Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000RAD and 15000RAD

The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools

CeCoIn5 - a quantum critical superfluid

We have made the first complete measurements of the London penetration depth $\lambda(T)$ of CeCoIn5, a quantum-critical metal where superconductivity arises from a non-Fermi-liquid normal state. Using a novel tunnel diode oscillator designed to avoid spurious contributions to $\lambda(T)$, we have established the existence of intrinsic and anomalous power-law behaviour at low temperature. A systematic analysis raises the possibility that the unusual observations are due to an extension of quantum criticality into the superconducting state.Comment: 5 pages, 3 figure

Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome☆☆Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under Accession No. EU879967-EU879988.

AbstractMammalian sex chromosomes are the remnants of an ancient autosomal pair present in the ancestral mammalian karyotype. As a consequence of random decay and chromosome rearrangements over evolutionary time, Y chromosome gene repertoires differ between eutherian lineages. To investigate the gene repertoire and transcriptional analysis of the domestic cat Y chromosome, and their potential roles in spermatogenesis, we obtained full-length cDNA sequences for all known Y genes and their X chromosome gametologues and used those sequences to create a BAC-based physical map of the X-degenerate region. Our results indicate the domestic cat Y chromosome has retained most X-degenerate genes that were present on the ancestral eutherian Y chromosome. Transcriptional analysis revealed that most feline X-degenerate genes have retained housekeeping functions shared by their X chromosome partners and have not been specialized for testis-specific functions. Physical mapping data indicate that the cat SRY gene is present as multiple functional copies and that very little of the felid Y chromosome may be single copy. X-Y gene divergence time estimates obtained using Bayesian methods confirm an early origin of Stratum 1 genes prior to the origin of therian mammals. We observed no statistical difference in the ages of Stratum 2 and Stratum 3 gene pairs, suggesting that eutherian and marsupial Stratum 2 genes may have been independently retained in each lineage

A high resolution RH map of the bovine major histocompatibility complex

<p>Abstract</p> <p>Background</p> <p>The cattle MHC is termed the bovine leukocyte antigen (BoLA) and, along with the MHCs of other ruminants, is unique in its genomic organization. Consequently, correct and reliable gene maps and sequence information are critical to the study of the BoLA region. The bovine genome sequencing project has produced two assemblies (Btau_3.1 and 4.0) that differ substantially from each other and from conventional gene maps in the BoLA region. To independently compare the accuracies of the different sequence assemblies, we have generated a high resolution map of BoLA using a 12,000_radradiation hybrid panel. Seventy-seven unique sequence tagged site (STS) markers chosen at approximately 50 kb intervals from the Btau 2.0 assembly and spanning the IIa-III-I and IIb regions of the bovine MHC were mapped on a 12,000_radbovine radiation hybrid (RH) panel to evaluate the different assemblies of the bovine genome sequence.</p> <p>Results</p> <p>Analysis of the data generated a high resolution RH map of BoLA that was significantly different from the Btau_3.1 assembly of the bovine genome but in good agreement with the Btau_4.0 assembly. Of the few discordancies between the RH map and Btau_4.0, most could be attributed to closely spaced markers that could not be precisely ordered in the RH panel. One probable incorrectly-assembled sequence and three missing sequences were noted in the Btau_4.0 assembly. The RH map of BoLA is also highly concordant with the sequence-based map of HLA (NCBI build 36) when reordered to account for the ancestral inversion in the ruminant MHC.</p> <p>Conclusion</p> <p>These results strongly suggest that studies using Btau_3.1 for analyses of the BoLA region should be reevaluated in light of the Btau_4.0 assembly and indicate that additional research is needed to produce a complete assembly of the BoLA genomic sequences.</p

Effects of precompetition state anxiety interventions on performance time and accuracy among amateur soccer players: Revisiting the matching hypothesis

In this study, we tested the matching ypothesis, which contends that administration of a cognitive or somatic anxiety intervention should be matched to a participant's dominant anxiety response. Sixty-one male soccer players (mean age 31.6 years, s=6.3) were assigned to one of four groups based on their responses to the Competitive State Anxiety Inventory-2, which was modified to include a directional scale. Interventions were randomly administered in a counterbalanced order 10 min before each performance trial on a soccer skill test. The dominantly cognitive anxious group (n=17), the dominantly somatic anxious group (n=17), and the non-anxious control intervention group (n=14) completed a baseline performance trial. The second and third trials were completed with random administration of brief cognitive and somatic interventions. The non-anxious control group (n=13) completed three trials with no intervention. A mixed-model, GroupTreatment multivariate analysis of variance indicated significant (P0.05), or performance time or accuracy (P>0.05). The present findings do not provide support for the matching hypothesis for state anxiety intensity and direction, or for performance

Developing an Optical Microlever for Stable and Unsupported Force Amplification

— Optical micromachines have the potential to im prove the capabilities of optical tweezers by amplifying forces and allowing for indirect handling and probing of specimens. However, systematic design and testing of micromachine per formance is still an emerging field. In this work we have designed and tested an unsupported microlever, suitable for general-purpose optical tweezer studies, that demonstrates stable trapping performance and repeatable doubling of applied forces. Stable trapping was ensured by analysing images to monitor focus shift when levers oscillated repeatedly, before the best-performing design was selected for force amplification. This study also shows that direct measurement of trap stiffness using the equipartition theorem appears to be a valid method for measuring applied forces on the spherical handles of microlevers

Modelling of discharges from baltic sea shipping

This paper describes the new developments of the Ship Traffic Emission Assessment Model (STEAM) which enable the modelling of pollutant discharges to water from ships. These include nutrients from black/grey water discharges as well as from food waste. Further, the modelling of contaminants in ballast, black, grey and scrubber water, bilge discharges, and stern tube oil leaks are also described as well as releases of contaminants from antifouling paints. Each of the discharges is regulated by different sections of the IMO MARPOL convention, and emission patterns of different pollution releases vary significantly. The discharge patterns and total amounts for the year 2012 in the Baltic Sea area are reported and open-loop SOx scrubbing effluent was found to be the second-largest pollutant stream by volume. The scrubber discharges have increased significantly in recent years, and their environmental impacts need to be investigated in detail

Novel Gene Acquisition on Carnivore Y Chromosomes

Despite its importance in harboring genes critical for spermatogenesis and male-specific functions, the Y chromosome has been largely excluded as a priority in recent mammalian genome sequencing projects. Only the human and chimpanzee Y chromosomes have been well characterized at the sequence level. This is primarily due to the presumed low overall gene content and highly repetitive nature of the Y chromosome and the ensuing difficulties using a shotgun sequence approach for assembly. Here we used direct cDNA selection to isolate and evaluate the extent of novel Y chromosome gene acquisition in the genome of the domestic cat, a species from a different mammalian superorder than human, chimpanzee, and mouse (currently being sequenced). We discovered four novel Y chromosome genes that do not have functional copies in the finished human male-specific region of the Y or on other mammalian Y chromosomes explored thus far. Two genes are derived from putative autosomal progenitors, and the other two have X chromosome homologs from different evolutionary strata. All four genes were shown to be multicopy and expressed predominantly or exclusively in testes, suggesting that their duplication and specialization for testis function were selected for because they enhance spermatogenesis. Two of these genes have testis-expressed, Y-borne copies in the dog genome as well. The absence of the four newly described genes on other characterized mammalian Y chromosomes demonstrates the gene novelty on this chromosome between mammalian orders, suggesting it harbors many lineage-specific genes that may go undetected by traditional comparative genomic approaches. Specific plans to identify the male-specific genes encoded in the Y chromosome of mammals should be a priority

Seeds of good anthropocenes: developing sustainability scenarios for Northern Europe

Scenario development helps people think about a broad variety of possible futures; however, the global environmental change community has thus far developed few positive scenarios for the future of the planet and humanity. Those that have been developed tend to focus on the role of a few common, large-scale external drivers, such as technology or environmental policy, even though pathways of positive change are often driven by surprising or bottom-up initiatives that most scenarios assume are unchanging. We describe an approach, pioneered in Southern Africa and tested here in a new context in Northern Europe, to developing scenarios using existing bottom-up transformative initiatives to examine plausible transitions towards positive, sustainable futures. By starting from existing, but marginal initiatives, as well as current trends, we were able to identify system characteristics that may play a key role in sustainability transitions (e.g., gender issues, inequity, governance, behavioral change) that are currently under-explored in global environmental scenarios. We suggest that this approach could be applied in other places to experiment further with the methodology and its potential applications, and to explore what transitions to desirables futures might be like in different places

Absolute values of the London penetration depth in YBa2Cu3O6+y measured by zero field ESR spectroscopy on Gd doped single crystals

Zero-field electron spin resonance (ESR) of dilute Gd ions substituted for Y in the cuprate superconductor YBa$_2$Cu$_3$O$_{\rm 6+y}$ is used as a novel technique for measuring the absolute value of the low temperature magnetic penetration depth $\lambda(T\to 0)$. The Gd ESR spectrum of samples with $\approx 1$ substitution was obtained with a broadband microwave technique that measures power absorption bolometrically from 0.5 GHz to 21 GHz. This ESR spectrum is determined by the crystal field that lifts the level degeneracy of the spin 7/2 Gd$^{3+}$ ion and details of this spectrum provide information concerning oxygen ordering in the samples. The magnetic penetration depth is obtained by relating the number of Gd ions exposed to the microwave magnetic field to the frequency-integrated intensity of the observed ESR transitions. This technique has allowed us to determine precise values of $\lambda$ for screening currents flowing in the three crystallographic orientations ($\hat a$, $\hat b$ and $\hat c$) in samples of Gd$_{\rm x}$Y$_{\rm 1-x}$Ba$_2$Cu$_3$O$_{6+{\rm y}}$ of three different oxygen contents ${\rm y}=0.993$ ($T_c = 89$ K), ${\rm y}=0.77$ ($T_c=75$ K) and ${\rm y}=0.52$ ($T_c=56$ K). The in-plane values are found to depart substantially from the widely reported relation $T_c\propto 1/\lambda^2$.Comment: 14 pages, 12 figures; version to appear in PR