Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the “Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)” to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs

Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs

Magnetization of coupled spin clusters in Ladder Geometry

In this paper, we construct a class of spin-1/2 antiferromagnetic (AFM) two-chain ladder models consisting of blocks of n-spin tetrahedral clusters alternating with two-spin rungs. For n=4 and 6 and in extended parameter regimes, the exact ground state of the ladder is shown to be a product of the ground states of the rungs and the n-spin blocks, in both zero and finite magnetic fields. In the latter case, magnetization/site (m) versus magenetic field (h) plot exhibits well-defined magnetization plateaus.Comment: 9 pages, latex, 6 figures, To be published in Phys. Rev.

Teenage Visitor Experience: Classification of Behavioral Dynamics in Museums

Teenagers' engagement in museums is much talked about but little research has been done to understand their behavior and inform design. Findings from co-design sessions with teenagers suggested they value games and stories when thinking about enjoyable museum tours. Informed by these findings and working with a natural history museum, we designed: a story-based tour (Turning Point) and a game-based tour (Haunted Encounters), informed by similar content. The two strategies were evaluated with 78 teenagers (15-19 years old) visiting the museum as part of an educational school trip. We assessed teenagers' personality in class; qualitative and quantitative data on their engagement, experience, and usability of the apps were collected at the museum. The triangulation of quantitative and qualitative data show personality traits mapping into different behaviors. We offer implications for the design of museum apps targeted to teenagers, a group known as difficult to reach

Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome

Additional file 3. This file contains all supplementary tables relating to lncRNA identification via the conservation of synteny. Table S3. lncRNAs inferred in one species by the genomic alignment of a transcript assembled with the RNA-seq libraries from a related spdecies. Table S12. Presence of intergenic lncRNAs both in sheep and cattle, in regions of conserved synteny. Table S13. Presence of intergenic lncRNAs both in sheep and goat, in regions of conserved synteny. Table S14. Presence of intergenic lncRNAs both in cattle and goat, in regions of conserved synteny. Table S15. Presence of intergenic lncRNAs both in sheep and humans, in regions of conserved synteny. Table S16. Presence of intergenic lncRNAs both in goat and humans, in regions of conserved synteny. Table S17. Presence of intergenic lncRNAs both in cattle and humans, in regions of conserved synteny. Table S18. High-confidence lncRNA pairs, those conserved across species both sequentially and positionally

Probe effects on the local gas holdup conditions in a fluidized bed

Fluidized beds are found in the energy production industry, and knowing their hydrodynamic conditions, such as local gas holdup or volumetric gas fraction, is important for effective operation. Local measurement probes are commonly used to measure local gas holdup. Although the probes are typically as small as possible to mitigate their influence on the local conditions, the invasive nature of this measurement technique has the potential to alter the fluidized bed behavior. This study used a noninvasive measurement technique, X-ray computed tomography (CT) imaging, to determine the local time-average gas holdup everywhere within a 10.2 cm diameter fluidized bed filled with 500–600 μm glass beads in which simulated probes were inserted. Three different simulated probe tips (pointed, rounded, and flat) and two different orientations (horizontal and vertical) were investigated at four different bed heights and two different fluidization velocities. The results show increases in local time-average gas holdup when the probes were present, but the scale of the effects was dependent upon the height at which the probes were placed; the lower the probe within the fluidized bed, the larger the local effects. The shape of the probe tip did not show any differences in the local gas holdup. On the other hand, probe orientation was an important factor, with the horizontal orientation showing a sustained increase in gas holdup values farther from the probe. The two different flow rates used in this study (1.5Umf and 3Umf, where Umf is the minimum fluidization velocity) also showed differences in the amount of variation in gas holdup, but the trends were inconsistent. Overall, the local hydrodynamic effects of the simulated invasive probes of this work were minimized when: (i) the probes were placed in the central part of the bed, outside the aeration region and top of the bed, (ii) the fluidized bed was operated at higher superficial gas velocities, and (iii) the probes were mounted in a vertical orientation.This is a manuscript of the article Published as Whitemarsh, Emily A., David R. Escudero, and Theodore J. Heindel. "Probe effects on the local gas holdup conditions in a fluidized bed." Powder Technology 294 (2016): 191-201. doi: https://doi.org/10.1016/j.powtec.2016.02.035. © 2016 by Elsevier. This manuscript is made available under the Elsevier user license. https://www.elsevier.com/open-access/userlicense/1.0/. CC BY-NC-ND