scholarly journals Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor

2021 ◽  
Vol 7 (8) ◽  
pp. eabe3516
Author(s):  
Kang Wang ◽  
Honghong Wang ◽  
Conghui Li ◽  
Zhinang Yin ◽  
Ruijing Xiao ◽  
...  
Keyword(s):  
High Resolution ◽  
Independent Method ◽  
Binding Domain ◽  
Human Diseases ◽  
Genomic Profiling ◽  
Biological Processes ◽  
Artificial Dna

An R loop is a unique triple-stranded structure that participates in multiple key biological processes and is relevant to human diseases. Accurate and comprehensive R loop profiling is a prerequisite for R loops studies. However, current R loop mapping methods generate large discrepancies, therefore an independent method is in urgent need. Here, we establish an independent R loop CUT&Tag (Tn5-based cleavage under targets and tagmentation) method by combining CUT&Tag and GST-His6-2×HBD (glutathione S-transferase–hexahistidine–2× hybrid-binding domain), an artificial DNA-RNA hybrid sensor that specifically recognizes the DNA-RNA hybrids. We demonstrate that the R loop CUT&Tag is sensitive, reproducible, and convenient for native R loop mapping with high resolution, and find that the capture strategies, instead of the specificity of sensors, largely contribute to the disparities among different methods. Together, we provide an independent strategy for genomic profiling of native R loops and help resolve discrepancies among multiple R loop mapping methods.

Twin stars as tracers of binary evolution in the Kepler era

2021 ◽  
Author(s):  
Sara Bulut ◽  
Baris Hoyman ◽  
Ahmet Dervisoglu ◽  
Orkun Özdarcan ◽  
Ömür Cakilrli
Keyword(s):  
High Resolution ◽  
Internal Structure ◽  
Spectroscopic Analysis ◽  
Independent Method ◽  
Eclipsing Binaries ◽  
Physical Parameters ◽  
Evolutionary Status ◽  
Mass Ratio ◽  
Orbital Parameters ◽  
Binary Evolution

Abstract We present results of the combined photometric and spectroscopic analysis of four systems, which are eclipsing binaries with a twin–component (mass ratio q ≃ 1). These are exceptional tools to provide information for probing the internal structure of stars. None of the systems were previously recognized as twin binaries. We used a number of high–resolution optical spectra to calculate the radial velocities and later combined them with photometry to derive orbital parameters. Temperatures and metallicities of systems were estimated from high-resolution spectra. For each binary, we obtained a full set of orbital and physical parameters, reaching precision below 3 per cent in masses and radii for whole pairs. By comparing our results with PARSEC and MIST isochrones, we assess the distance, age and evolutionary status of the researched objects. The primary and/or secondary stars of EPIC 216075815 and EPIC 202843107 are one of the cases where asteroseismic parameters of δ Sct and γ Dor pulsators were confirmed by an independent method and rare examples of the twin–eclipsing binaries, therefore the following analyses and results concern the pulsating nature of the components.

scholarly journals Robust polarity establishment occurs via an endocytosis-based cortical corralling mechanism

2013 ◽  
Vol 200 (4) ◽  
pp. 407-418 ◽  
Author(s):  
Mini Jose ◽  
Sylvain Tollis ◽  
Deepak Nair ◽  
Jean-Baptiste Sibarita ◽  
Derek McCusker
Keyword(s):  
High Resolution ◽  
Membrane Trafficking ◽  
In Vivo Studies ◽  
Biological Processes ◽  
Constant Frequency ◽  
In Silico Modeling ◽  
Resolution Imaging ◽  
Polarity Establishment ◽  
Endocytic Vesicles

Formation of a stable polarity axis underlies numerous biological processes. Here, using high-resolution imaging and complementary mathematical modeling we find that cell polarity can be established via the spatial coordination of opposing membrane trafficking activities: endocytosis and exocytosis. During polarity establishment in budding yeast, these antagonistic processes become apposed. Endocytic vesicles corral a central exocytic zone, tightening it to a vertex that establishes the polarity axis for the ensuing cell cycle. Concomitantly, the endocytic system reaches an equilibrium where internalization events occur at a constant frequency. Endocytic mutants that failed to initiate periodic internalization events within the corral displayed wide, unstable polarity axes. These results, predicted by in silico modeling and verified by high resolution in vivo studies, identify a requirement for endocytic corralling during robust polarity establishment.

scholarly journals Longitudinal in vivo evaluation of bone regeneration by combined measurement of multi-pinhole SPECT and micro-CT for tissue engineering

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Philipp S. Lienemann ◽  
Stéphanie Metzger ◽  
Anna-Sofia Kiveliö ◽  
Alain Blanc ◽  
Panagiota Papageorgiou ◽  
...  
Keyword(s):  
Computed Tomography ◽  
High Resolution ◽  
Bone Formation ◽  
Bone Regeneration ◽  
Bone Defects ◽  
Histological Evaluation ◽  
Biological Processes ◽  
Micro Ct ◽  
Pinhole Spect

Abstract Over the last decades, great strides were made in the development of novel implants for the treatment of bone defects. The increasing versatility and complexity of these implant designs request for concurrent advances in means to assess in vivo the course of induced bone formation in preclinical models. Since its discovery, micro-computed tomography (micro-CT) has excelled as powerful high-resolution technique for non-invasive assessment of newly formed bone tissue. However, micro-CT fails to provide spatiotemporal information on biological processes ongoing during bone regeneration. Conversely, due to the versatile applicability and cost-effectiveness, single photon emission computed tomography (SPECT) would be an ideal technique for assessing such biological processes with high sensitivity and for nuclear imaging comparably high resolution (<1 mm). Herein, we employ modular designed poly(ethylene glycol)-based hydrogels that release bone morphogenetic protein to guide the healing of critical sized calvarial bone defects. By combined in vivo longitudinal multi-pinhole SPECT and micro-CT evaluations we determine the spatiotemporal course of bone formation and remodeling within this synthetic hydrogel implant. End point evaluations by high resolution micro-CT and histological evaluation confirm the value of this approach to follow and optimize bone-inducing biomaterials.

Time and taphonomy: Actualistic evidence for time-averaging of benthic foraminiferal assemblages

1993 ◽  
Vol 6 ◽  
pp. 34-56 ◽  
Author(s):  
Ronald E. Martin
Keyword(s):  
High Resolution ◽  
Ecosystem Management ◽  
Deep Sea ◽  
Time Averaging ◽  
Biological Processes ◽  
Exploration And Exploitation ◽  
Short Term ◽  
Resource Exploration ◽  
To Come ◽  
Paleoclimate Modelling

For more than half a century, microfossils–especially foraminifera–have been widely used as stratigraphic markers and paleoenvironmental indicators. Although increasing emphasis has been placed on their use in high-resolution paleoclimate studies, the time-scales involved in most microfossil-based stratigraphic investigations have remained relatively coarse (hundreds-of-thousands to millions of years). My intent herein is to try to come to grips with the interplay between time-averaging of benthic foraminiferal assemblages and stratigraphic resolution, and the implications for recognition of short-term physical and biological processes. These sorts of considerations deserve much closer scrutiny as the applied Earth sciences continue to move from a base of resource exploration and exploitation to one of paleoclimate modelling and ecosystem management (Martin, 1991; Corliss, 1993). The potential stratigraphic and paleoenvironmental resolution of foraminiferal assemblages is assessed using concepts derived from the age analysis of deep-sea assemblages.

scholarly journals High-resolution crystal structures of alternate forms of the human CD44 hyaluronan-binding domain reveal a site for protein interaction

2014 ◽  
Vol 70 (9) ◽  
pp. 1155-1161 ◽  
Author(s):  
Li-Kai Liu ◽  
Barry Finzel
Keyword(s):  
High Resolution ◽  
Crystal Structures ◽  
Crystal Form ◽  
Binding Domain ◽  
Structural Deformation ◽  
Monoclinic Form ◽  
Alternate Forms ◽  
Binding Groove ◽  
A Site ◽  
Hyaluronan Binding

Two new crystal structures of the extracellular hyaluronan-binding domain of human CD44 are described at high resolution. A hexagonal crystal form at 1.60 Å resolution and a monoclinic form at 1.08 Å resolution both have two molecules in the asymmetric unit arranged about a similar noncrystallographic twofold axis of symmetry. These structures are compared with those previously reported at 2.20 Å resolution to show that the fold is quite resistant to structural deformation in different crystal environments. Unexpectedly, a short peptide is found in the monoclinic crystals at a site remote from the known hyaluronan-binding groove. The peptide with a valine at the carboxy-terminus must have co-purified from the bacterial expression host and binds on the opposite side of the domain from the known hyaluronan-binding groove. This opportunistic binding may identify a site of interaction used as CD44 assembles with other proteins to accomplish effective signaling regarding changes to the extracellular environment.

Abstract 809: High-resolution genomic profiling reveals gains of CCND1 and EGFR associated with disease progression in Taiwanese oral cavity squamous cell carcinomas.

2013 ◽  
Author(s):  
Huei-Tzu Chien ◽  
Shiang-Fu Huang ◽  
I-How Chen ◽  
Chun-Ta Liao ◽  
Hung-Ming Wang ◽  
...  
Keyword(s):  
High Resolution ◽  
Oral Cavity ◽  
Disease Progression ◽  
Squamous Cell ◽  
Squamous Cell Carcinomas ◽  
Genomic Profiling

High-resolution solution structure of the 18 kDa substrate-binding domain of the mammalian chaperone protein Hsc70 1 1Edited by P. E. Wright

1999 ◽  
Vol 289 (5) ◽  
pp. 1387-1403 ◽  
Author(s):  
Robert C Morshauser ◽  
Weidong Hu ◽  
Hong Wang ◽  
Yuxi Pang ◽  
Gregory C Flynn ◽  
...  
Keyword(s):  
High Resolution ◽  
Solution Structure ◽  
Substrate Binding ◽  
Binding Domain ◽  
Chaperone Protein ◽  
Substrate Binding Domain

Comprehensive high-resolution genomic profiling and cytogenetics of two pediatric and one adult medulloblastoma

2013 ◽  
Vol 209 (9) ◽  
pp. 541-547 ◽  
Author(s):  
Heidrun Holland ◽  
Li-Xin Xu ◽  
Peter Ahnert ◽  
Holger Kirsten ◽  
Ronald Koschny ◽  
...  
Keyword(s):  
High Resolution ◽  
Genomic Profiling ◽  
Adult Medulloblastoma
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