127 research outputs found
Identification and Characterization of Bovine Pol III Promoters to Express a Short-Hairpin RNA
The use of molecular biology as a means to advance agriculture has proven beneficial in many fields. However, the development lentiviral vectors that utilize a livestock promoter to express short hairpin RNA (shRNA) has been limited to date. The goal of this research project was to develop and characterize lentiviral bovine Pol III mir30 shRNA expression vectors for future use in livestock research. The bovine Pol III promoter (7sk, U6-2, or H1) was inserted directly upstream of a mir30 shRNA expression sequence in the lentiviral vector pNef-GT. A transient luciferase knockdown assay in human embryonic kidney (HEK) 293T cells was used to compare the functionality of these vectors. The bPol III mir30 shRNA expression vector was co-transfected with the pGL3 luciferase expression vector and the renilla expression vector pLB at a ratio of 5:10:1 respectively. The vectors were allowed 48 hrs to produce their respective products before luciferase activity was measured with the Stop-n-Glo Assay (Promega). Each bPol III promoter was able to express a functional shRNA resulting in a reduction of luciferase activity greater than 68 percent. The bH1 and bU6-2 Luc shRNA vectors were the most effective vectors when transfected with >76 percent (p-value <0.05) reduced luciferase activity. To confirm that these promoters were functional after integration into a bovine genome, recombinant lentivirus was made from these vectors. These particles were then used to transduce a bovine kidney (MDBK) cell line that expressed luciferase. After transduction, transgenic cells were selected by the addition of the antibiotic, Geneticin to the culture media until a population of 100 percent bPol III expression cells were observed for two passages and luciferase activity was measured. The 7sk promoter was the most effective bPol III promoter that reduced luciferase activity in these cells by 72 percent (p-value <0.05), while the bU6-2 and bH1 were moderately effective at reducing luciferase levels (37 percent, 46 percent respectively). These experiments were the first to quantify the bovine Pol III promoter function after integration into a bovine genome. While variability was observed, for livestock based research, the b7sk lentiviral vector appears to be the best choice to express a shRNA from the genome of a bovine genome
The Angular Correlation Function of Galaxies from Early SDSS Data
The Sloan Digital Sky Survey is one of the first multicolor photometric and
spectroscopic surveys designed to measure the statistical properties of
galaxies within the local Universe. In this Letter we present some of the
initial results on the angular 2-point correlation function measured from the
early SDSS galaxy data. The form of the correlation function, over the
magnitude interval 18<r*<22, is shown to be consistent with results from
existing wide-field, photographic-based surveys and narrower CCD galaxy
surveys. On scales between 1 arcminute and 1 degree the correlation function is
well described by a power-law with an exponent of ~ -0.7. The amplitude of the
correlation function, within this angular interval, decreases with fainter
magnitudes in good agreement with analyses from existing galaxy surveys. There
is a characteristic break in the correlation function on scales of
approximately 1-2 degrees. On small scales, < 1', the SDSS correlation function
does not appear to be consistent with the power-law form fitted to the 1'<
theta <0.5 deg data. With a data set that is less than 2% of the full SDSS
survey area, we have obtained high precision measurements of the power-law
angular correlation function on angular scales 1' < theta < 1 deg, which are
robust to systematic uncertainties. Because of the limited area and the highly
correlated nature of the error covariance matrix, these initial results do not
yet provide a definitive characterization of departures from the power-law form
at smaller and larger angles. In the near future, however, the area of the SDSS
imaging survey will be sufficient to allow detailed analysis of the small and
large scale regimes, measurements of higher-order correlations, and studies of
angular clustering as a function of redshift and galaxy type
The Fifth Data Release of the Sloan Digital Sky Survey
This paper describes the Fifth Data Release (DR5) of the Sloan Digital Sky
Survey (SDSS). DR5 includes all survey quality data taken through June 2005 and
represents the completion of the SDSS-I project (whose successor, SDSS-II will
continue through mid-2008). It includes five-band photometric data for 217
million objects selected over 8000 square degrees, and 1,048,960 spectra of
galaxies, quasars, and stars selected from 5713 square degrees of that imaging
data. These numbers represent a roughly 20% increment over those of the Fourth
Data Release; all the data from previous data releases are included in the
present release. In addition to "standard" SDSS observations, DR5 includes
repeat scans of the southern equatorial stripe, imaging scans across M31 and
the core of the Perseus cluster of galaxies, and the first spectroscopic data
from SEGUE, a survey to explore the kinematics and chemical evolution of the
Galaxy. The catalog database incorporates several new features, including
photometric redshifts of galaxies, tables of matched objects in overlap regions
of the imaging survey, and tools that allow precise computations of survey
geometry for statistical investigations.Comment: ApJ Supp, in press, October 2007. This paper describes DR5. The SDSS
Sixth Data Release (DR6) is now public, available from http://www.sdss.or
SMARCB1 regulates the hypoxic stress response in sickle cell trait during the pathogenesis of renal medullary carcinoma.
View full abstracthttps://openworks.mdanderson.org/leading-edge/1058/thumbnail.jp
The Seventh Data Release of the Sloan Digital Sky Survey
This paper describes the Seventh Data Release of the Sloan Digital Sky Survey
(SDSS), marking the completion of the original goals of the SDSS and the end of
the phase known as SDSS-II. It includes 11663 deg^2 of imaging data, with most
of the roughly 2000 deg^2 increment over the previous data release lying in
regions of low Galactic latitude. The catalog contains five-band photometry for
357 million distinct objects. The survey also includes repeat photometry over
250 deg^2 along the Celestial Equator in the Southern Galactic Cap. A
coaddition of these data goes roughly two magnitudes fainter than the main
survey. The spectroscopy is now complete over a contiguous area of 7500 deg^2
in the Northern Galactic Cap, closing the gap that was present in previous data
releases. There are over 1.6 million spectra in total, including 930,000
galaxies, 120,000 quasars, and 460,000 stars. The data release includes
improved stellar photometry at low Galactic latitude. The astrometry has all
been recalibrated with the second version of the USNO CCD Astrograph Catalog
(UCAC-2), reducing the rms statistical errors at the bright end to 45
milli-arcseconds per coordinate. A systematic error in bright galaxy photometr
is less severe than previously reported for the majority of galaxies. Finally,
we describe a series of improvements to the spectroscopic reductions, including
better flat-fielding and improved wavelength calibration at the blue end,
better processing of objects with extremely strong narrow emission lines, and
an improved determination of stellar metallicities. (Abridged)Comment: 20 pages, 10 embedded figures. Accepted to ApJS after minor
correction
Cosmological parameters from SDSS and WMAP
We measure cosmological parameters using the three-dimensional power spectrum
P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in
combination with WMAP and other data. Our results are consistent with a
``vanilla'' flat adiabatic Lambda-CDM model without tilt (n=1), running tilt,
tensor modes or massive neutrinos. Adding SDSS information more than halves the
WMAP-only error bars on some parameters, tightening 1 sigma constraints on the
Hubble parameter from h~0.74+0.18-0.07 to h~0.70+0.04-0.03, on the matter
density from Omega_m~0.25+/-0.10 to Omega_m~0.30+/-0.04 (1 sigma) and on
neutrino masses from <11 eV to <0.6 eV (95%). SDSS helps even more when
dropping prior assumptions about curvature, neutrinos, tensor modes and the
equation of state. Our results are in substantial agreement with the joint
analysis of WMAP and the 2dF Galaxy Redshift Survey, which is an impressive
consistency check with independent redshift survey data and analysis
techniques. In this paper, we place particular emphasis on clarifying the
physical origin of the constraints, i.e., what we do and do not know when using
different data sets and prior assumptions. For instance, dropping the
assumption that space is perfectly flat, the WMAP-only constraint on the
measured age of the Universe tightens from t0~16.3+2.3-1.8 Gyr to
t0~14.1+1.0-0.9 Gyr by adding SDSS and SN Ia data. Including tensors, running
tilt, neutrino mass and equation of state in the list of free parameters, many
constraints are still quite weak, but future cosmological measurements from
SDSS and other sources should allow these to be substantially tightened.Comment: Minor revisions to match accepted PRD version. SDSS data and ppt
figures available at http://www.hep.upenn.edu/~max/sdsspars.htm
Multi-disciplinary efforts to evaluate the therapeutic potential of CDK11, a novel transcription associated cyclin dependent kinase.
View full abstracthttps://openworks.mdanderson.org/leading-edge/1043/thumbnail.jp
Meiotic Chromosome Pairing Is Promoted by Telomere-Led Chromosome Movements Independent of Bouquet Formation
Chromosome pairing in meiotic prophase is a prerequisite for the high fidelity of chromosome segregation that haploidizes the genome prior to gamete formation. In the budding yeast Saccharomyces cerevisiae, as in most multicellular eukaryotes, homologous pairing at the cytological level reflects the contemporaneous search for homology at the molecular level, where DNA double-strand broken ends find and interact with templates for repair on homologous chromosomes. Synapsis (synaptonemal complex formation) stabilizes pairing and supports DNA repair. The bouquet stage, where telomeres have formed a transient single cluster early in meiotic prophase, and telomere-promoted rapid meiotic prophase chromosome movements (RPMs) are prominent temporal correlates of pairing and synapsis. The bouquet has long been thought to contribute to the kinetics of pairing, but the individual roles of bouquet and RPMs are difficult to assess because of common dependencies. For example, in budding yeast RPMs and bouquet both require the broadly conserved SUN protein Mps3 as well as Ndj1 and Csm4, which link telomeres to the cytoskeleton through the intact nuclear envelope. We find that mutants in these genes provide a graded series of RPM activity: wild-type>mps3-dCC>mps3-dAR>ndj1Δ>mps3-dNT = csm4Δ. Pairing rates are directly correlated with RPM activity even though only wild-type forms a bouquet, suggesting that RPMs promote homologous pairing directly while the bouquet plays at most a minor role in Saccharomyces cerevisiae. A new collision trap assay demonstrates that RPMs generate homologous and heterologous chromosome collisions in or before the earliest stages of prophase, suggesting that RPMs contribute to pairing by stirring the nuclear contents to aid the recombination-mediated homology search
PRMT1-dependent regulation of RNA metabolism and DNA damage response sustains pancreatic ductal adenocarcinoma
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer that has remained clinically challenging to manage. Here we employ an RNAi-based in vivo functional genomics platform to determine epigenetic vulnerabilities across a panel of patient-derived PDAC models. Through this, we identify protein arginine methyltransferase 1 (PRMT1) as a critical dependency required for PDAC maintenance. Genetic and pharmacological studies validate the role of PRMT1 in maintaining PDAC growth. Mechanistically, using proteomic and transcriptomic analyses, we demonstrate that global inhibition of asymmetric arginine methylation impairs RNA metabolism, which includes RNA splicing, alternative polyadenylation, and transcription termination. This triggers a robust downregulation of multiple pathways involved in the DNA damage response, thereby promoting genomic instability and inhibiting tumor growth. Taken together, our data support PRMT1 as a compelling target in PDAC and informs a mechanism-based translational strategy for future therapeutic development.
Statement of significance
PDAC is a highly lethal cancer with limited therapeutic options. This study identified and characterized PRMT1-dependent regulation of RNA metabolism and coordination of key cellular processes required for PDAC tumor growth, defining a mechanism-based translational hypothesis for PRMT1 inhibitors
Teixobactin kills bacteria by a two-pronged attack on the cell envelope
Antibiotics that use novel mechanisms are needed to combat antimicrobial resistance1–3. Teixobactin4 represents a new class of antibiotics with a unique chemical scaffold and lack of detectable resistance. Teixobactin targets lipid II, a precursor of peptidoglycan5. Here we unravel the mechanism of teixobactin at the atomic level using a combination of solid-state NMR, microscopy, in vivo assays and molecular dynamics simulations. The unique enduracididine C-terminal headgroup of teixobactin specifically binds to the pyrophosphate-sugar moiety of lipid II, whereas the N terminus coordinates the pyrophosphate of another lipid II molecule. This configuration favours the formation of a β-sheet of teixobactins bound to the target, creating a supramolecular fibrillar structure. Specific binding to the conserved pyrophosphate-sugar moiety accounts for the lack of resistance to teixobactin4. The supramolecular structure compromises membrane integrity. Atomic force microscopy and molecular dynamics simulations show that the supramolecular structure displaces phospholipids, thinning the membrane. The long hydrophobic tails of lipid II concentrated within the supramolecular structure apparently contribute to membrane disruption. Teixobactin hijacks lipid II to help destroy the membrane. Known membrane-acting antibiotics also damage human cells, producing undesirable side effects. Teixobactin damages only membranes that contain lipid II, which is absent in eukaryotes, elegantly resolving the toxicity problem. The two-pronged action against cell wall synthesis and cytoplasmic membrane produces a highly effective compound targeting the bacterial cell envelope. Structural knowledge of the mechanism of teixobactin will enable the rational design of improved drug candidates
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