is the first report of an underwater audiogram from a dolphin in a capture-and-release scenario. Two bow-riding white-beaked dolphins Lagenorhynchus albirostris (a female and a male) were captured using the hoop-net technique in Faxaflói Bay, Iceland. The dolphins were transferred to a stretcher and hoisted into a plastic research tank on board a small fishing vessel. Two underwater transducers were used to cover the frequency range from 16 to 215 kHz. Two human EEG electrodes mounted in suction cups, one placed near the blow hole and the other on the dorsal fin, picked up bioelectrical responses to acoustic stimuli. Responses to about 1000 sinusoidal amplitude modulated stimuli for each amplitude/frequency combination were averaged and analyzed using a fast Fourier transform to obtain an evoked auditory response. Threshold was defined as the zero crossing of the response using linear regression. Two threshold frequencies at 50 kHz and 64 kHz were obtained from the female. An audiogram ranging from 16 to 181 kHz was obtained from an adult male and showed the typical ;U' shaped curve for odontocetes. The thresholds for both white-beaks were comparable and demonstrated the most sensitive high frequency hearing of any known dolphin and were as sensitive as the harbor porpoise.

Carbon monoxide adsorption on low-silica zeolites: from single to dual and to multiple cation sites.

Infrared spectra of CO adsorbed on the Al-rich Na-A zeolite were analysed by using a combined theoretical and experimental approach, showing that such spectra cannot be interpreted by assigning each IR band to CO interacting with a specific type of single cation site. This concept, which usually works well for high-silica zeolites, should not be uncritically extended to Al-rich zeolites that are crowded with cations in configurations which lead to preferential formation of CO adsorption complexes involving more than one cation site.

Thermodynamics of reversible gas adsorption on alkali-metal exchanged zeolites--the interplay of infrared spectroscopy and theoretical calculations.

Detailed understanding of weak solid-gas interactions giving rise to reversible gas adsorption on zeolites and related materials is relevant to both, fundamental studies on gas adsorption and potential improvement on a number of (adsorption based) technological processes. Combination of variable-temperature infrared spectroscopy with theoretical calculations constitutes a fruitful approach towards both of these aims. Such an approach is demonstrated here (mainly) by reviewing recent studies on hydrogen and carbon monoxide adsorption (at a low temperature) on alkali-metal exchanged ferrierite. However, the methodology discussed, which involves the interplay of experimental measurements and theoretical calculations at the periodic DFT level, should be equally valid for many other gas-solid systems. Specific aspects considered are the identification of gas adsorption complexes and thermodynamic studies related to standard adsorption enthalpy and entropy.

Single and dual cation sites in zeolites: theoretical calculations and FTIR spectroscopic studies on CO adsorption on K-FER.

Interaction of CO with K-FER zeolite was investigated by a combination of variable-temperature IR spectroscopy and computational study. Calculations were performed using omega(CO)/r(CO) correlation method in combination with a periodic density functional theory model. On the basis of agreement between experimental and calculated results, the following carbonyl complexes were identified: (i) mono- and dicarbonyl C-down complexes on single K(+) sites characterized by IR absorption bands at 2163 and 2161 cm(-1), respectively; (ii) complexes formed by CO bridging two K(+) ions separated by about 7-8 A (dual sites) characterized by a band at 2148 cm(-1); and (iii) isocarbonyl (O-down) complexes characterized by a band at 2116 cm(-1). The bridged carbonyl complexes on dual K(+) sites are about 5 kJ/mol more stable than monodentate (monocarbonyl) CO complexes. The C-O stretching frequency of monocarbonyl species in K-FER depends on K(+) location in the zeolite, and not on K(+) coordination to the framework. A combination of theoretical calculations using a periodic density functional model and experimental results showed formation of two types of monocarbonyls. The most abundant type appears at 2163 cm(-1), and the less abundant one at 2172 cm(-1). These experimentally determined wavenumber values coincide, within +/-2 cm(-1), with those derived from theoretical calculations.

FTIR spectroscopic and computational studies on hydrogen adsorption on the zeolite Li-FER.

The interaction, at a low temperature, between molecular hydrogen and the zeolite Li-FER was studied by means of variable temperature infrared spectroscopy and theoretical calculations using a periodic DFT model. The adsorbed dihydrogen molecule becomes infrared active, giving a characteristic IR absorption band (H-H stretching) at 4090 cm(-1). Three different Li(+) site types with respect to H(2) adsorption were found in the zeolite, two of which adsorb H(2). Calculations showed a similar interaction energy for these two sites, which was found to agree with the experimentally determined value of standard adsorption enthalpy of DeltaH(0) = -4.1 (+/-0.8) kJ mol(-1). The results are discussed in the broader context of previously reported data for H(2) adsorption on Na-FER and K-FER.

Combined theoretical and FTIR spectroscopic studies on hydrogen adsorption on the zeolites Na-FER and K-FER.

The interaction between molecular hydrogen and the alkali-metal-exchanged zeolites Na-FER and K-FER at a low temperature was investigated by combining variable-temperature infrared spectroscopy and theoretical calculations by using a periodic DFT model. The experimentally determined values of standard adsorption enthalpy, DeltaH degrees , were -6.0 (+/-0.8) and -3.5 (+/-0.8) kJ mol(-1) for Na-FER and K-FER, respectively. These results were found to be in agreement with corresponding DeltaH degrees values obtained from calculations on the periodic model. Two types of alkali-metal cation sites in FER were found: channel intersection sites and channel wall sites. Calculations showed a similar interaction energy for both site types, and similar structures of adsorption complexes. Up to two dihydrogen molecules can be physisorbed on the alkali-metal cation located on the intersection of two channels, while only one H2 molecule is physisorbed on the cation at the channel wall site. The adsorption enthalpies of H2 on alkali-metal-exchanged FER are significantly smaller than those found previously for the MFI-type zeolites Na-ZSM-5 and K-ZSM-5, which is likely due to a difference in the alkali-metal cation coordination in the two zeolite frameworks.

Classification of electronically generated phantom targets by an Atlantic bottlenose dolphin (Tursiops truncatus).

Animal behavior experiments require not only stimulus control of the animal's behavior, but also precise control of the stimulus itself. In discrimination experiments with real target presentation, the complex interdependence between the physical dimensions and the backscattering process of an object make it difficult to extract and control relevant echo parameters separately. In other phantom-echo experiments, the echoes were relatively simple and could only simulate certain properties of targets. The echo-simulation method utilized in this paper can be used to transform any animal echolocation sound into phantom echoes of high fidelity and complexity. The developed phantom-echo system is implemented on a digital signal-processing board and gives an experimenter fully programmable control over the echo-generating process and the echo structure itself. In this experiment, the capability of a dolphin to discriminate between acoustically simulated phantom replicas of targets and their real equivalents was tested. Phantom replicas were presented in a probe technique during a materials discrimination experiment. The animal accepted the phantom echoes and classified them in the same manner as it classified real targets.

Monitoring of progesterone in captive female false killer whales, Pseudorca crassidens.

The present study describes progesterone profiles to enhance understanding of general reproductive patterns in three female captive false killer whales and analyzes potential relationships in progesterone concentrations between plasma, salivary, and ocular secretions. Plasma progesterone concentrations reflected ovarian activity for most of the year, with increased concentrations in the spring and summer, indicating that the two adult female false killer whales were spontaneous ovulators and seasonally polyestrus. Elevated progesterone concentrations were determined at intervals, for up to 10 consecutive months, in one female. There were also varying periods of no apparent ovarian activity from 3 to 10 consecutive months. Correlation coefficients between progesterone concentrations in plasma, salivary, and ocular secretions ranged between -0.23 and 0.16. It is concluded that blood collection should not be replaced by salivary or ocular secretion collection for the measurement of progesterone in the false killer whale.

Dolphin hearing: relative sensitivity as a function of point of application of a contact sound source in the jaw and head region.

The auditory input area of the dolphin head was investigated in an unrestrained animal trained to beach itself and to accept noninvasive electroencephalograph (EEG) electrodes for the recording of the auditory brain-stem response (ABR). The stimulus was a synthetic dolphin click, transmitted from a piezo-electric transducer and coupled to the skin via a small volume of water. The results conform with earlier experiments on acute preparations that show best auditory sensitivity at the middle of the lower jaw. Minimum latency was found at the rear of the lower jaw. A shaded receiver configuration for the dolphin ear is proposed.