The Southern Ocean Exchange: porous boundaries between humpback whale breeding populations in southern polar waters.

Humpback whales (Megaptera novaeangliae) are a cosmopolitan species and perform long annual migrations between low-latitude breeding areas and high-latitude feeding areas. Their breeding populations appear to be spatially and genetically segregated due to long-term, maternally inherited fidelity to natal breeding areas. In the Southern Hemisphere, some humpback whale breeding populations mix in Southern Ocean waters in summer, but very little movement between Pacific and Atlantic waters has been identified to date, suggesting these waters constituted an oceanic boundary between genetically distinct populations. Here, we present new evidence of summer co-occurrence in the West Antarctic Peninsula feeding area of two recovering humpback whale breeding populations from the Atlantic (Brazil) and Pacific (Central and South America). As humpback whale populations recover, observations like this point to the need to revise our perceptions of boundaries between stocks, particularly on high latitude feeding grounds. We suggest that this "Southern Ocean Exchange" may become more frequent as populations recover from commercial whaling and climate change modifies environmental dynamics and humpback whale prey availability.

miR-675 mediates downregulation of Twist1 and Rb in AFP-secreting hepatocellular carcinoma.

BACKGROUND: Alpha-fetoprotein (AFP)-secreting hepatocellular carcinomas (HCC) represent a genetically distinct subset of tumors often associated with a worse prognosis. However, the molecular mechanisms that underlie these phenotypic differences remain poorly understood. METHODS: HCC tumor samples from 27 patients were profiled using the Affymetrix 133 Plus 2.0 GeneChips. GeneGO Metacore software was used to identify altered biologic pathways. Expression validation was confirmed by RT-PCR. Manipulation of miR-675 by overexpression and antagomir-mediated knockdown was carried out with subsequent evaluation of effects on cell behavior by cell cycle, proliferation, invasion, and growth in soft agar assays. RESULTS: We identified a strong relationship between primary tumor H19 gene expression and elevated serum AFP. H19 has recently been identified to encode microRNA-675 (miR-675), and we confirmed the relationship in an independent sample of patients. Pathway analyses of the effect of miR-675 overexpression in hepatoma cells revealed a predominant upregulation of cell adhesion and cell cycle initiation pathways. We have demonstrated that miR-675 mediates increases in proliferation and an accumulation of cells with tetraploid DNA content associated with a repression of Rb. We also demonstrated that overexpression of miR-675 alters cellular morphology, reduces invasive potential, and increases anchorage-independent growth capacity. These findings are consistent with a mesenchymal-to-epithelial transition, associated with a reduction in the expression of the key EMT mediator, Twist1. CONCLUSIONS: Expression of the miR-675 in hepatocellular carcinoma links a dramatic upregulation of proliferative and growth capacity with inhibition of motility in HCC cells.

A new context-based approach to assess marine mammal behavioral responses to anthropogenic sounds.

Acute effects of anthropogenic sounds on marine mammals, such as from military sonars, energy development, and offshore construction, have received considerable international attention from scientists, regulators, and industry. Moreover, there has been increasing recognition and concern about the potential chronic effects of human activities (e.g., shipping). It has been demonstrated that increases in human activity and background noise can alter habitats of marine animals and potentially mask communications for species that rely on sound to mate, feed, avoid predators, and navigate. Without exception, regulatory agencies required to assess and manage the effects of noise on marine mammals have addressed only the acute effects of noise on hearing and behavior. Furthermore, they have relied on a single exposure metric to assess acute effects: the absolute sound level received by the animal. There is compelling evidence that factors other than received sound level, including the activity state of animals exposed to different sounds, the nature and novelty of a sound, and spatial relations between sound source and receiving animals (i.e., the exposure context) strongly affect the probability of a behavioral response. A more comprehensive assessment method is needed that accounts for the fact that multiple contextual factors can affect how animals respond to both acute and chronic noise. We propose a three-part approach. The first includes measurement and evaluation of context-based behavioral responses of marine mammals exposed to various sounds. The second includes new assessment metrics that emphasize relative sound levels (i.e., ratio of signal to background noise and level above hearing threshold). The third considers the effects of chronic and acute noise exposure. All three aspects of sound exposure (context, relative sound level, and chronic noise) mediate behavioral response, and we suggest they be integrated into ecosystem-level management and the spatial planning of human offshore activities.

Current problems in the management of marine fisheries.

The public perception of fisheries is that they are in crisis and have been for some time. Numerous scientific and popular articles have pointed to the failures of fisheries management that have caused this crisis. These are widely accepted to be overcapacity in fishing fleets, a failure to take the ecosystem effects of fishing into account, and a failure to enforce unpalatable but necessary reductions in fishing effort on fishing fleets and communities. However, the claims of some analysts that there is an inevitable decline in the status of fisheries is, we believe, incorrect. There have been successes in fisheries management, and we argue that the tools for appropriate management exist. Unfortunately, they have not been implemented widely. Our analysis suggests that management authorities need to develop legally enforceable and tested harvest strategies, coupled with appropriate rights-based incentives to the fishing community, for the future of fisheries to be better than their past.

Short- and long-term changes in right whale calling behavior: the potential effects of noise on acoustic communication.

The impact of anthropogenic noise on marine mammals has been an area of increasing concern over the past two decades. Most low-frequency anthropogenic noise in the ocean comes from commercial shipping which has contributed to an increase in ocean background noise over the past 150 years. The long-term impacts of these changes on marine mammals are not well understood. This paper describes both short- and long-term behavioral changes in calls produced by the endangered North Atlantic right whale (Eubalaena glacialis) and South Atlantic right whale (Eubalaena australis) in the presence of increased low-frequency noise. Right whales produce calls with a higher average fundamental frequency and they call at a lower rate in high noise conditions, possibly in response to masking from low-frequency noise. The long-term changes have occurred within the known lifespan of individual whales, indicating that a behavioral change, rather than selective pressure, has resulted in the observed differences. This study provides evidence of a behavioral change in sound production of right whales that is correlated with increased noise levels and indicates that right whales may shift call frequency to compensate for increased band-limited background noise.

Underwater, low-frequency noise in a coastal sea turtle habitat.

Underwater sound was recorded in one of the major coastal foraging areas for juvenile sea turtles in the Peconic Bay Estuary system in Long Island, New York. The recording season of the underwater environment coincided with the sea turtle activity season in an inshore area where there is considerable boating and recreational activity, especially during the summer between Independence Day and Labor Day. Within the range of sea turtle hearing, average noise pressure reached 110 dB during periods of high human activity and diminished proportionally, down to 80 dB, with decreasing human presence. Therefore, during much of the season when sea turtles are actively foraging in New York waters, their coastal habitats are flooded with underwater noise. During the period of highest human activity, average noise pressures within the range of frequencies heard by sea turtles were greater by over two orders of magnitude (26 dB) than during the lowest period of human activity. Sea turtles undoubtedly are exposed to high levels of noise, most of which is anthropogenic. Results suggest that continued exposure to existing high levels of pervasive anthropogenic noise in vital sea turtle habitats and any increase in noise could affect sea turtle behavior and ecology.

Microscopic structure of a vortex line in a dilute superfluid fermi gas.

The microscopic properties of a single vortex in a dilute superfluid Fermi gas at zero temperature are examined within the framework of self-consistent Bogoliubov-de Gennes theory. Using only physical parameters as input, we study the pair potential, the density, the energy, and the current distribution. Comparison of the numerical results with analytical expressions clearly indicates that the energy of the vortex is governed by the zero-temperature BCS coherence length.

Superfluid-to-solid crossover in a rotating Bose-Einstein condensate.

The properties of a rotating Bose-Einstein condensate confined in a prolate cylindrically symmetric trap are explored both analytically and numerically. As the rotation frequency increases, an ever greater number of vortices are energetically favored. Though the cloud anisotropy and moment of inertia approach those of a classical fluid at high frequencies, the observed vortex density is consistently lower than the solid-body estimate. Furthermore, the vortices are found to arrange themselves in highly regular triangular arrays, with little distortion even near the condensate surface. These results are shown to be a direct consequence of the inhomogeneous confining potential.

Biogenetically inspired approach to the Strychnos alkaloids. Concise syntheses of (+/-)-akuammicine and (+/-)-strychnine.

A linear synthesis of the indole alkaloid (+/-)-akuammicine (2) was completed by a novel sequence of reactions requiring only 10 steps from commercially available starting materials. The approach features a tandem vinylogous Mannich addition and an intramolecular hetero Diels-Alder reaction to rapidly assemble the pentacyclic heteroyohimboid derivative 8 from the readily available hydrocarboline 6. Oxidation of the E ring of 8 gave the lactone 9 that was converted into deformylgeissoschizine (11). The subsequent elaboration of 11 into 2 was effected by a biomimetically patterned transformation that involved sequential oxidation and base-induced skeletal reorganization. A variation of these tactics was then applied to the synthesis of the C(18) hydroxylated akuammicine derivative 36. Because 36 had previously been converted into strychnine (1) in four steps, its preparation constitutes a concise, formal synthesis of this complex alkaloid.

Watching dark solitons decay into vortex rings in a Bose-Einstein condensate.

We have created spatial dark solitons in two-component Bose-Einstein condensates in which the soliton exists in one of the condensate components and the soliton nodal plane is filled with the second component. The filled solitons are stable for hundreds of milliseconds. The filling can be selectively removed, making the soliton more susceptible to dynamical instabilities. For a condensate in a spherically symmetric potential, these instabilities cause the dark soliton to decay into stable vortex rings. We have imaged the resulting vortex rings.

Anomalous modes drive vortex dynamics in confined Bose-Einstein condensates.

The dynamics of vortices in trapped Bose-Einstein condensates are investigated both analytically and numerically. In axially symmetric traps, the critical rotation frequency for metastability of an isolated vortex coincides with the largest vortex precession frequency (or anomalous mode) in the Bogoliubov excitation spectrum. The number of anomalous modes increases for an elongated condensate. The largest mode frequency exceeds the thermodynamic critical frequency and the nucleation frequency at which vortices are created dynamically. Thus, anomalous modes describe both vortex precession and the critical rotation frequency for creation of the first vortex in an elongated condensate.

The effect of dominance on food hoarding: a game theoretical model.

Many food hoarding animals live in small groups structured by rank. The presence of conspecifics in the hoarding area increases the risk of losing stored supplies. The possibility of stealing from others depends on a forager's rank in the group. Highly ranked individuals can steal from subordinates and also protect their own caches. Since storing incurs both costs and benefits, the optimal hoarding investment will differ between individuals of different rank. In a game theoretical model, we investigate how dominant and subordinate individuals should optimize their hoarding effort. Our model imagines animals that are large-scale hoarders in autumn and dependent on stored supplies for winter survival. Many examples can be found in the bird families Paridae and Corvidae, but the model can be used for any hoarding species that forage in groups. Predictions from the model are as follows: First, subordinates should store more than dominants, but in a predictable environment, this difference will decrease as the environment gets harsher. Under harsh conditions, dominants should store almost as much as subordinates and, later, spend almost as much time retrieving their own caches as subordinates. Second, if on the other hand, bad winter conditions were not expected when storing, dominants should spend more time pilfering caches from subordinates. Third, in populations that are highly dependent on stored supplies, dominants should store relatively more than in populations that are less dependent on stored supplies. Fourth, harsher environments will favor hoarding. And finally, if dominant individuals store, it implies that hoarders have a selfish recovery advantage over conspecific pilferers.

Behavioral responses of humpback whales (Megaptera novaeangliae) to full-scale ATOC signals.

Loud (195 dB re 1 microPa at 1 m) 75-Hz signals were broadcast with an ATOC projector to measure ocean temperature. Respiratory and movement behaviors of humpback whales off North Kauai, Hawaii, were examined for potential changes in response to these transmissions and to vessels. Few vessel effects were observed, but there were fewer vessels operating during this study than in previous years. No overt responses to ATOC were observed for received levels of 98-109 dB re 1 microPa. An analysis of covariance, using the no-sound behavioral rate as a covariate to control for interpod variation, found that the distance and time between successive surfacings of humpbacks increased slightly with an increase in estimated received ATOC sound level. These responses are very similar to those observed in response to scaled-amplitude playbacks of ATOC signals [Frankel and Clark, Can. J. Zool. 76, 521-535 (1998)]. These similar results were obtained with different sound projectors, in different years and locations, and at different ranges creating a different sound field. The repeatability of the findings for these two different studies indicates that these effects, while small, are robust. This suggests that at least for the ATOC signal, the received sound level is a good predictor of response.

The use of biomagnetic separation to recover DNA suitable for PCR from Claviceps species.

DNA analysis of agriculturally important fungi using polymerase chain reaction (PCR)-based methods is becoming routine in research and for diagnostic purposes. Rapid, small-scale DNA isolation methods that take advantage of the sensitivity, speed and automation potential of PCR technology are needed for timely analysis of important plant pathogens. DNA isolated from Claviceps africana (causal agent of ergot of sorghum) using several standard DNA extraction protocols was found to be unamplifiable using PCR. The standard methods apparently failed to separate DNA from substances inhibitory to the Taq polymerase enzyme. We obtained DNA amenable to PCR analysis using a novel method involving magnetic beads and high salt extraction buffer. The biomagnetic purification method allowed us to obtain reliable PCR amplification of the internal transcribed spacer (ITS) regions of rDNA of Claviceps africana, making genetic comparisons possible.

Calibration and comparison of the acoustic location methods used during the spring migration of the bowhead whale, Balaena mysticetus, off Pt. Barrow, Alaska, 1984-1993.

Between 1984 and 1993, visual and acoustic methods were combined to census the Bering-Chukchi-Beaufort bowhead whale, Balaena mysticetus, population. Passive acoustic location was based on arrival-time differences of transient bowhead sounds detected on sparse arrays of three to five hydrophones distributed over distances of 1.5-4.5 km along the ice edge. Arrival-time differences were calculated from either digital cross correlation of spectrograms (old method), or digital cross correlation of time waveforms (new method). Acoustic calibration was conducted in situ in 1985 at five sites with visual site position determined by triangulation using two theodolites. The discrepancy between visual and acoustic locations was <1%-5% of visual range and less than 0.7 degrees of visual bearing for either method. Comparison of calibration results indicates that the new method yielded slightly more precise and accurate positions than the old method. Comparison of 217 bowhead whale call locations from both acoustic methods showed that the new method was more precise, with location errors 3-4 times smaller than the old method. Overall, low-frequency bowhead transients were reliably located out to ranges of 3-4 times array size. At these ranges in shallow water, signal propagation appears to be dominated by the fundamental mode and is not corrupted by multipath.

Recognizing transient low-frequency whale sounds by spectrogram correlation.

A method is described for the automatic recognition of transient animal sounds. Automatic recognition can be used in wild animal research, including studies of behavior, population, and impact of anthropogenic noise. The method described here, spectrogram correlation, is well-suited to recognition of animal sounds consisting of tones and frequency sweeps. For a sound type of interest, a two-dimensional synthetic kernel is constructed and cross-correlated with a spectrogram of a recording, producing a recognition function--the likelihood at each point in time that the sound type was present. A threshold is applied to this function to obtain discrete detection events, instants at which the sound type of interest was likely to be present. An extension of this method handles the temporal variation commonly present in animal sounds. Spectrogram correlation was compared to three other methods that have been used for automatic call recognition: matched filters, neural networks, and hidden Markov models. The test data set consisted of bowhead whale (Balaena mysticetus) end notes from songs recorded in Alaska in 1986 and 1988. The method had a success rate of about 97.5% on this problem, and the comparison indicated that it could be especially useful for detecting a call type when relatively few (5-200) instances of the call type are known.

Accelerating Scientific Discovery Through Computation and Visualization.

The rate of scientific discovery can be accelerated through computation and visualization. This acceleration results from the synergy of expertise, computing tools, and hardware for enabling high-performance computation, information science, and visualization that is provided by a team of computation and visualization scientists collaborating in a peer-to-peer effort with the research scientists. In the context of this discussion, high performance refers to capabilities beyond the current state of the art in desktop computing. To be effective in this arena, a team comprising a critical mass of talent, parallel computing techniques, visualization algorithms, advanced visualization hardware, and a recurring investment is required to stay beyond the desktop capabilities. This article describes, through examples, how the Scientific Applications and Visualization Group (SAVG) at NIST has utilized high performance parallel computing and visualization to accelerate condensate modeling, (2) fluid flow in porous materials and in other complex geometries, (3) flows in suspensions, (4) x-ray absorption, (5) dielectric breakdown modeling, and (6) dendritic growth in alloys.

The differentiation of Phytophthora species that are pathogenic on potatoes by an asymmetric PCR combined with single-strand conformation polymorphism analysis.

The goal of this study was to develop a polymerase chain reaction (PCR) capable of differentiating Phytophthora species that are pathogenic on potatoes using a single primer pair. To achieve this objective, primers were derived from conserved regions flanking variable sequences in the internal transcribed spacer 1 (ITS1) of Phytophthora species. One primer pair produced a 140 bp product from P. infestans, P. erythroseptica and P. nicotianae. The PCR products were purified and used in an asymmetric PCR (A-PCR) protocol to generate single-strand DNA (ssDNA). The ssDNA of the Phytophthora potato pathogens reproducibly migrated in non-denaturing polyacrylamide gels in a species-specific manner.

Characterization of bacterial cell membrane attachment sites of plasmid R6K.

In vitro binding studies revealed that plasmid R6K could attach to both inner and outer membrane fractions of its host cell, Escherichia coli. Derivatives of R6K carrying one or two of its three origins of replication could not bind stably to the same membrane fractions in the presence of salt. However, the derivative, pRK35, carrying the intact three origins of replication could bind stably to membrane fractions from its host in the presence or absence of salt. These observations suggest that the three origins of DNA replication must be contiguous for stable binding of the plasmid to the cell membrane. The results of binding experiments showed that plasmid R6K bound competitively with pRK35 as well as the heterologous plasmid, pl524.