Enhancer Priming Enables Fast and Sustained Transcriptional Responses to Notch Signaling.

Information from developmental signaling pathways must be accurately decoded to generate transcriptional outcomes. In the case of Notch, the intracellular domain (NICD) transduces the signal directly to the nucleus. How enhancers decipher NICD in the real time of developmental decisions is not known. Using the MS2-MCP system to visualize nascent transcripts in single cells in Drosophila embryos, we reveal how two target enhancers read Notch activity to produce synchronized and sustained profiles of transcription. By manipulating the levels of NICD and altering specific motifs within the enhancers, we uncover two key principles. First, increased NICD levels alter transcription by increasing duration rather than frequency of transcriptional bursts. Second, priming of enhancers by tissue-specific transcription factors is required for NICD to confer synchronized and sustained activity; in their absence, transcription is stochastic and bursty. The dynamic response of an individual enhancer to NICD thus differs depending on the cellular context.Wellcome Trus

Marginalized Populations’ Access to Transit: Journeys from Home and Work to Transit

Previous scholarship has shown that low-income individuals who also might identify as racial, ethnic, and gender minorities (such as transgender and gender nonconforming) are more likely to be dependent on public transportation. What remains understudied is how these marginalized groups, given their intersectional identities of oppression, might experience transit. The primary research question guiding this project is how do people with intersecting marginal identities experience social exclusion as they travel via mass transit? To answer the above research question, we employed a photovoice methodology and video-call interviewing, in Portland, OR, and Salt Lake City, UT. Across these two sites we interviewed 35 BIPOC (Black, Indigenous and other People of Color) with an income level less than $35,000 per person per year or$70,000 per family per year who use transit regularly, who were ethnically diverse, and included immigrants and people with other marginalized identities. In the interviews we found that people from these historically marginalized communities experience economic barriers, discrimination, harassment, and violence on transit and in public areas such as sidewalks, bus stops, and transit platforms when accessing transit related to their intersecting identities (e.g., being a woman of color). We examined how to make transit more accessible; for example, transit passes for low-income individuals, higher frequency of buses, lighting in dark areas, Spanish messaging in stations and on buses, to mention a few. We found that transit workers were key to feelings of safety by marginalized riders, where they could create a sense of welcome and community and fairly and consistently support policies that facilitated access for all. In addition, technology could be a mechanism for safety and ease of travel, but also widen socioeconomic gaps. Our findings are a starting point about what not only Salt Lake City and Portland planners, policymakers, social service providers, and case managers can do, but also what other municipalities could expect in terms of improving transportation and services for these vulnerable populations

Computation in Classical Mechanics

There is a growing consensus that physics majors need to learn computational skills, but many departments are still devoid of computation in their physics curriculum. Some departments may lack the resources or commitment to create a dedicated course or program in computational physics. One way around this difficulty is to include computation in a standard upper-level physics course. An intermediate classical mechanics course is particularly well suited for including computation. We discuss the ways we have used computation in our classical mechanics courses, focusing on how computational work can improve students' understanding of physics as well as their computational skills. We present examples of computational problems that serve these two purposes. In addition, we provide information about resources for instructors who would like to include computation in their courses.Comment: 6 pages, 3 figures, submitted to American Journal of Physic

Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism.

BackgroundCrassulacean acid metabolism (CAM), a specialized mode of photosynthesis, enables plant adaptation to water-limited environments and improves photosynthetic efficiency via an inorganic carbon-concentrating mechanism. Kalanchoë fedtschenkoi is an obligate CAM model featuring a relatively small genome and easy stable transformation. However, the molecular responses to light quality and intensity in CAM plants remain understudied.ResultsHere we present a genome-wide expression atlas of K. fedtschenkoi plants grown under 12 h/12 h photoperiod with different light quality (blue, red, far-red, white light) and intensity (0, 150, 440, and 1,000 μmol m-2 s-1) based on RNA sequencing performed for mature leaf samples collected at dawn (2 h before the light period) and dusk (2 h before the dark period). An eFP web browser was created for easy access of the gene expression data. Based on the expression atlas, we constructed a light-responsive co-expression network to reveal the potential regulatory relationships in K. fedtschenkoi. Measurements of leaf titratable acidity, soluble sugar, and starch turnover provided metabolic indicators of the magnitude of CAM under the different light treatments and were used to provide biological context for the expression dataset. Furthermore, CAM-related subnetworks were highlighted to showcase genes relevant to CAM pathway, circadian clock, and stomatal movement. In comparison with white light, monochrome blue/red/far-red light treatments repressed the expression of several CAM-related genes at dusk, along with a major reduction in acid accumulation. Increasing light intensity from an intermediate level (440 μmol m-2 s-1) of white light to a high light treatment (1,000 μmol m-2 s-1) increased expression of several genes involved in dark CO2 fixation and malate transport at dawn, along with an increase in organic acid accumulation.ConclusionsThis study provides a useful genomics resource for investigating the molecular mechanism underlying the light regulation of physiology and metabolism in CAM plants. Our results support the hypothesis that both light intensity and light quality can modulate the CAM pathway through regulation of CAM-related genes in K. fedtschenkoi

Multiplatform characterization of dynamic changes in breast milk during lactation

The multicomponent analysis of human breast milk (BM) by metabolic profiling is a new area of study applied to determining milk composition, and is capable of associating BM composition with maternal characteristics, and subsequent infant health outcomes. A multiplatform approach combining HPLC‐MS and ultra‐performance LC‐MS, GC‐MS, CE‐MS, and 1H NMR spectroscopy was used to comprehensively characterize metabolic profiles from seventy BM samples. A total of 710 metabolites spanning multiple molecular classes were defined. The utility of the individual and combined analytical platforms was explored in relation to numbers of metabolites identified, as well as the reproducibility of the methods. The greatest number of metabolites was identified by the single phase HPLC‐MS method, while CE‐MS uniquely profiled amino acids in detail and NMR was the most reproducible, whereas GC‐MS targeted volatile compounds and short chain fatty acids. Dynamic changes in BM composition were characterized over the first 3 months of lactation. Metabolites identified as altering in abundance over lactation included fucose, di‐ and triacylglycerols, and short chain fatty acids, known to be important for infant immunological, neurological, and gastrointestinal development, as well as being an important source of energy. This extensive metabolic coverage of the dynamic BM metabolome provides a baseline for investigating the impact of maternal characteristics, as well as establishing the impact of environmental and dietary factors on the composition of BM, with a focus on the downstream health consequences this may have for infants

The semiannual oscillation of the tropical zonal wind in the middle atmosphere derived from satellite geopotential height retrievals

Abstract The dominant mode of seasonal variability in the global tropical upper-stratosphere and mesosphere zonal wind is the semiannual oscillation (SAO). However, it is notoriously difficult to measure winds at these heights from satellite or ground-based remote sensing. Here, the balance wind relationship is used to derive monthly and zonally averaged zonal winds in the tropics from satellite retrievals of geopotential height. Data from the Aura Microwave Limb Sounder (MLS) cover about 12.5 yr, and those from the Thermosphere, Ionosphere, Mesosphere Energetics and Dynamics (TIMED) Sounding of the Atmosphere Using Broadband Emission Radiometry (SABER) cover almost 15 yr. The derived winds agree with direct wind observations below 10 hPa and above 80 km; there are no direct wind observations for validation in the intervening layers of the middle atmosphere. The derived winds show the following prominent peaks associated with the SAO: easterly maxima near the solstices at 1.0 hPa, westerly maxima near the equinoxes at 0.1 hPa, and easterly maxima near the equinoxes at 0.01 hPa. The magnitudes of these three wind maxima are stronger during the first cycle (January at 1.0 hPa and March at 0.1 and 0.01 hPa). The month and pressure level of the wind maxima shift depending on the phase of the quasi-biennial oscillation (QBO) at 10 hPa. During easterly QBO, the westerly maxima are shifted upward, are about 10 m s−1 stronger, and occur approximately 1 month later than those during the westerly QBO phase.</jats:p

Brane Interaction as the Origin of Inflation

We reanalyze brane inflation with brane-brane interactions at an angle, which include the special case of brane-anti-brane interaction. If nature is described by a stringy realization of the brane world scenario today (with arbitrary compactification), and if some additional branes were present in the early universe, we find that an inflationary epoch is generically quite natural, ending with a big bang when the last branes collide. In an interesting brane inflationary scenario suggested by generic string model-building, we use the density perturbation observed in the cosmic microwave background and the coupling unification to find that the string scale is comparable to the GUT scale.Comment: 28 pages, 8 figures, 2 tables, JHEP forma

Roles and Programming of Arabidopsis ARGONAUTE Proteins During Turnip Mosaic Virus Infection

In eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has ten AGO genes of which AGO1, AGO2, and AGO7 have been shown to play roles in antiviral defense. A genetic analysis was used to identify and characterize the roles of AGO proteins in antiviral defense against Turnip mosaic virus (TuMV) in Arabidopsis. AGO1, AGO2 and AGO10 promoted anti-TuMV defense in a modular way in various organs, with AGO2 providing a prominent antiviral role in leaves. AGO5, AGO7 and AGO10 had minor effects in leaves. AGO1 and AGO10 had overlapping antiviral functions in inflorescence tissues after systemic movement of the virus, although the roles of AGO1 and AGO10 accounted for only a minor amount of the overall antiviral activity. By combining AGO protein immunoprecipitation with high-throughput sequencing of associated small RNAs, AGO2, AGO10, and to a lesser extent AGO1 were shown to associate with siRNAs derived from silencing suppressor (HC-Pro)-deficient TuMV-AS9, but not with siRNAs derived from wild-type TuMV. Co-immunoprecipitation and small RNA sequencing revealed that viral siRNAs broadly associated with wild-type HC-Pro during TuMV infection. These results support the hypothesis that suppression of antiviral silencing during TuMV infection, at least in part, occurs through sequestration of virus-derived siRNAs away from antiviral AGO proteins by HC-Pro. These findings indicate that distinct AGO proteins function as antiviral modules, and provide a molecular explanation for the silencing suppressor activity of HC-Pro

Cancer associated fibroblasts predict for poor outcome and promote periostin-dependent invasion in oesophageal adenocarcinoma

Interactions between cancer cells and cancer-associated fibroblasts (CAF) play an important role in tumour development and progression. In this study we investigated the functional role of CAF in oesophageal adenocarcinoma (EAC). We used immunochemistry to analyse a cohort of EAC patients (183 patients) for CAF markers related to disease mortality. We characterized CAF and normal oesophageal fibroblasts (NOF) using western blotting, immunofluorescence and gel contraction. Transwell assays, 3-D organotypic culture and xenograft models were used to examine effects on EAC cell function, and dissect molecular mechanisms regulating invasion. Most EAC (93%) contained CAF with a myofibroblastic (?-SMA-positive) phenotype, which correlated significantly with poor survival (p?=?0.016; HR 7. 1 (1.7-29.4). Primary CAF, isolated from EAC, have a contractile, myofibroblastic phenotype, and promote EAC cell invasion in vitro (Transwell assays, p?=?&lt;0.05; organotypic culture, p?&lt;?0.001) and in vivo (p?=?&lt;0.05). In vitro, this pro-invasive effect is modulated through the matricellular protein periostin. Periostin is secreted by CAF, and acts as a ligand for EAC cell integrins ?v?3 and ?v?5, promoting activation of the PI3kinase/Akt pathway. In patient samples, periostin expression at the tumour cell/stromal interface correlates with poor overall and disease-free survival. Our study highlights the importance of the tumour stroma in EAC progression. Paracrine interaction between CAF-secreted periostin and EAC-expressed integrins results in PI3 kinase/Akt activation and increased tumour cell invasion. Most EAC contain a myofibroblastic CAF-rich stroma; this may explain the aggressive, highly infiltrative nature of the disease, and suggests that stromal targeting may produce therapeutic benefit in EAC patient