92 research outputs found
Genetically-Directed, Cell Type-Specific Sparse Labeling for the Analysis of Neuronal Morphology
Background: In mammals, genetically-directed cell labeling technologies have not yet been applied to the morphologic analysis of neurons with very large and complex arbors, an application that requires extremely sparse labeling and that is only rendered practical by limiting the labeled population to one or a few predetermined neuronal subtypes. Methods and Findings: In the present study we have addressed this application by using CreER technology to noninvasively label very small numbers of neurons so that their morphologies can be fully visualized. Four lines of IRES-CreER knock-in mice were constructed to permit labeling selectively in cholinergic or catecholaminergic neurons [choline acetyltransferase (ChAT)-IRES-CreER or tyrosine hydroxylase (TH)-IRES-CreER], predominantly in projection neurons [neurofilament light chain (NFL)-IRES-CreER], or broadly in neurons and some glia [vesicle-associated membrane protein2 (VAMP2)-IRES-CreER]. When crossed to the Z/AP reporter and exposed to 4-hydroxytamoxifen in the early postnatal period, the number of neurons expressing the human placental alkaline phosphatase reporter can be reproducibly lowered to fewer than 50 per brain. Sparse Cre-mediated recombination in ChAT-IRES-CreER;Z/AP mice shows the full axonal and dendritic arbors of individual forebrain cholinergic neurons, the first time that the complete morphologies of these very large neurons have been revealed in any species. Conclusions: Sparse genetically-directed, cell type-specific neuronal labeling with IRES-creER lines should prove useful fo
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Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.
Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs\u27 recapitulation of human tumors
MagAO Imaging of Long-period Objects (MILO). II. A Puzzling White Dwarf around the Sun-like Star HD 11112
The version of record, Rodigas, T. J. et al, 'MagAO Imaging of long-period objects (MILO). II. A puzzling white dwarf around the sun-like star HD 11112', The Astrophysical Journal, 831:177, November 2016, is available online via doi: 10.3847/0004-637X/831/2/177 © 2016. The American Astronomical Society. All rights reserved.HD 11112 is an old, Sun-like star that has a long-term radial velocity (RV) trend indicative of a massive companion on a wide orbit. Here we present direct images of the source responsible for the trend using the Magellan Adaptive Optics system. We detect the object (HD 11112B) at a separation of 2\fasec 2 (100 AU) at multiple wavelengths spanning 0.6-4 \microns ~and show that it is most likely a gravitationally-bound cool white dwarf. Modeling its spectral energy distribution (SED) suggests that its mass is 0.9-1.1 \msun, which corresponds to very high-eccentricity, near edge-on orbits from Markov chain Monte Carlo analysis of the RV and imaging data together. The total age of the white dwarf is discrepant with that of the primary star under most assumptions. The problem can be resolved if the white dwarf progenitor was initially a double white dwarf binary that then merged into the observed high-mass white dwarf. HD 11112B is a unique and intriguing benchmark object that can be used to calibrate atmospheric and evolutionary models of cool white dwarfs and should thus continue to be monitored by RV and direct imaging over the coming years.Peer reviewedFinal Published versio
The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe
The preponderance of matter over antimatter in the early Universe, the
dynamics of the supernova bursts that produced the heavy elements necessary for
life and whether protons eventually decay --- these mysteries at the forefront
of particle physics and astrophysics are key to understanding the early
evolution of our Universe, its current state and its eventual fate. The
Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed
plan for a world-class experiment dedicated to addressing these questions. LBNE
is conceived around three central components: (1) a new, high-intensity
neutrino source generated from a megawatt-class proton accelerator at Fermi
National Accelerator Laboratory, (2) a near neutrino detector just downstream
of the source, and (3) a massive liquid argon time-projection chamber deployed
as a far detector deep underground at the Sanford Underground Research
Facility. This facility, located at the site of the former Homestake Mine in
Lead, South Dakota, is approximately 1,300 km from the neutrino source at
Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino
charge-parity symmetry violation and mass ordering effects. This ambitious yet
cost-effective design incorporates scalability and flexibility and can
accommodate a variety of upgrades and contributions. With its exceptional
combination of experimental configuration, technical capabilities, and
potential for transformative discoveries, LBNE promises to be a vital facility
for the field of particle physics worldwide, providing physicists from around
the globe with opportunities to collaborate in a twenty to thirty year program
of exciting science. In this document we provide a comprehensive overview of
LBNE's scientific objectives, its place in the landscape of neutrino physics
worldwide, the technologies it will incorporate and the capabilities it will
possess.Comment: Major update of previous version. This is the reference document for
LBNE science program and current status. Chapters 1, 3, and 9 provide a
comprehensive overview of LBNE's scientific objectives, its place in the
landscape of neutrino physics worldwide, the technologies it will incorporate
and the capabilities it will possess. 288 pages, 116 figure
Finishing the euchromatic sequence of the human genome
The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead
Effects of a balanced translocation between chromosomes 1 and 11 disrupting the DISC1 locus on white matter integrity
Objective
Individuals carrying rare, but biologically informative genetic variants provide a unique opportunity to model major mental illness and inform understanding of disease mechanisms. The rarity of such variations means that their study involves small group numbers, however they are amongst the strongest known genetic risk factors for major mental illness and are likely to have large neural effects. DISC1 (Disrupted in Schizophrenia 1) is a gene containing one such risk variant, identified in a single Scottish family through its disruption by a balanced translocation of chromosomes 1 and 11; t(1;11) (q42.1;q14.3).
Method
Within the original pedigree, we examined the effects of the t(1;11) translocation on white matter integrity, measured by fractional anisotropy (FA). This included family members with (n = 7) and without (n = 13) the translocation, along with a clinical control sample of patients with psychosis (n = 34), and a group of healthy controls (n = 33).
Results
We report decreased white matter integrity in five clusters in the genu of the corpus callosum, the right inferior fronto-occipital fasciculus, acoustic radiation and fornix. Analysis of the mixed psychosis group also demonstrated decreased white matter integrity in the above regions. FA values within the corpus callosum correlated significantly with positive psychotic symptom severity.
Conclusions
We demonstrate that the t(1;11) translocation is associated with reduced white matter integrity in frontal commissural and association fibre tracts. These findings overlap with those shown in affected patients with psychosis and in DISC1 animal models and highlight the value of rare but biologically informative mutations in modeling psychosis
A PCNA-derived cell permeable peptide selectively inhibits neuroblastoma cell growth.
Proliferating cell nuclear antigen (PCNA), through its interaction with various proteins involved in DNA synthesis, cell cycle regulation, and DNA repair, plays a central role in maintaining genome stability. We previously reported a novel cancer associated PCNA isoform (dubbed caPCNA), which was significantly expressed in a broad range of cancer cells and tumor tissues, but not in non-malignant cells. We found that the caPCNA-specific antigenic site lies between L126 and Y133, a region within the interconnector domain of PCNA that is known to be a major binding site for many of PCNA's interacting proteins. We hypothesized that therapeutic agents targeting protein-protein interactions mediated through this region may confer differential toxicity to normal and malignant cells. To test this hypothesis, we designed a cell permeable peptide containing the PCNA L126-Y133 sequence. Here, we report that this peptide selectively kills human neuroblastoma cells, especially those with MYCN gene amplification, with much less toxicity to non-malignant human cells. Mechanistically, the peptide is able to block PCNA interactions in cancer cells. It interferes with DNA synthesis and homologous recombination-mediated double-stranded DNA break repair, resulting in S-phase arrest, accumulation of DNA damage, and enhanced sensitivity to cisplatin. These results demonstrate conceptually the utility of this peptide for treating neuroblastomas, particularly, the unfavorable MYCN-amplified tumors
Inhibition of DNA replication and induction of S-phase arrest and apoptosis by R9-caPep.
<p>a) SK-N-BE(2)c cells were pulsed in 10 µM of BrdU for 30 min after being pre-treated with R9-caPep or R9-srbPep for 7.5 h. The relative abundances of BrdU-positive cells in triplicates were averaged and graphed plus/minus standard deviations. b) Nuclear extracts from SK-N-BE(2)c cells were incubated with the indicated concentrations of R9-caPep (grey bars) or R9-srbPep (black bars) for 20 min. SV40 T-antigen was then added to the nuclear extracts along with premixed reaction buffer containing <sup>32</sup>P dCTP. A complete reaction mixture except for SV40 T-antigen was used as control for T-antigen-independent nucleotide incorporation. The polymerized radioactivity was measured by a scintillation counter. The T-antigen-dependent incorporation of <sup>32</sup>P dCTP was calculated by subtracting T-antigen-independent radioactivity from the total radioactivity and was normalized to the T-antigen-dependent radioactivity in PBS-treated samples. Triplicates of normalized T-antigen-dependent radioactivity for each treatment condition were averaged and graphed plus/minus standard deviations. c) SK-N-BE(2)c and non-malignant 7SM0032 cells were fixed and stained with propidium iodide (PI) after being treated with the indicated concentrations of R9-caPeptide for 48 h. The cellular PI fluorescence intensity determined by flow cytometry was analyzed by the FlowJo to model various cell populations. d) Cells grown on chamber slides were treated by R9-caPep or R9-srbPep at 40 µM for 48 h. Cells were fixed and analyzed by a TUNEL assay. Cells were imaged by a confocal microscope. TMR-red is the fluorophore that was attached to the free DNA ends. DAPI (blue) indicates the location of nuclei. The pink dots derived from the merged TMR-red and DAPI staining indicate apoptosis. e) The abundance of apoptotic cells relative to the total number of cells in six randomly selected fields were averaged and graphed plus/minus standard deviations (right). The dark and gray bars represent results from 7SM0032 and SK-N-BE(2)c cells respectively.</p
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