303 research outputs found
RNA interference in marine and freshwater sponges
Background: The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not been available.
Results: We show that soaking developing freshwater sponges in double-stranded RNA and/or feeding marine and freshwater sponges bacteria expressing double-stranded RNA can lead to RNA interference and reduction of targeted transcript levels. These methods, first utilized in C. elegans, have been adapted for the development and feeding style of easily cultured marine and freshwater poriferans. We demonstrate phenotypic changes result from âknocking downâ expression of the actin gene.
Conclusion: This technique provides an easy, efficient loss-of-function manipulation for developmental and gene regulatory studies in these important non-bilaterian animals
LHS 1610A: A Nearby Mid-M Dwarf with a Companion That is Likely A Brown Dwarf
We present the spectroscopic orbit of LHS 1610A, a newly discovered
single-lined spectroscopic binary with a trigonometric distance placing it at
9.9 pm 0.2 pc. We obtained spectra with the TRES instrument on the 1.5m
Tillinghast Reflector at the Fred Lawrence Whipple Observatory located on Mt.
Hopkins in AZ. We demonstrate the use of the TiO molecular bands at 7065 --
7165 Angstroms to measure radial velocities and achieve an average estimated
velocity uncertainty of 28 m/s. We measure the orbital period to be 10.6 days
and calculate a minimum mass of 44.8 pm 3.2 Jupiter masses for the secondary,
indicating that it is likely a brown dwarf. We place an upper limit to 3 sigma
of 2500 K on the effective temperature of the companion from infrared
spectroscopic observations using IGRINS on the 4.3m Discovery Channel
Telescope. In addition, we present a new photometric rotation period of 84.3
days for the primary star using data from the MEarth-South Observatory, with
which we show that the system does not eclipse.Comment: 10 pages, 5 figures; accepted for publication in the Astronomical
Journa
Avalanches on a conical bead pile: scaling with tuning parameters
Uniform spherical beads were used to explore the behavior of a granular
system near its critical angle of repose on a conical bead pile. We found two
tuning parameters that could take the system to a critical point where a simple
power-law described the avalanche size distribution as predicted by
self-organized criticality, which proposed that complex dynamical systems
self-organize to a critical point without need for tuning. Our distributions
were well described by a simple power-law with the power {\tau} = 1.5 when
dropping beads slowly onto the apex of a bead pile from a small height.
However, we could also move the system from the critical point using either of
two tuning parameters: the height from which the beads fell onto the top of the
pile or the region over which the beads struck the pile. As the drop height
increased, the system did not reach the critical point yet the resulting
distributions were independent of the bead mass, coefficient of friction, or
coefficient of restitution. All our apex-dropping distributions for any type of
bead (glass, stainless steel, zirconium) showed universality by scaling onto a
common curve with {\tau} = 1.5 and {\sigma} = 1.0, where 1/{\sigma} is the
power of the tuning parameter. From independent calculations using the moments
of the distribution, we find values for {\tau} = 1.6 \pm 0.1 and {\sigma} =
0.91 \pm 0.15. When beads were dropped across the surface of the pile instead
of solely on the apex, then the system also moved from the critical point and
again the avalanche size distributions fell on a common curve when scaled
similarly using the same values of {\tau} and {\sigma}. We also observed that
an hcp structure on the base of the pile caused an emergent structure in the
pile that had six faces with some fcc or hcp structure.Comment: 8 pages, 6 figures; submitted to Granular Matter; Reformatted into
LaTeX from Word; Fixed typo in uncertainty of tau; Rearranged two paragraphs
to improve flo
RNA interference in marine and freshwater sponges: actin knockdown in Tethya wilhelma and Ephydatia muelleri by ingested dsRNA expressing bacteria
Background: The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not been available. Results: We show that soaking developing freshwater sponges in double-stranded RNA and/or feeding marine and freshwater sponges bacteria expressing double-stranded RNA can lead to RNA interference and reduction of targeted transcript levels. These methods, first utilized in C. elegans, have been adapted for the development and feeding style of easily cultured marine and freshwater poriferans. We demonstrate phenotypic changes result from `knocking down' expression of the actin gene. Conclusion: This technique provides an easy, efficient loss-of-function manipulation for developmental and gene regulatory studies in these important non-bilaterian animals
Identification of PSD-95 in the Postsynaptic Density Using MiniSOG and EM Tomography
Combining tomography with electron microscopy (EM) produces images at definition sufficient to visualize individual protein molecules or molecular complexes in intact neurons. When freeze-substituted hippocampal cultures in plastic sections are imaged by EM tomography, detailed structures emerging from 3D reconstructions reveal putative glutamate receptors and membrane-associated filaments containing scaffolding proteins such as postsynaptic density (PSD)-95 family proteins based on their size, shape, and known distributions. In limited instances, structures can be identified with enhanced immuno-Nanogold labeling after light fixation and subsequent freeze-substitution. Molecular identification of structure can be corroborated in their absence after acute protein knockdown or gene knockout. However, additional labeling methods linking EM level structure to molecules in tomograms are needed. A recent development for labeling structures for TEM employs expression of endogenous proteins carrying a green fluorescent tag, miniSOG, to photoconvert diaminobenzidine (DAB) into osmiophilic polymers. This approach requires initial mild chemical fixation but many of structural features in neurons can still be discerned in EM tomograms. The photoreaction product, which appears as electron-dense, fine precipitates decorating protein structures in neurons, may diffuse to fill cytoplasm of spines, thus obscuring specific localization of proteins tagged with miniSOG. Here we develop an approach to minimize molecular diffusion of the DAB photoreaction product in neurons, which allows miniSOG tagged molecule/complexes to be identified in tomograms. The examples reveal electron-dense clusters of reaction product labeling membrane-associated vertical filaments, corresponding to the site of miniSOG fused at the C-terminal end of PSD-95-miniSOG, allowing identification of PSD-95 vertical filaments at the PSD. This approach, which results in considerable improvement in the precision of labeling PSD-95 in tomograms without complications due to the presence of antibody complexes in immunogold labeling, may be applicable for identifying other synaptic proteins in intact neurons
Automated NMR relaxation dispersion data analysis using NESSY
<p>Abstract</p> <p>Background</p> <p>Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear Magnetic Resonance (NMR) relaxation dispersion experiments are used to measure motion of discrete nuclei within the micro to millisecond timescale. Information about conformational/chemical exchange, populations of exchanging states and chemical shift differences are extracted from these experiments. To ensure these parameters are correctly extracted, accurate and careful analysis of these experiments is necessary.</p> <p>Results</p> <p>The software introduced in this article is designed for the automatic analysis of relaxation dispersion data and the extraction of the parameters mentioned above. It is written in Python for multi platform use and highest performance. Experimental data can be fitted to different models using the Levenberg-Marquardt minimization algorithm and different statistical tests can be used to select the best model. To demonstrate the functionality of this program, synthetic data as well as NMR data were analyzed. Analysis of these data including the generation of plots and color coded structures can be performed with minimal user intervention and using standard procedures that are included in the program.</p> <p>Conclusions</p> <p>NESSY is easy to use open source software to analyze NMR relaxation data. The robustness and standard procedures are demonstrated in this article.</p
TESS Discovery of an ultra-short-period planet around the nearby M dwarf LHS 3844
Data from the newly-commissioned \textit{Transiting Exoplanet Survey
Satellite} (TESS) has revealed a "hot Earth" around LHS 3844, an M dwarf
located 15 pc away. The planet has a radius of and
orbits the star every 11 hours. Although the existence of an atmosphere around
such a strongly irradiated planet is questionable, the star is bright enough
(, ) for this possibility to be investigated with transit and
occultation spectroscopy. The star's brightness and the planet's short period
will also facilitate the measurement of the planet's mass through Doppler
spectroscopy.Comment: 10 pages, 4 figures. Submitted to ApJ Letters. This letter makes use
of the TESS Alert data, which is currently in a beta test phase, using data
from the pipelines at the TESS Science Office and at the TESS Science
Processing Operations Cente
- âŠ