House and home

If asked to imagine home, most of us will come to think of a particular house or building. And, for many of us, the quintessential image of home remains the place we grew up in. This close association between house and home has long marked anthropological literature. And yet, when we imagine home, it is often not the structures themselves but the feelings, practices, and relationships within familiar spaces which give home a powerful sense of belonging. Home may be the scent of a grandmother’s cooking, the familiar fuzz of a worn cushion, the seemingly defiant thrill of hanging posters on the wall as a teenager, or the knot of tension in the stomach of a child listening to an argument in the adjoining room. Recent anthropological studies have hence looked beyond physical structures to understand home in terms of a diverse array of practices, meaningful and imaginative forms, and feelings which surround a sense of groundedness within the world. Understood in such terms, home becomes something much less solid than a structure of stone or wood. It tends to be contestable and fragile, a domain not only of belonging but also of potential alienation when attempts to make home fail or are subverted. This flourishing literature increasingly suggests that while physical shelter may be a basic existential need, it is houses and homes, wrapped up in the desire and struggle for belonging, which underpin human sociality

Sub-kHz-level relative stabilization of an intracavity doubled continuous wave optical parametric oscillator using Pound-Drever-Hall scheme

We report the relative frequency stabilization of an intracavity frequency doubled singly resonant optical parametric oscillator on a Fabry-Perot\'etalon. The red/orange radiation produced by the frequency doubling of the intracavity resonant idler is stabilized using the Pound-Drever-Hall locking technique. The relative frequency noise of this orange light, when integrated from 1 Hz to 50 kHz, corresponds to a standard deviation of 700 Hz. The frequency noise of the pump laser is shown experimentally to be transferred to the non resonant signal beam

Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing

Variations in transcription start site (TSS) selection reflect diversity of preinitiation complexes and can impact on post-transcriptional RNA fates. Most metazoan polymerase II-transcribed genes carry canonical initiation with pyrimidine/purine (YR) dinucleotide, while translation machinery-associated genes carry polypyrimidine initiator (5'-TOP or TCT). By addressing the developmental regulation of TSS selection in zebrafish we uncovered a class of dual-initiation promoters in thousands of genes, including snoRNA host genes. 5'-TOP/TCT initiation is intertwined with canonical initiation and used divergently in hundreds of dual-initiation promoters during maternal to zygotic transition. Dual-initiation in snoRNA host genes selectively generates host and snoRNA with often different spatio-temporal expression. Dual-initiation promoters are pervasive in human and fruit fly, reflecting evolutionary conservation. We propose that dual-initiation on shared promoters represents a composite promoter architecture, which can function both coordinately and divergently to diversify RNAs

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release

Quality science from quality measurement: The role of measurement type with respect to replication and effect size magnitude in psychological research

Copyright: © 2018 Kornbrot et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The quality of psychological studies is currently a major concern. The Many Labs Project (MLP) and the Open-Science-Collaboration (OSC) have collected key data on replicability and statistical effect sizes. We build on this work by investigating the role played by three measurement types: ratings, proportions and unbounded (measures without conceptual upper limits, e.g. time). Both replicability and effect sizes are dependent on the amount of variability due to extraneous factors. We predicted that the role of such extraneous factors might depend on measurement type, and would be greatest for ratings, intermediate for proportions and least for unbounded. Our results support this conjecture. OSC replication rates for unbounded, 43% and proportion 40% combined are reliably higher than those for ratings at 20% (effect size, w = .20). MLP replication rates for the original studies are: pro- portion = .74, ratings = .40 (effect size w = .33). Original effect sizes (Cohen’s d) are highest for: unbounded OSC cognitive = 1.45, OSC social = .90); next for proportions (OSC cogni- tive = 1.01, OSC social = .84, MLP = .82); and lowest for ratings (OSC social = .64, MLP = .31). These findings are of key importance to scientific methodology and design, even if the reasons for their occurrence are still at the level of conjecture.Peer reviewe

Quest for barley canopy architecture genes in the hortillus population and whealbi germplasm collection

Barley grains are predominantly used for animal feed and malting, and breeding traditionally focused on increase of grain yield by partitioning biomass from straw to grains. The increasing demand for renewable energy sources makes straw, and specially barley straw characterized by the largest content of carbohydrates among the cereals, a valuable product for its potential conversion into biofuels and other products. The BarPLUS project aims at finding genes, alleles and candidate lines related to barley canopy architecture and photosynthesis, to maximize barley biomass and yield (https://barplus.wordpress.com/). In this framework, our research group focuses on identifying genes and alleles controlling tillering, leaf size and leaf angle traits in barley by exploiting both induced and natural allelic variation. Using a forward genetics approach, we screened the HorTILLUS population (Szurman-Zubrzycka et al., 2018) under both field and controlled conditions, identifying 5 mutants with increased tillering and/or erect leaves. After crossing with four reference cultivars, pools of F2 wild-type and mutant plants were selected to map and identify the underlying genes by exome sequencing (Mascher et al., 2014). In parallel, TILLING of the HorTILLUS population identified four lines carrying mutations in the LBO (Lateral branching oxidoreductase) gene involved in tiller number. In order to explore also natural genetic variation, we are taking advantage of the \u2018WHEALBI\u2019 germplasm collection, which includes 403 exome sequenced diverse accessions (BustosKorts et al., 2019): a field trial on a subset of 240 lines (Fiorenzuola d\u2019Arda, Italy) allowed us to conduct a preliminary genome wide association study based on high-throughput phenotyping for leaf angle (PocketPlant3D smartphone app) and quantitative image-analysis for leaf size. Results will be compared with those from a greenhouse experiment on the same 240 accessions to analyze a wide range of morphological traits and identify associated markers and genomic regions

Robot life: simulation and participation in the study of evolution and social behavior.

This paper explores the case of using robots to simulate evolution, in particular the case of Hamilton's Law. The uses of robots raises several questions that this paper seeks to address. The first concerns the role of the robots in biological research: do they simulate something (life, evolution, sociality) or do they participate in something? The second question concerns the physicality of the robots: what difference does embodiment make to the role of the robot in these experiments. Thirdly, how do life, embodiment and social behavior relate in contemporary biology and why is it possible for robots to illuminate this relation? These questions are provoked by a strange similarity that has not been noted before: between the problem of simulation in philosophy of science, and Deleuze's reading of Plato on the relationship of ideas, copies and simulacra

Control of developmentally primed erythroid genes by combinatorial co-repressor actions

How transcription factors (TFs) cooperate within large protein complexes to allow rapid modulation of gene expression during development is still largely unknown. Here we show that the key haematopoietic LIM-domain-binding protein-1 (LDB1) TF complex contains several activator and repressor components that together maintain an erythroid-specific gene expression programme primed for rapid activation until differentiation is induced. A combination of proteomics, functional genomics and in vivo studies presented here identifies known and novel co-repressors, most notably the ETO2 and IRF2BP2 proteins, involved in maintaining this primed state. The ETO2-IRF2BP2 axis, interacting with the NCOR1/SMRT co-repressor complex, suppresses the expression of the vast majority of archetypical erythroid genes and pathways until its decommissioning at the onset of terminal erythroid differentiation. Our experiments demonstrate that multimeric regulatory complexes feature a dynamic interplay between activating and repressing components that determines lineage-specific gene expression and cellular differentiation

Feedback between p21 and reactive oxygen production is necessary for cell senescence

The sustained activation of CDKN1A (p21/Waf1/Cip1) by a DNA damage response induces mitochondrial dysfunction and reactive oxygen species (ROS) production via signalling through CDKN1A-GADD45A-MAPK14- GRB2-TGFBR2-TGFbeta in senescing primary human and mouse cells in vitro and in vivo.Enhanced ROS production in senescing cells generates additional DNA damage. Although this damage is repairable and transient, it elevates the average levels of DNA damage response permanently, thus forming a positive feedback loop.This loop is necessary and sufficient to maintain the stability of growth arrest until a ‘point of no return' is reached during establishment of senescence

Conservative route to genome compaction in a miniature annelid

The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact 73.8-megabase genome of Dimorphilus gyrociliatus, a meiobenthic segmented worm. The D. gyrociliatus genome retains traits classically associated with larger and slower-evolving genomes, such as an ordered, intact Hox cluster, a generally conserved developmental toolkit and traces of ancestral bilaterian linkage. Unlike some other animals with small genomes, the analysis of the D. gyrociliatus epigenome revealed canonical features of genome regulation, excluding the presence of operons and trans-splicing. Instead, the gene-dense D. gyrociliatus genome presents a divergent Myc pathway, a key physiological regulator of growth, proliferation and genome stability in animals. Altogether, our results uncover a conservative route to genome compaction in annelids, reminiscent of that observed in the vertebrate Takifugu rubripes