De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

On which timescales do gas transfer velocities control North Atlantic CO2 flux variability?

This is the final version of the article. Available from AGU via the DOI in this record.The North Atlantic is an important basin for the global ocean's uptake of anthropogenic and natural carbon dioxide (CO 2 ), but the mechanisms controlling this carbon flux are not fully understood. The air-sea flux of CO 2 , F, is the product of a gas transfer velocity, k, the air-sea CO 2 concentration gradient, ΔpCO 2 , and the temperature- and salinity-dependent solubility coefficient, α. k is difficult to constrain, representing the dominant uncertainty in F on short (instantaneous to interannual) timescales. Previous work shows that in the North Atlantic, ΔpCO 2 and k both contribute significantly to interannual F variability but that k is unimportant for multidecadal variability. On some timescale between interannual and multidecadal, gas transfer velocity variability and its associated uncertainty become negligible. Here we quantify this critical timescale for the first time. Using an ocean model, we determine the importance of k, ΔpCO 2 , and α on a range of timescales. On interannual and shorter timescales, both ΔpCO 2 and k are important controls on F. In contrast, pentadal to multidecadal North Atlantic flux variability is driven almost entirely by ΔpCO 2 ; k contributes less than 25%. Finally, we explore how accurately one can estimate North Atlantic F without a knowledge of nonseasonal k variability, finding it possible for interannual and longer timescales. These findings suggest that continued efforts to better constrain gas transfer velocities are necessary to quantify interannual variability in the North Atlantic carbon sink. However, uncertainty in k variability is unlikely to limit the accuracy of estimates of longer-term flux variability.This work was supported the RAGNARoCC NERC directed research program (NE/K002546/1, NE/K00249X/1, and NE/K002473/1)

Morphological evolution of a barchan dune migrating past an offshore wind farm foundation

As the number of manmade structures installed on the seafloor is increasing rapidly, we seek to understand the impact of these immobile obstacles on marine geomorphological processes, such as the evolution of bedforms. A 5.8 m diameter monopile foundation was installed at the case study offshore windfarm approximately 30 m ahead of an approaching barchan (crescent‐shaped) dune. The impact of the monopile on the dune's evolution was analysed using six multibeam bathymetry surveys spanning 20 years. To substantiate this analysis, coupled three‐dimensional numerical modelling of flows and sediment was conducted in which the scour inducing bed shear stresses were calculated from the modelled turbulent kinetic energy. Following the installation of the monopile, the mid‐section of the dune accelerated and stretched in the direction of the wake of the monopile. Four years after the monopile's installation the rest of the dune had caught up, flattening out the slip face within half the dune's length downstream of the monopile. Due to the modified flow field, the dune was scoured deeply at the base of the monopile to a depth of 6.8 m (supported by the model results that predicted a scour depth exceeding 2 m over a period of just a few days). The surveyed volume of material scoured amounted to 8% of the total dune volume. Whilst the process of scouring occurs at a timescale of days to weeks, the dune migrated on average by 25 m/yr. The difference in the timescale of the two processes allowed the scouring to occur through the full thickness of the dune. The scoured dune profile recovered rapidly once the dune migrated downstream of the monopile. This article demonstrates how large geomorphological features can intercept and migrate past a monopile foundation without long‐lasting impacts on the integrity of the feature or the foundation

Primary Transgenic Bovine Cells and Their Rejuvenated Cloned Equivalents Show Transgene-Specific Epigenetic Differences

Cell-mediated transgenesis, based on somatic cell nuclear transfer (SCNT), provides the opportunity to shape the genetic make-up of cattle. Bovine primary fetal fibroblasts, commonly used cells for SCNT, have a limited lifespan, and complex genetic modifications that require sequential transfections can be challenging time and cost-wise. To overcome these limitations, SCNT is frequently used to rejuvenate the cell lines and restore exhausted growth potential. We have designed a construct to be used in a 2-step cassette exchange experiment. Our transgene contains a puromycin resistance marker gene and an enhanced green fluorescence protein (EGFP) expression cassette, both driven by a strong mammalian promoter, and flanked by loxP sites and sequences from the bovine β-casein locus. Several transgenic cell lines were generated by random insertion into primary bovine cell lines. Two of these original cell lines were rederived by SCNT and new primary cells, with the same genetic makeup as the original donors, were established. While the original cell lines were puromycin-resistant and had a characteristic EGFP expression profile, all rejuvenated cell lines were sensitive to puromycin, and displayed varied EGFP expression, indicative of various degrees of silencing. When the methylation states of individual CpG sites within the transgene were analyzed, a striking increase in transgene-specific methylation was observed in all rederived cell lines. The results indicate that original transgenic donor cells and their rejuvenated derivatives may not be equivalent and differ in the functionality of their transgene sequences

A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific

peer-reviewedBackground: Spermatozoa have a remarkable epigenome in line with their degree of specialization, their unique nature and different requirements for successful fertilization. Accordingly, perturbations in the establishment of DNA methylation patterns during male germ cell differentiation have been associated with infertility in several species.Background: Spermatozoa have a remarkable epigenResults: The quantification of DNA methylation at CCGG sites using luminometric methylation assay (LUMA) highlighted the undermethylation of bull sperm compared to the sperm of rams, stallions, mice, goats and men. Total blood cells displayed a similarly high level of methylation in bulls and rams, suggesting that undermethylation of the bovine genome was specific to sperm. Annotation of CCGG sites in different species revealed no striking bias in the distribution of genome features targeted by LUMA that could explain undermethylation of bull sperm. To map DNA methylation at a genome-wide scale, bull sperm was compared with bovine liver, fibroblasts and monocytes using reduced representation bisulfite sequencing (RRBS) and immunoprecipitation of methylated DNA followed by microarray hybridization (MeDIP-chip). These two methods exhibited differences in terms of genome coverage, and consistently, two independent sets of sequences differentially methylated in sperm and somatic cells were identified for RRBS and MeDIP-chip. Remarkably, in the two sets most of the differentially methylated sequences were hypomethylated in sperm. In agreement with previous studies in other species, the sequences that were specifically hypomethylated in bull sperm targeted processes relevant to the germline differentiation program (piRNA metabolism, meiosis, spermatogenesis) and sperm functions (cell adhesion, fertilization), as well as satellites and rDNA repeats. Conclusions: These results highlight the undermethylation of bull spermatozoa when compared with both bovine somatic cells and the sperm of other mammals, and raise questions regarding the dynamics of DNA methylation in bovine male germline. Whether sperm undermethylation has potential interactions with structural variation in the cattle genome may deserve further attention. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bull spermatozoa is still scarce. The purpose of this study was therefore to characterize the bull sperm methylome relative to both bovine somatic cells and the sperm of other mammals through a multiscale analysis

Contribution of ocean physics and dynamics at different scales to heat uptake in low-resolution AOGCMs

Using an ensemble of atmosphere-ocean general circulation models (AOGCMs) in an idealized climate change experiment, this study quantifies the contributions to ocean heat uptake (OHU) from ocean physical parameterizations and resolved dynamical processes operating at different scales. Analysis of heat budget diagnostics reveals a leading-order global heat balance in the sub-surface upper ocean in a steady state between the large-scale circulation warming it and mesoscale processes cooling it, and shows that there are positive contributions from processes on all scales to the subsurface OHU during climate change. There is better agreement among the AOGCMs in the net OHU than in the individual scales/processes contributing to it. In the upper ocean and at high latitudes, OHU is dominated by small-scale diapycnal processes. Below 400 m, OHU is dominated by the super-residual transport, representing large-scale ocean dynamics combined with all parameterized mesoscale and submesoscale eddy effects. Weakening of the AMOC leads to less heat convergence in the subpolar North Atlantic and less heat divergence at lower latitudes, with a small overall effect on the net Atlantic heat content. At low latitudes, the dominance of advective heat redistribution is contrary to the diffusive OHU mechanism assumed by the commonly used upwelling-diffusion model. Using a density watermass framework, it is found that most of the OHU occurs along isopycnal directions. This feature of OHU is used to accurately reconstruct the global vertical ocean warming profile from the surface heat flux anomalies, supporting advective (rather than diffusive) models of OHU and sea-level rise

Ocean‐Only FAFMIP: Understanding Regional Patterns of Ocean Heat Content and Dynamic Sea Level Change

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Molecular Plasticity of E-Cadherin and Sialyl Lewis X Expression, in Two Comparative Models of Mammary Tumorigenesis

The process of metastasis involves a series of steps and interactions between the tumor embolus and the microenvironment. Key alterations in adhesion molecules are known to dictate progression from the invasive to malignant phenotype followed by colonization at a distant site. The invasive phenotype results from the loss of expression of the E-cadherin adhesion molecule, whereas the malignant phenotype is associated with an increased expression of the carbohydrate ligand-binding epitopes, (e.g. Sialyl Lewis (x/a)) that bind endothelial E-selectin of the lymphatics and vasculature.Our study analyzed the expression of two adhesion molecules, E-cadherin and Sialyl Lewis x (sLe(x)), in both a canine mammary carcinoma and human inflammatory breast cancer (IBC) model, using double labelled immunofluorescence staining.Our results demonstrate that canine mammary carcinoma and human IBC exhibit an inversely correlated cellular expression of E-cadherin and sLe(x) within the same tumor embolus.Our results in these two comparative models (canine and human) suggest the existence of a biologically coordinated mechanism of E-cadherin and sLe(x) expression (i.e. molecular plasticity) essential for tumor establishment and metastatic progression

What causes the spread of model projections of ocean dynamic sea-level change in response to greenhouse gas forcing?

Sea levels of different atmosphere-ocean general circulation models (AOGCMs) respond to climate change forcing in different ways, representing a crucial uncertainty in climate change research. We isolate the role of the ocean dynamics in setting the spatial pattern of dynamic sea-level (zeta) change by forcing several AOGCMs with prescribed identical heat, momentum (wind) and freshwater flux perturbations. This method produces a zeta projection spread comparable in magnitude to the spread that results from greenhouse gas forcing, indicating that the differences in ocean model formulation are the cause, rather than diversity in surface flux change. The heat flux change drives most of the global pattern of zeta change, while the momentum and water flux changes cause locally confined features. North Atlantic heat uptake causes large temperature and salinity driven density changes, altering local ocean transport and zeta. The spread between AOGCMs here is caused largely by differences in their regional transport adjustment, which redistributes heat that was already in the ocean prior to perturbation. The geographic details of the zeta change in the North Atlantic are diverse across models, but the underlying dynamic change is similar. In contrast, the heat absorbed by the Southern Ocean does not strongly alter the vertically coherent circulation. The Arctic zeta change is dissimilar across models, owing to differences in passive heat uptake and circulation change. Only the Arctic is strongly affected by nonlinear interactions between the three air-sea flux changes, and these are model specific.Peer reviewe

Overcoming Barriers to Skills Training in Borderline Personality Disorder: A Qualitative Interview Study

Despite evidence suggesting that skills training is an important mechanism of change in dialectical behaviour therapy, little research exploring facilitators and barriers to this process has been conducted. The study aimed to explore clients’ experiences of barriers to dialectical behaviour therapy skills training and how they felt they overcame these barriers, and to compare experiences between treatment completers and dropouts. In-depth qualitative interviews were conducted with 40 clients with borderline personality disorder who had attended a dialectical behaviour therapy programme. A thematic analysis of participants’ reported experiences found that key barriers to learning the skills were anxiety during the skills groups and difficulty understanding the material. Key barriers to using the skills were overwhelming emotions which left participants feeling unable or unwilling to use them. Key ways in which participants reported overcoming barriers to skills training were by sustaining their commitment to attending therapy and practising the skills, personalising the way they used them, and practising them so often that they became an integral part of their behavioural repertoire. Participants also highlighted a number of key ways in which they were supported with their skills training by other skills group members, the group therapists, their individual therapist, friends and family. Treatment dropouts were more likely than completers to describe anxiety during the skills groups as a barrier to learning, and were less likely to report overcoming barriers to skills training via the key processes outlined above. The findings of this qualitative study require replication, but could be used to generate hypotheses for testing in further research on barriers to skills training, how these relate to dropout, and how they can be overcome. The paper outlines several such suggestions for further research