Advances in Engineering the Fly Genome with the CRISPR-Cas System.

Drosophila has long been a premier model for the development and application of cutting-edge genetic approaches. The CRISPR-Cas system now adds the ability to manipulate the genome with ease and precision, providing a rich toolbox to interrogate relationships between genotype and phenotype, to delineate and visualize how the genome is organized, to illuminate and manipulate RNA, and to pioneer new gene drive technologies. Myriad transformative approaches have already originated from the CRISPR-Cas system, which will likely continue to spark the creation of tools with diverse applications. Here, we provide an overview of how CRISPR-Cas gene editing has revolutionized genetic analysis in Drosophila and highlight key areas for future advances

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos.

The regulation of transcription requires the coordination of numerous activities on DNA, yet how transcription factors mediate these activities remains poorly understood. Here, we use lattice light-sheet microscopy to integrate single-molecule and high-speed 4D imaging in developing Drosophila embryos to study the nuclear organization and interactions of the key transcription factors Zelda and Bicoid. In contrast to previous studies suggesting stable, cooperative binding, we show that both factors interact with DNA with surprisingly high off-rates. We find that both factors form dynamic subnuclear hubs, and that Bicoid binding is enriched within Zelda hubs. Remarkably, these hubs are both short lived and interact only transiently with sites of active Bicoid-dependent transcription. Based on our observations, we hypothesize that, beyond simply forming bridges between DNA and the transcription machinery, transcription factors can organize other proteins into hubs that transiently drive multiple activities at their gene targets.Editorial noteThis article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter)

Comparative Direct Analysis of Type Ia Supernova Spectra. IV. Postmaximum

A comparative study of optical spectra of Type Ia supernovae (SNe Ia) obtained near 1 week, 3 weeks, and 3 months after maximum light is presented. Most members of the four groups that were defined on the basis of maximum light spectra in Paper II (core normal, broad line, cool, and shallow silicon) develop highly homogeneous postmaximum spectra, although there are interesting exceptions. Comparisons with SYNOW synthetic spectra show that most of the spectral features can be accounted for in a plausible way. The fits show that 3 months after maximum light, when SN Ia spectra are often said to be in the nebular phase and to consist of forbidden emission lines, the spectra actually remain dominated by resonance scattering features of permitted lines, primarily those of Fe II. Even in SN 1991bg, which is said to have made a very early transition to the nebular phase, there is no need to appeal to forbidden lines at 3 weeks postmaximum, and at 3 months postmaximum the only clear identification of a forbidden line is [Ca II] 7291, 7324. Recent studies of SN Ia rates indicate that most of the SNe Ia that have ever occurred have been "prompt" SNe Ia, produced by young (100,000,000 yr) stellar populations, while most of the SNe Ia that occur at low redshift today are "tardy", produced by an older (several Gyrs) population. We suggest that the shallow silicon SNe Ia tend to be the prompt ones.Comment: Accepted by PAS

Repetitive negative thinking in the perinatal period and its relationship with anxiety and depression

Background: Rumination and worry represent two types of repetitive negative thinking (RNT), and their predictive and maintaining roles are well-established in depression and anxiety, respectively. Furthermore, there is an emerging literature on the link between RNT and psychological wellbeing in the perinatal period. Methods: We conducted a scoping review of studies that have investigated the relationship between RNT and perinatal depression and anxiety. We identified 87 papers eligible for inclusion in the review; they included cross-sectional and longitudinal studies, as well as treatment evaluations (pilot trials and randomised controlled trials). Results: Cross-sectional studies provided evidence of an association between RNT (i.e., rumination and worry) and depression and anxiety, in both pregnancy and postpartum. Longitudinal findings were mixed. Whilst antenatal worry consistently predicted subsequent depression and anxiety (both later in pregnancy and postpartum), rumination did not consistently predict depression. However, there was some evidence that RNT interacted with other processes to predict later psychopathology. Three randomised controlled trials evaluated whether psychological treatments reduce RNT in the perinatal period, only one of which included a clinical sample. Limitations: No experimental investigations were eligible for inclusion in the review. Conclusions: Further studies are needed to further our understanding of the nature and role of RNT in pregnancy and postpartum, and its consequences for maternal mental health. These include (but are not limited to) experimental investigations, studies with large clinical samples, and RCTs evaluating the effectiveness of psychological interventions targeting RNT to prevent and treat perinatal depression and anxiety

Upper extremity transplantation in non-human primates: an orthotopic model for translational research

Vascularized composite allotransplantation (VCA) offers unparalleled restoration of function and form following devastating musculoskeletal and soft tissue injury. However, the potential adverse effects of life-long immunosuppression remain a significant cause for concern. Therefore, while the surgical techniques necessary for VCA have developed rapidly, the immunological aspects of these procedures and the potential functional significance of immunological processes on vascularized composite allografts remain areas in which further research is required. The functional complexity of these procedures, combined with the preclinical nature of many of the research questions, necessitates the use of large animal models to most effectively address some of the outstanding hypotheses. Cynomolgus macaques are among the premier large animal models for immunological research. This manuscript describes development of an orthotopic model of upper extremity transplantation in cynomolgus macaques. Following study of the anatomy to determine feasibility, in vivo proof of concept was achieved by autologous amputation and replantation in two animals, following which a preliminary series of four allotransplants was performed. The anatomy encountered and techniques required for successful transplantation are closely comparable to those in clinical upper extremity transplantation. This is a technically challenging model, but offers a rigorous pre-clinical platform for translational research in transplant immunology, and is suitable for detailed study of the impact of immunologic processes on functional outcomes following VCA

Rapamycin‐mediated lifespan increase in mice is dose and sex dependent and metabolically distinct from dietary restriction

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/107367/1/acel12194.pd

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo

The transition from a specified germ cell to a population of pluripotent cells occurs rapidly following fertilization. During this developmental transition, the zygotic genome is largely transcriptionally quiescent and undergoes significant chromatin remodeling. In Drosophila, the DNA-binding protein Zelda (also known as Vielfaltig) is required for this transition and for transcriptional activation of the zygotic genome. Open chromatin is associated with Zelda-bound loci, as well as more generally with regions of active transcription. Nonetheless, the extent to which Zelda influences chromatin accessibility across the genome is largely unknown. Here we used formaldehyde-assisted isolation of regulatory elements to determine the role of Zelda in regulating regions of open chromatin in the early embryo. We demonstrate that Zelda is essential for hundreds of regions of open chromatin. This Zelda-mediated chromatin accessibility facilitates transcription-factor recruitment and early gene expression. Thus, Zelda possesses some key characteristics of a pioneer factor. Unexpectedly, chromatin at a large subset of Zelda-bound regions remains open even in the absence of Zelda. The GAGA factor-binding motif and embryonic GAGA factor binding are specifically enriched in these regions. We propose that both Zelda and GAGA factor function to specify sites of open chromatin and together facilitate the remodeling of the early embryonic genome