Discrete model for laser driven etching and microstructuring of metallic surfaces

We present a unidimensional discrete solid-on-solid model evolving in time using a kinetic Monte Carlo method to simulate micro-structuring of kerfs on metallic surfaces by means of laser-induced jet-chemical etching. The precise control of the passivation layer achieved by this technique is responsible for the high resolution of the structures. However, within a certain range of experimental parameters, the microstructuring of kerfs on stainless steel surfaces with a solution of $\mathrm{H}_3\mathrm{PO}_4$ shows periodic ripples, which are considered to originate from an intrinsic dynamics. The model mimics a few of the various physical and chemical processes involved and within certain parameter ranges reproduces some morphological aspects of the structures, in particular ripple regimes. We analyze the range of values of laser beam power for the appearance of ripples in both experimental and simulated kerfs. The discrete model is an extension of one that has been used previously in the context of ion sputtering and is related to a noisy version of the Kuramoto-Sivashinsky equation used extensively in the field of pattern formation.Comment: Revised version. Etching probability distribution and new simulations adde

Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation

Naive human embryonic stem cells (hESCs) can be derived from primed hESCs or directly from blastocysts, but their X chromosome state has remained unresolved. Here, we show that the inactive X chromosome (Xi) of primed hESCs was reactivated in naive culture conditions. Like cells of the blastocyst, the resulting naive cells contained two active X chromosomes with XIST expression and chromosome-wide transcriptional dampening and initiated XIST-mediated X inactivation upon differentiation. Both establishment of and exit from the naive state (differentiation) happened via an XIST-negative XaXaintermediate. Together, these findings identify a cell culture system for functionally exploring the two X chromosome dosage compensation processes in early human development: X dampening and X inactivation. However, remaining differences between naive hESCs and embryonic cells related to mono-allelic XIST expression and non-random X inactivation highlight the need for further culture improvement. As the naive state resets Xiabnormalities seen in primed hESCs, it may provide cells better suited for downstream applications

Wainwright’s West Yorkshire: affect and landscape in the television drama of Sally Wainwright

Over the past two decades RED Production Company's key presence in British television drama has been grounded in its regional focus on the North of England. It shares this commitment with Sally Wainwright, whose work with and outside of RED is built around a strong affective engagement with its characters’ experiences. These stories offer intimate explorations of family dynamics and female relationships, situated within and interwoven with the spaces and places of West Yorkshire. From her adaptation of Wuthering Heights in Sparkhouse (BBC, 2002) to her 2016 Christmas biopic of the Brontë sisters To Walk Invisible (BBC, 2016), through Last Tango in Halifax (BBC, 2012–16) and Happy Valley (BBC, 2014–) these are distinctly regional narratives whose female-led familial melodrama, psychodrama and romance are embedded within and return to the landscapes of the region, spaces which blend the stolid and torrid. Wide and spectacular aerial shots follow cars that track through the green and brown expanses between the Harrogate and Halifax families of the elderly couple in Last Tango, the beauty of the Calder Valley pens in the stark bleakness that is foundational to Happy Valley, and the Brontë sisters stride across heathered hills and are silhouetted against grey skies in To Walk Invisible. This article explores the visual dynamics of Wainwright's work and her engagement with the landscapes of the region in both her writing and direction, evoking their numerous literary and cultural connotations in her interweaving of West Yorkshire's stark, dynamic beauty with her stories of intimate female affect

RNA promotes the formation of spatial compartments in the nucleus

The nucleus is a highly organized arrangement of RNA, DNA, and protein molecules that are compartmentalized within three-dimensional (3D) structures involved in shared functional and regulatory processes. Although RNA has long been proposed to play a global role in organizing nuclear structure, exploring the role of RNA in shaping nuclear structure has remained a challenge because no existing methods can simultaneously measure RNA-RNA, RNA-DNA, and DNA-DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the location of all RNAs relative to DNA and other RNAs. Using this approach, we identify many RNAs that are localized near their transcriptional loci (RNA-DNA) together with other diffusible ncRNAs (RNA-RNA) within higher-order DNA structures (DNA-DNA). These RNA-chromatin compartments span three major classes of nuclear functions: RNA processing (including ribosome biogenesis, mRNA splicing, snRNA biogenesis, and histone mRNA processing), heterochromatin assembly, and gene regulation. More generally, we identify hundreds of ncRNAs that form stable nuclear compartments in spatial proximity to their transcriptional loci. We find that dozens of nuclear compartments require RNA to guide protein regulators into these 3D structures, and focusing on several ncRNAs, we show that these ncRNAs specifically regulate heterochromatin assembly and the expression of genes contained within these compartments. Together, our results demonstrate a unique mechanism by which RNA acts to shape nuclear structure by forming high concentration territories immediately upon transcription, binding to diffusible regulators, and guiding them into spatial compartments to regulate a wide range of essential nuclear functions

RNA promotes the formation of spatial compartments in the nucleus

The nucleus is a highly organized arrangement of RNA, DNA, and protein molecules that are compartmentalized within three-dimensional (3D) structures involved in shared functional and regulatory processes. Although RNA has long been proposed to play a global role in organizing nuclear structure, exploring the role of RNA in shaping nuclear structure has remained a challenge because no existing methods can simultaneously measure RNA-RNA, RNA-DNA, and DNA-DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the location of all RNAs relative to DNA and other RNAs. Using this approach, we identify many RNAs that are localized near their transcriptional loci (RNA-DNA) together with other diffusible ncRNAs (RNA-RNA) within higher-order DNA structures (DNA-DNA). These RNA-chromatin compartments span three major classes of nuclear functions: RNA processing (including ribosome biogenesis, mRNA splicing, snRNA biogenesis, and histone mRNA processing), heterochromatin assembly, and gene regulation. More generally, we identify hundreds of ncRNAs that form stable nuclear compartments in spatial proximity to their transcriptional loci. We find that dozens of nuclear compartments require RNA to guide protein regulators into these 3D structures, and focusing on several ncRNAs, we show that these ncRNAs specifically regulate heterochromatin assembly and the expression of genes contained within these compartments. Together, our results demonstrate a unique mechanism by which RNA acts to shape nuclear structure by forming high concentration territories immediately upon transcription, binding to diffusible regulators, and guiding them into spatial compartments to regulate a wide range of essential nuclear functions

Does personality affect premating isolation between locally-adapted populations?

Background: One aspect of premating isolation between diverging, locally-adapted population pairs is female mate choice for resident over alien male phenotypes. Mating preferences often show considerable individual variation, and whether or not certain individuals are more likely to contribute to population interbreeding remains to be studied. In the Poecilia mexicana-species complex different ecotypes have adapted to hydrogen sulfide (H2S)-toxic springs, and females from adjacent non-sulfidic habitats prefer resident over sulfide-adapted males. We asked if consistent individual differences in behavioral tendencies (animal personality) predict the strength and direction of the mate choice component of premating isolation in this system. Results: We characterized focal females for their personality and found behavioral measures of ‘novel object exploration’, ‘boldness’ and ‘activity in an unknown area’ to be highly repeatable. Furthermore, the interaction term between our measures of exploration and boldness affected focal females’ strength of preference (SOP) for the resident male phenotype in dichotomous association preference tests. High exploration tendencies were coupled with stronger SOPs for resident over alien mating partners in bold, but not shy, females. Shy and/or little explorative females had an increased likelihood of preferring the non-resident phenotype and thus, are more likely to contribute to rare population hybridization. When we offered large vs. small conspecific stimulus males instead, less explorative females showed stronger preferences for large male body size. However, this effect disappeared when the size difference between the stimulus males was small. Conclusions: Our results suggest that personality affects female mate choice in a very nuanced fashion. Hence, population differences in the distribution of personality types could be facilitating or impeding reproductive isolation between diverging populations depending on the study system and the male trait(s) upon which females base their mating decisions, respectively

Turbulence, instream wood and fish: ecohydraulic interactions under field conditions

This is the pre-peer reviewed version of the following article: Trinci, G, Harvey, GL, Henshaw, AJ, Bertoldi, W, Hölker, F. Turbulence, instream wood and fish: Ecohydraulic interactions under field conditions. Ecohydrology. 2020;e2211. https://doi.org/10.1002/eco.2211 , which has been published in final form at https://doi.org/10.1002/eco.2211. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions