745 research outputs found
GIVE: portable genome browsers for personal websites.
Growing popularity and diversity of genomic data demand portable and versatile genome browsers. Here, we present an open source programming library called GIVE that facilitates the creation of personalized genome browsers without requiring a system administrator. By inserting HTML tags, one can add to a personal webpage interactive visualization of multiple types of genomics data, including genome annotation, "linear" quantitative data, and genome interaction data. GIVE includes a graphical interface called HUG (HTML Universal Generator) that automatically generates HTML code for displaying user chosen data, which can be copy-pasted into user's personal website or saved and shared with collaborators. GIVE is available at: https://www.givengine.org/
Bridging Time Scales in Cellular Decision Making with a Stochastic Bistable Switch
Cellular transformations which involve a significant phenotypical change of
the cell's state use bistable biochemical switches as underlying decision
systems. In this work, we aim at linking cellular decisions taking place on a
time scale of years to decades with the biochemical dynamics in signal
transduction and gene regulation, occuring on a time scale of minutes to hours.
We show that a stochastic bistable switch forms a viable biochemical mechanism
to implement decision processes on long time scales. As a case study, the
mechanism is applied to model the initiation of follicle growth in mammalian
ovaries, where the physiological time scale of follicle pool depletion is on
the order of the organism's lifespan. We construct a simple mathematical model
for this process based on experimental evidence for the involved genetic
mechanisms. Despite the underlying stochasticity, the proposed mechanism turns
out to yield reliable behavior in large populations of cells subject to the
considered decision process. Our model explains how the physiological time
constant may emerge from the intrinsic stochasticity of the underlying gene
regulatory network. Apart from ovarian follicles, the proposed mechanism may
also be of relevance for other physiological systems where cells take binary
decisions over a long time scale.Comment: 14 pages, 4 figure
Adaptation of a Smoking Cessation and Prevention Website for Urban American Indian/Alaska Native Youth
Tobacco use among American Indian youth is a disproportionately significant problem. We adapted and modified an existing web-based and youth-focused tobacco control program to make it appropriate for young urban American Indian/Alaska Natives (AI/ANs). The results of the focus group indicate that AI/AN youth were very receptive to the use of a web-based Zine-style intervention tool. They wanted the look and feel of the website to be more oriented toward their cultural images. Future research should examine if successful programs for reducing non-ceremonial tobacco use among urban AI/AN youth can keep young irregular smokers from becoming adult smokers
X-Ray Spectroscopy of Stars
(abridged) Non-degenerate stars of essentially all spectral classes are soft
X-ray sources. Low-mass stars on the cooler part of the main sequence and their
pre-main sequence predecessors define the dominant stellar population in the
galaxy by number. Their X-ray spectra are reminiscent, in the broadest sense,
of X-ray spectra from the solar corona. X-ray emission from cool stars is
indeed ascribed to magnetically trapped hot gas analogous to the solar coronal
plasma. Coronal structure, its thermal stratification and geometric extent can
be interpreted based on various spectral diagnostics. New features have been
identified in pre-main sequence stars; some of these may be related to
accretion shocks on the stellar surface, fluorescence on circumstellar disks
due to X-ray irradiation, or shock heating in stellar outflows. Massive, hot
stars clearly dominate the interaction with the galactic interstellar medium:
they are the main sources of ionizing radiation, mechanical energy and chemical
enrichment in galaxies. High-energy emission permits to probe some of the most
important processes at work in these stars, and put constraints on their most
peculiar feature: the stellar wind. Here, we review recent advances in our
understanding of cool and hot stars through the study of X-ray spectra, in
particular high-resolution spectra now available from XMM-Newton and Chandra.
We address issues related to coronal structure, flares, the composition of
coronal plasma, X-ray production in accretion streams and outflows, X-rays from
single OB-type stars, massive binaries, magnetic hot objects and evolved WR
stars.Comment: accepted for Astron. Astrophys. Rev., 98 journal pages, 30 figures
(partly multiple); some corrections made after proof stag
Statistical Analysis of Molecular Signal Recording
A molecular device that records time-varying signals would enable new approaches in neuroscience. We have recently proposed such a device, termed a âmolecular ticker tapeâ, in which an engineered DNA polymerase (DNAP) writes time-varying signals into DNA in the form of nucleotide misincorporation patterns. Here, we define a theoretical framework quantifying the expected capabilities of molecular ticker tapes as a function of experimental parameters. We present a decoding algorithm for estimating time-dependent input signals, and DNAP kinetic parameters, directly from misincorporation rates as determined by sequencing. We explore the requirements for accurate signal decoding, particularly the constraints on (1) the polymerase biochemical parameters, and (2) the amplitude, temporal resolution, and duration of the time-varying input signals. Our results suggest that molecular recording devices with kinetic properties similar to natural polymerases could be used to perform experiments in which neural activity is compared across several experimental conditions, and that devices engineered by combining favorable biochemical properties from multiple known polymerases could potentially measure faster phenomena such as slow synchronization of neuronal oscillations. Sophisticated engineering of DNAPs is likely required to achieve molecular recording of neuronal activity with single-spike temporal resolution over experimentally relevant timescales.United States. Defense Advanced Research Projects Agency. Living Foundries ProgramGoogle (Firm)New York Stem Cell Foundation. Robertson Neuroscience Investigator AwardNational Institutes of Health (U.S.) (EUREKA Award 1R01NS075421)National Institutes of Health (U.S.) (Transformative R01 1R01GM104948)National Institutes of Health (U.S.) (Single Cell Grant 1 R01 EY023173)National Institutes of Health (U.S.) (Grant 1R01DA029639)National Institutes of Health (U.S.) (Grant 1R01NS067199)National Science Foundation (U.S.) (CAREER Award CBET 1053233)National Science Foundation (U.S.) (Grant EFRI0835878)National Science Foundation (U.S.) (Grant DMS1042134)Paul G. Allen Family Foundation (Distinguished Investigator in Neuroscience Award
Hv-CBF2A overexpression in barley accelerates COR gene transcript accumulation and acquisition of freezing tolerance during cold acclimation
Abstract C-Repeat Binding Factors (CBFs) are DNAbinding
transcriptional activators of gene pathways imparting
freezing tolerance. Poaceae contain three CBF subfamilies,
two of which, HvCBF3/CBFIII and HvCBF4/CBFIV,
are unique to this taxon. To gain mechanistic insight into
HvCBF4/CBFIV CBFs we overexpressed Hv-CBF2A in
spring barley (Hordeum vulgare) cultivar âGolden Promiseâ.
The Hv-CBF2A overexpressing lines exhibited stunted
growth, poor yield, and greater freezing tolerance compared
to non-transformed âGolden Promiseâ. Differences in
freezing tolerance were apparent only upon cold acclimation.
During cold acclimation freezing tolerance of the
Hv-CBF2A overexpressing lines increased more rapidly
than that of âGolden Promiseâ and paralleled the freezing
tolerance of the winter hardy barley âDicktooâ. Transcript
levels of candidate CBF target genes, COR14B and DHN5
were increased in the overexpressor lines at warm temperatures,
and at cold temperatures they accumulated to much
higher levels in the Hv-CBF2A overexpressors than in
âGolden Promiseâ. Hv-CBF2A overexpression also
increased transcript levels of other CBF genes at FROST
RESISTANCE-H2-H2 (FR-H2) possessing CRT/DRE sites
in their upstream regions, the most notable of which was
CBF12. CBF12 transcript levels exhibited a relatively constant
incremental increase above levels in âGolden Promiseâ
both at warm and cold. These data indicate that Hv-CBF2A
activates target genes at warm temperatures and that transcript
accumulation for some of these targets is greatly
enhanced by cold temperatures
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