Characterization of ten novel Ty1/copia-like retrotransposon families of the grapevine genome

BACKGROUND: Retrotransposons make a significant contribution to the size, organization and genetic diversity of their host genomes. To characterize retrotransposon families in the grapevine genome (the fourth crop plant genome sequenced) we have combined two approaches: a PCR-based method for the isolation of RnaseH-LTR sequences with a computer-based sequence similarity search in the whole-genome sequence of PN40024. RESULTS: Supported by a phylogenic analysis, ten novel Ty1/copia families were distinguished in this study. To select a canonical reference element sequence from amongst the various insertions in the genome belonging to each retroelement family, the following screening criteria were adopted to identify the element sequence with: (1) perfect 5 bp-duplication of target sites, (2) the highest level of identity between 5’ and 3’-LTR within a single insertion sequence, and (3) longest, un-interrupted coding capacity within the gag-pol ORF. One to eight copies encoding a single putatively functional gag-pol polyprotein were found for three families, indicating that these families could be still autonomous and active. For the others, no autonomous copies were identified. However, a subset of copies within the presumably non-autonomous families had perfect identity between their 5’ and 3’ LTRs, indicating a recent insertion event. A phylogenic study based on the sequence alignment of the region located between reverse transcriptase domains I and VII distinguished these 10 families from other plant retrotransposons. Including the previously characterized Ty1/copia-like grapevine retrotransposons Tvv1 and Vine 1 and the Ty3/gypsy-like Gret1 in this assessment, a total of 1709 copies were identified for the 13 retrotransposon families, representing 1.24% of the sequenced genome. The copy number per family ranged from 91-212 copies. We performed insertion site profiling for 8 out of the 13 retrotransposon families and confirmed multiple insertions of these elements across the Vitis genus. Insertional polymorphism analysis and dating of full-length copies based on their LTR divergence demonstrated that each family has a particular amplification history, with 71% of the identified copies being inserted within the last 2 million years. CONCLUSION: The strategy we used efficiently delivered new Ty1/copia-like retrotransposon sequences, increasing the total number of characterized grapevine retrotrotransposons from 3 to 13. We provide insights into the representation and dynamics of the 13 families in the genome. Our data demonstrated that each family has a particular amplification pattern, with 7 families having copies recently inserted within the last 0.2 million year. Among those 7 families with recent insertions, three retain the capacity for activity in the grape genome today

Telecommunications systems design techniques handbook

Handbook presents design and analysis of tracking, telemetry, and command functions utilized in these systems with particular emphasis on deep-space telecommunications. Antenna requirements are also discussed. Handbook provides number of tables outlining various performance criteria. Block diagrams and performance charts are also presented

Contributions to the Nearby Stars (NStars) Project: Spectroscopy of Stars Earlier than M0 within 40 parsecs: The Northern Sample I

We have embarked on a project, under the aegis of the Nearby Stars (NStars)/ Space Interferometry Mission Preparatory Science Program to obtain spectra, spectral types, and, where feasible, basic physical parameters for the 3600 dwarf and giant stars earlier than M0 within 40 parsecs of the sun. In this paper we report on the results of this project for the first 664 stars in the northern hemisphere. These results include precise, homogeneous spectral types, basic physical parameters (including the effective temperature, surface gravity and the overall metallicity, [M/H]) and measures of the chromospheric activity of our program stars. Observed and derived data presented in this paper are also available on the project's website at http://stellar.phys.appstate.edu/

Physical aspects of oracles for randomness, and Hadamard's conjecture

We analyze the physical aspects and origins of currently proposed oracles for (absolute) randomness.Comment: 10 pages, 3 figures. arXiv admin note: substantial text overlap with arXiv:1405.140

Modulating medial prefrontal cortex activity using real-time fMRI neurofeedback: Effects on reality monitoring performance and associated functional connectivity

Neuroimaging studies have found ‘reality monitoring’, our ability to distinguish internally generated experiences from those derived from the external world, to be associated with activity in the medial prefrontal cortex (mPFC) of the brain. Here we probe the functional underpinning of this ability using real-time fMRI neurofeedback to investigate the involvement of mPFC in recollection of the source of self-generated information. Thirty-nine healthy individuals underwent neurofeedback training in a between groups study receiving either Active feedback derived from the paracingulate region of the mPFC (21 subjects) or Sham feedback based on a similar level of randomised signal (18 subjects). Compared to those in the Sham group, participants receiving Active signal showed increased mPFC activity over the course of three real-time neurofeedback training runs undertaken in a single scanning session. Analysis of resting state functional connectivity associated with changes in reality monitoring accuracy following Active neurofeedback revealed increased connectivity between dorsolateral frontal regions of the fronto-parietal network (FPN) and the mPFC region of the default mode network (DMN), together with reduced connectivity within ventral regions of the FPN itself. However, only a trend effect was observed in the interaction of the recollection of the source of Imagined information compared with recognition memory between participants receiving Active and Sham neurofeedback, pre- and post- scanning. As such, these findings demonstrate that neurofeedback can be used to modulate mPFC activity and increase cooperation between the FPN and DMN, but the effects on reality monitoring performance are less clear

A dilemma in representing observables in quantum mechanics

There are self-adjoint operators which determine both spectral and semispectral measures. These measures have very different commutativity and covariance properties. This fact poses a serious question on the physical meaning of such a self-adjoint operator and its associated operator measures.Comment: 10 page

Canonical and kinetic forms of the electromagnetic momentum in an ad hoc quantization scheme for a dispersive dielectric

An ad hoc quantization scheme for the electromagnetic field in a weakly dispersive, transparent dielectric leads to the definition of canonical and kinetic forms for the momentum of the electromagnetic field in a dispersive medium. The canonical momentum is uniquely defined as the operator that generates spatial translations in a uniform medium, but the quantization scheme suggests two possible choices for the kinetic momentum operator, corresponding to the Abraham or the Minkowski momentum in classical electrodynamics. Another implication of this procedure is that a wave packet containing a single dressed photon travels at the group velocity through the medium. The physical significance of the canonical momentum has already been established by considerations of energy and momentum conservation in the atomic recoil due to spontaneous emission, the Cerenkov effect, the Doppler effect, and phase matching in nonlinear optical processes. In addition, the data of the Jones and Leslie radiation pressure experiment is consistent with the assignment of one ?k unit of canonical momentum to each dressed photon. By contrast, experiments in which the dielectric is rigidly accelerated by unbalanced electromagnetic forces require the use of the Abraham momentum.Comment: 21 pages, 1 figure, aip style, submitted to PR

Overcoming cross-cultural group work tensions: mixed student perspectives on the role of social relationships

As universities worldwide rapidly internationalise, higher education classrooms have become unique spaces for collaboration between students from different countries. One common way to encourage collaboration between diverse peers is through group work. However, previous research has highlighted that cross-cultural group work can be challenging and has hinted at potential social tensions. To understand this notion better, we have used robust quantitative tools in this study to select 20 participants from a larger classroom of 860 students to take part in an in-depth qualitative interview about cross-cultural group work experiences. Participant views on social tensions in cross-cultural group work were elicited using a unique mediating artefact method to encourage reflection and in-depth discussion. In our analysis of emergent interview themes, we compared student perspectives on the role of social relationships in group work by their academic performance level. Our findings indicated that all students interviewed desired the opportunity to form social relationships with their group work members, but their motivations for doing so varied widely by academic performance level

Population consequences of the Deepwater Horizon oil spill on pelagic cetaceans

This research was made possible by a grant from the Gulf of Mexico Research Initiative to the Consortium for Advanced Research on Marine Mammal Health Assessment (CARMMHA). T.A.M. acknowledges partial support by CEAUL (funded by FCT−Fundação para a Ciência e a Tecnologia, Portugal, through project UIDB/00006/2020).The Deepwater Horizon disaster resulted in the release of 490000 m3 of oil into the northern Gulf of Mexico. We quantified population consequences for pelagic cetaceans, including sperm whales, beaked whales and 11 species of delphinids. We used existing spatial density models to establish pre-spill population size and distribution, and overlaid an oil footprint to estimate the proportion exposed to oil. This proportion ranged from 0.058 (Atlantic spotted dolphin, 95% CI = 0.041-0.078) to 0.377 (spinner dolphin, 95% CI = 0.217-0.555). We adapted a population dynamics model, developed for an estuarine population of bottlenose dolphins, to each pelagic species by scaling demographic parameters using literature-derived estimates of gestation duration. We used expert elicitation to translate knowledge from dedicated studies of oil effects on bottlenose dolphins to pelagic species and address how density dependence may affect reproduction. We quantified impact by comparing population trajectories under baseline and oil-impacted scenarios. The number of lost cetacean years (difference between trajectories, summed over years) ranged from 964 (short-finned pilot whale, 95% CI = 385-2291) to 32584 (oceanic bottlenose dolphin, 95% = CI 13377-71967). Maximum proportional population decrease ranged from 1.3% (Atlantic spotted dolphin 95% CI = 0.5-2.3) to 8.4% (spinner dolphin 95% CI = 3.2-17.7). Estimated time to recover to 95% of baseline was >10 yr for spinner dolphin (12 yr, 95% CI = 0-21) and sperm whale (11 yr, 95% CI = 0-21), while 7 taxonomic units remained within 95% of the baseline population size (time to recover, therefore, as per its definition, was 0). We investigated the sensitivity of results to alternative plausible inputs. Our methods are widely applicable for estimating population effects of stressors in the absence of direct measurements.Publisher PDFPeer reviewe