149 research outputs found
Developing a biotic index for Colorado stream quality
November 1994.Also listed online under Open file reports list as no. 8.Includes bibliographical references (pages 114-118).Financed in part by the U.S. Dept. of the Interior, Geological Survey, grant no. 14-08-0001-G2008/3 11
Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin
Extracting kinetic models from single
molecule data is an important
route to mechanistic insight in biophysics, chemistry, and biology.
Data collected from force spectroscopy can probe discrete hops of
a single molecule between different conformational states. Model extraction
from such data is a challenging inverse problem because single molecule
data are noisy and rich in structure. Standard modeling methods normally
assume (i) a prespecified number of discrete states and (ii) that
transitions between states are Markovian. The data set is then fit
to this predetermined model to find a handful of rates describing
the transitions between states. We show that it is unnecessary to
assume either (i) or (ii) and focus our analysis on the zipping/unzipping
transitions of an RNA hairpin. The key is in starting with a very
broad class of non-Markov models in order to let the data guide us
toward the best model from this very broad class. Our method suggests
that there exists a folding intermediate for the P5ab RNA hairpin
whose zipping/unzipping is monitored by force spectroscopy experiments.
This intermediate would not have been resolved if a Markov model had
been assumed from the onset. We compare the merits of our method with
those of others
The Free Energy Landscape of Small Molecule Unbinding
The spontaneous dissociation of six small ligands from the active site of FKBP
(the FK506 binding protein) is investigated by explicit water molecular dynamics
simulations and network analysis. The ligands have between four
(dimethylsulphoxide) and eleven (5-diethylamino-2-pentanone) non-hydrogen atoms,
and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the
FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each
ligand) are grouped according to a set of intermolecular distances into nodes of
a network, and the direct transitions between them are the links. The network
analysis reveals that the bound state consists of several subbasins, i.e.,
binding modes characterized by distinct intermolecular hydrogen bonds and
hydrophobic contacts. The dissociation kinetics show a simple (i.e.,
single-exponential) time dependence because the unbinding barrier is much higher
than the barriers between subbasins in the bound state. The unbinding transition
state is made up of heterogeneous positions and orientations of the ligand in
the FKBP active site, which correspond to multiple pathways of dissociation. For
the six small ligands of FKBP, the weaker the binding affinity the closer to the
bound state (along the intermolecular distance) are the transition state
structures, which is a new manifestation of Hammond behavior. Experimental
approaches to the study of fragment binding to proteins have limitations in
temporal and spatial resolution. Our network analysis of the unbinding
simulations of small inhibitors from an enzyme paints a clear picture of the
free energy landscape (both thermodynamics and kinetics) of ligand
unbinding
Poorly processed reusable surface disinfection tissue dispensers may be a source of infection
SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids
Kidney failure is frequently observed during and after COVID-19, but it remains elusive whether this is a direct effect of the virus. Here, we report that SARS-CoV-2 directly infects kidney cells and is associated with increased tubule-interstitial kidney fibrosis in patient autopsy samples. To study direct effects of the virus on the kidney independent of systemic effects of COVID-19, we infected human-induced pluripotent stem-cell-derived kidney organoids with SARS-CoV-2. Single-cell RNA sequencing indicated injury and dedifferentiation of infected cells with activation of profibrotic signaling pathways. Importantly, SARS-CoV-2 infection also led to increased collagen 1 protein expression in organoids. A SARS-CoV-2 protease inhibitor was able to ameliorate the infection of kidney cells by SARS-CoV-2. Our results suggest that SARS-CoV-2 can directly infect kidney cells and induce cell injury with subsequent fibrosis. These data could explain both acute kidney injury in COVID-19 patients and the development of chronic kidney disease in long COVID
Ptychography
Ptychography is a computational imaging technique. A detector records an extensive data set consisting of many inference patterns obtained as an object is displaced to various positions relative to an illumination field. A computer algorithm of some type is then used to invert these data into an image. It has three key advantages: it does not depend upon a good-quality lens, or indeed on using any lens at all; it can obtain the image wave in phase as well as in intensity; and it can self-calibrate in the sense that errors that arise in the experimental set up can be accounted for and their effects removed. Its transfer function is in theory perfect, with resolution being wavelength limited. Although the main concepts of ptychography were developed many years ago, it has only recently (over the last 10 years) become widely adopted. This chapter surveys visible light, x-ray, electron, and EUV ptychography as applied to microscopic imaging. It describes the principal experimental arrangements used at these various wavelengths. It reviews the most common inversion algorithms that are nowadays employed, giving examples of meta code to implement these. It describes, for those new to the field, how to avoid the most common pitfalls in obtaining good quality reconstructions. It also discusses more advanced techniques such as modal decomposition and strategies to cope with three-dimensional () multiple scattering
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