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First record of Larsonella pumilus (Teleostei: Gobiidae) from Japan, with phylogenetic placement of the genus Larsonella
Get PDFDuring a survey of deep-sea fauna, using a Remotely Operated Vehicle, a single specimen (21.6 mm in standard length) of Larsonella pumilus (Larson & Hoese, 1980) was collected at a depth of 214 m off the coast of Okinawa Island, Japan. It represents the first record of this species from Japan. The collection site was far deeper than previous reports for this species. This suggests that the main habitat of L. pumilus is deeper than previously recognized and it may explain the paucity of records of this species. As the previously available morphological description of L. pumilus was based on only a single specimen (holotype), this new specimen is described herein. Its morphology corresponds closely to the original description of the holotype, except that faint melanophores are arranged radially around the eyes and scattered on the trunk and the fins. Mitochondrial genome sequences of L. pumilus and 19 related species demonstrate close relationships between L. pumilus and the genus Priolepis. These data also indicate that the genus Priolepis is not monophyletic.journal articl
Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals
Get PDFVenom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon (Solenodon paradoxus). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 (KLK1) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions.journal articl
New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis
Get PDFBobtail squid are emerging models for host-microbe interactions, behavior, and development, yet their species diversity and distribution remain poorly characterized. Here, we combine mitochondrial and transcriptome sequences with morphological analysis to describe three species of bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu archipelago, and compare them with related taxa. One Ryukyuan type was previously unknown, and is described here as Euprymna brenneri sp. nov. Another Ryukyuan type is morphologically indistinguishable from Sepiola parva Sasaki, 1913. Molecular analyses, however, place this taxon within the genus Euprymna Steenstrup, 1887, and additional morphological investigation led to formal rediagnosis of Euprymna and reassignment of this species as Euprymna parva comb. nov. While no adults from the third Ryukyuan type were found, sequences from hatchlings suggest a close relationship with E. pardalota Reid, 2011, known from Australia and East Timor. The broadly sampled transcriptomes reported here provide a foundation for future phylogenetic and comparative studies.journal articl
Error-Speed Correlations in Biopolymer Synthesis
Get PDFSynthesis of biopolymers such as DNA, RNA, and proteins are biophysical processes aided by enzymes. The performance of these enzymes is usually characterized in terms of their average error rate and speed. However, because of thermal fluctuations in these single-molecule processes, both error and speed are inherently stochastic quantities. In this Letter, we study fluctuations of error and speed in biopolymer synthesis and show that they are in general correlated. This means that, under equal conditions, polymers that are synthesized faster due to a fluctuation tend to have either better or worse errors than the average. The error-correction mechanism implemented by the enzyme determines which of the two cases holds. For example, discrimination in the forward reaction rates tends to grant smaller errors to polymers with faster synthesis. The opposite occurs for discrimination in monomer rejection rates. Our results provide an experimentally feasible way to identify error-correction mechanisms by measuring the error-speed correlations.journal articl
A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans
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Roadmap on STIRAP applications
Get PDFSTIRAP (stimulated Raman adiabatic passage) is a powerful laser-based method, usually involving two photons, for efficient and selective transfer of populations between quantum states. A particularly interesting feature is the fact that the coupling between the initial and the final quantum states is via an intermediate state, even though the lifetime of the latter can be much shorter than the interaction time with the laser radiation. Nevertheless, spontaneous emission from the intermediate state is prevented by quantum interference. Maintaining the coherence between the initial and final state throughout the transfer process is crucial. STIRAP was initially developed with applications in chemical dynamics in mind. That is why the original paper of 1990 was published in The Journal of Chemical Physics. However, from about the year 2000, the unique capabilities of STIRAP and its robustness with respect to small variations in some experimental parameters stimulated many researchers to apply the scheme to a variety of other fields of physics. The successes of these efforts are documented in this collection of articles. In Part A the experimental success of STIRAP in manipulating or controlling molecules, photons, ions or even quantum systems in a solid-state environment is documented. After a brief introduction to the basic physics of STIRAP, the central role of the method in the formation of ultracold molecules is discussed, followed by a presentation of how precision experiments (measurement of the upper limit of the electric dipole moment of the electron or detecting the consequences of parity violation in chiral molecules) or chemical dynamics studies at ultralow temperatures benefit from STIRAP. Next comes the STIRAP-based control of photons in cavities followed by a group of three contributions which highlight the potential of the STIRAP concept in classical physics by presenting data on the transfer of waves (photonic, magnonic and phononic) between respective waveguides. The works on ions or ion strings discuss options for applications, e.g. in quantum information. Finally, the success of STIRAP in the controlled manipulation of quantum states in solid-state systems, which are usually hostile towards coherent processes, is presented, dealing with data storage in rare-earth ion doped crystals and in nitrogen vacancy (NV) centers or even in superconducting quantum circuits. The works on ions and those involving solid-state systems emphasize the relevance of the results for quantum information protocols. Part B deals with theoretical work, including further concepts relevant to quantum information or invoking STIRAP for the manipulation of matter waves. The subsequent articles discuss the experiments underway to demonstrate the potential of STIRAP for populating otherwise inaccessible high-lying Rydberg states of molecules, or controlling and cooling the translational motion of particles in a molecular beam or the polarization of angular-momentum states. The series of articles concludes with a more speculative application of STIRAP in nuclear physics, which, if suitable radiation fields become available, could lead to spectacular results.journal articl
The turbulent flow in a slug: a re-examination
Get PDFThe transition to turbulence in pipe flow proceeds through several distinct stages, eventually producing aggressively expanding regions of fluctuations, ‘slugs’, surrounded by laminar flow. By examining mean-velocity profiles, fluctuating-velocity profiles and Reynolds stress profiles, the seminal study of Wygnanski & Champagne (J. Fluid Mech., vol. 59 (2), 1973, 281–335) concluded that the flow inside slugs is ‘identical’ to fully turbulent flow. Although this conclusion is widely accepted, upon closer examination of their analysis, we find that their data cannot be used to substantiate this conclusion. We resolve this conflict via new experiments and simulations wherein we pair slugs and fully turbulent flow at the same value of Reynolds number (Re). We conclude that the flow inside a slug is indeed indistinguishable from a fully turbulent flow but only when the two flows share the same value of Re. Our work highlights the rich Re-dependence of transitional pipe flows.journal articl
Deficits in Conditional Discrimination Learning in Children with ADHD are Independent of Delay Aversion and Working Memory
Get PDFAdaptive behavior requires the adjustment of one's behavioral repertoire to situational demands. The learning of situationally appropriate choice behavior can be operationalized as a task of Conditional Discrimination Learning (CDL). CDL requires the acquisition of hierarchical reinforcement relations, which may pose a particular challenge for children with Attention Deficit Hyperactivity Disorder (ADHD), particularly in light of documented deficits in short-term/working memory and delay aversion in ADHD. Using an arbitrary Delayed Matching-To-Sample task, we investigated whether children with ADHD (N = 46), relative to Typically Developing children (TD, N = 55), show a deficit in CDL under different choice delays (0, 8, and 16 seconds) and whether these differences are mediated by short-term/working memory capacity and/or delay aversion. Children with ADHD demonstrated poorer CDL than TD children under 8 and 16-second delays. Non-delayed CDL performance did not differ between groups. CDL differences were not mediated by short-term/working memory performance or delay aversion. Moreover, CDL performance under an 8-second delay was a better predictor of clinical status than short-term/working memory performance or delay aversion. CDL, under conditions of delay, is impaired in children with ADHD. This may lead to difficulties discriminating between different situational demands and adapting behavior according to the prevailing reward contingencies or expectations.journal articl
Spectral link and macroscopic non-universality in turbulent plane Couette flow
Get PDFIn fully developed turbulent plane Couette flow the classical experimental data of frictional factor f versus Reynolds number Re display well-known disparities which have long remained unexplained. These disparities are accompanied by previously unnoticed disparities in the wakes, and only in the wakes, of the attendant mean-velocity profiles (MVPs). To help explain these experimental data, we apply the model of the 'spectral link' for MVPs to turbulent plane Couette flows. The model links the dissipative range, the inertial range, and the energetic range of the standard phenomenological model of the spectrum of turbulent kinetic energy to, respectively, the buffer layer, the log layer, and the wake of the MVPs. By assessing the empirical data using the spectral model, we argue for the existence, in plane Couette flow, of multiple states of turbulence which differ from one another only at the largest lengthscales in the flow, corresponding to the energetic range, where the spectrum is subject to finite-domain effects. Thus, the multiplicity of turbulent states is entirely consistent with small-scale universality, and the experimental data on plane Couette flow pose no challenge to the phenomenological theory of turbulence. Our findings might apply more broadly to a general class of flows engendered by moving boundaries.journal articl
Xenacoelomorph-Specific Hox Peptides: Insights into the Phylogeny of Acoels, Nemertodermatids, and Xenoturbellids
Get PDFXenacoelomorpha has recently been proposed as an animal taxon that includes acoels, nemertodermatids, and xenoturbellids. Their flattened bodies are very simple and lack discrete organs. The Acoela and Nemertodermatida (which comprise Acoelomorpha) were traditionally regarded as early-diverged extant orders of the class Turbellaria of the phylum Platyhelminthes. Recent anatomical studies and molecular phylogenetic studies demonstrate that the two groups belong to the phylum Xenacoelomorpha together with Xenoturbellida. However, debate remains in regard to whether Xenacoelomorpha is monophyletic, and whether xenacoelomorphs are sisters to all other bilaterians or have close affinity to ambulacrarians. The present study addresses the first question by examining the presence or absence of diagnostic peptide sequences shared by the three taxa. Hox genes have been used to investigate the phylogenetic relationships of metazoans. It has been shown that lophotrochozoans, rotifers, and chaetognaths share diagnostic peptide sequences in the C-terminal region of the Lox5 (Hox5/6/7) homeodomain proteins, which supports the clustering of these taxa. Examination of the decoded genome of the acoel Praesagittifera naikaiensis and reported xenacoelomorph Hox genes revealed that acoels share a peptide NLK(S/T)MSQ(V/I)D, which starts immediately after the homeodomain sequence of the central Hox4/5/6. In addition, we found another diagnostic peptide, KEGKL, in the C-terminal region of the anterior Hox1, which is shared by all the three groups of xenacoelomorphs, but not other bilaterians. Furthermore, two acoels, Praesagittifera naikaiensis and Symsagittifera roscoffensis, share another peptide SG(A/P)-PGM in the posterior Hox9/11/13. These results support the designation of the phylum Xenacoelomorpha, in which Acoela is a discrete group.journal articl