scholarly journals A cookbook for DNase Hi-C

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Maria Gridina ◽  
Evgeniy Mozheiko ◽  
Emil Valeev ◽  
Ludmila P. Nazarenko ◽  
Maria E. Lopatkina ◽  
...  
Keyword(s):  
Rational Design ◽  
Restriction Enzymes ◽  
Nucleotide Exchange ◽  
Computational Tools ◽  
3 Dimensional ◽  
Cultured Human Cells ◽  
Dna Ends ◽  
By Products ◽  
Robust Protocol

Abstract Background The Hi-C technique is widely employed to study the 3-dimensional chromatin architecture and to assemble genomes. The conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in nonuniform genomic coverage. Using sequence-agnostic restriction enzymes, such as DNAse I, could help to overcome this limitation. Results In this study, we compare different DNAse Hi-C protocols and identify the critical steps that significantly affect the efficiency of the protocol. In particular, we show that the SDS quenching strategy strongly affects subsequent chromatin digestion. The presence of biotinylated oligonucleotide adapters may lead to ligase reaction by-products, which can be avoided by rational design of the adapter sequences. Moreover, the use of nucleotide-exchange enzymes for biotin fill-in enables simultaneous labelling and repair of DNA ends, similar to the conventional Hi-C protocol. These improvements simplify the protocol, making it less expensive and time-consuming. Conclusions We propose a new robust protocol for the preparation of DNAse Hi-C libraries from cultured human cells and blood samples supplemented with experimental controls and computational tools for the evaluation of library quality.

Molecular Design of Peptide-Fc Fusion Drugs

2019 ◽  
Vol 20 (3) ◽  
pp. 203-208 ◽  
Author(s):  
Lin Ning ◽  
Bifang He ◽  
Peng Zhou ◽  
Ratmir Derda ◽  
Jian Huang
Keyword(s):  
Rational Design ◽  
Molecular Design ◽  
Computational Design ◽  
Fusion Technology ◽  
Computational Tools ◽  
Open Questions ◽  
Biological Therapeutics ◽  
Key Steps ◽  
Computational Resources ◽  
Tools And Methods

Background:Peptide-Fc fusion drugs, also known as peptibodies, are a category of biological therapeutics in which the Fc region of an antibody is genetically fused to a peptide of interest. However, to develop such kind of drugs is laborious and expensive. Rational design is urgently needed.Methods:We summarized the key steps in peptide-Fc fusion technology and stressed the main computational resources, tools, and methods that had been used in the rational design of peptide-Fc fusion drugs. We also raised open questions about the computer-aided molecular design of peptide-Fc.Results:The design of peptibody consists of four steps. First, identify peptide leads from native ligands, biopanning, and computational design or prediction. Second, select the proper Fc region from different classes or subclasses of immunoglobulin. Third, fuse the peptide leads and Fc together properly. At last, evaluate the immunogenicity of the constructs. At each step, there are quite a few useful resources and computational tools.Conclusion:Reviewing the molecular design of peptibody will certainly help make the transition from peptide leads to drugs on the market quicker and cheaper.

In situ nanoscale visualization of solvent effects on molecular crystal surfaces

CrystEngComm ◽  
2021 ◽  
Author(s):  
Mikkel Herzberg ◽  
Anders Støttrup Larsen ◽  
Tue Hassenkam ◽  
Anders Østergaard Madsen ◽  
Jukka Rantanen
Keyword(s):  
Solid Solution ◽  
Solvent Effects ◽  
Molecular Crystal ◽  
Rational Design ◽  
Molecular Level ◽  
Molecular Crystals ◽  
Crystal Surfaces ◽  
Solution Interface ◽  
Atomic Force

Solvents can dramatically affect molecular crystals. Obtaining favorable properties for these crystals requires rational design based on molecular level understanding of the solid-solution interface. Here we show how atomic force...

Rational Design and In-situ Formation of Nickel–Cobalt Nitride Multi-core/Hollow N-doped Carbon Shell Anode for Li-ion Batteries

2021 ◽  
pp. 129630
Author(s):  
Bong Kyun Kang ◽  
Yoo Jung Choi ◽  
Hyung Wook Choi ◽  
Seok Bin Kwon ◽  
Suji Kim ◽  
...  
Keyword(s):  
Rational Design ◽  
Carbon Shell ◽  
Li Ion Batteries ◽  
Nickel Cobalt ◽  
Li Ion ◽  
In Situ Formation

Oil spill modeling: computational tools, analytical frameworks, and emerging technologies

2018 ◽  
Vol 43 (1) ◽  
pp. 129-143 ◽  
Author(s):  
Jake R. Nelson ◽  
Tony H. Grubesic
Keyword(s):  
Oil Spill ◽  
Emerging Technologies ◽  
Computational Tools ◽  
Gis And Remote Sensing ◽  
Response Strategies ◽  
Wide Range ◽  
Oil Spill Modeling ◽  
In Situ Sensing ◽  
Analytical Frameworks

Following the Deepwater Horizon oil spill of 2010, a substantial body of research has focused on the development of computational tools and analytical frameworks for modeling oil spill events. Much of this work is dedicated to deepening our understanding of the interactions between oil, fragile ecosystems, and the environment, as well as the impacts of oil on human settlements which are vulnerable to spill events. These advances in oil spill modeling and associated analytics have not only increased the efficiency of spill interdiction and mitigation efforts, they have also helped to nurture proactive, versus reactive, response strategies and plans for local and regional stakeholders. The purpose of this paper is to provide a progress report on the wide range of computational tools, analytical frameworks, and emerging technologies which are necessary inputs for a complete oil spill modeling package. Specifically, we explore the use of relatively mature tools, such as dedicated spill modeling packages, geographic information systems (GIS), and remote sensing, as well emerging technologies such as aerial and aquatic drones and other in-situ sensing technologies. The integration of these technologies and the advantages associated with using a geographic lens for oil spill modeling are discussed.

scholarly journals Hematopoiesis in 3 dimensions: human and murine bone marrow architecture visualized by confocal microscopy

Blood ◽  
2010 ◽  
Vol 116 (15) ◽  
pp. e41-e55 ◽  
Author(s):  
Tomoiku Takaku ◽  
Daniela Malide ◽  
Jichun Chen ◽  
Rodrigo T. Calado ◽  
Sachiko Kajigaya ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Three Dimensional ◽  
Cell Types ◽  
Bone Marrow Tissue ◽  
Murine Bone Marrow ◽  
3 Dimensional ◽  
Vascular Structures ◽  
Bone Structures ◽  
Surrounding Bone

AbstractIn many animals, blood cell production occurs in the bone marrow. Hematopoiesis is complex, requiring self-renewing and pluripotent stem cells, differentiated progenitor and precursor cells, and supportive stroma, adipose tissue, vascular structures, and extracellular matrix. Although imaging is a vital tool in hematology research, the 3-dimensional architecture of the bone marrow tissue in situ remains largely uncharacterized. The major hindrance to imaging the intact marrow is the surrounding bone structures are almost impossible to cut/image through. We have overcome these obstacles and describe a method whereby whole-mounts of bone marrow tissue were immunostained and imaged in 3 dimensions by confocal fluorescence and reflection microscopy. We have successfully mapped by multicolor immunofluorescence the localization pattern of as many as 4 cell features simultaneously over large tiled views and to depths of approximately 150 μm. Three-dimensional images can be assessed qualitatively and quantitatively to appreciate the distribution of cell types and their interrelationships, with minimal perturbations of the tissue. We demonstrate its application to normal mouse and human marrow, to murine models of marrow failure, and to patients with aplastic anemia, myeloid, and lymphoid cell malignancies. The technique should be generally adaptable for basic laboratory investigation and for clinical diagnosis of hematologic diseases.

scholarly journals N–doped hierarchical porous carbon nanoscrolls towards efficient oxygen reduction reaction in Zn–air batteries via interior and exterior modification

2021 ◽  
Author(s):  
Binhong He ◽  
Yangyang Chen ◽  
Da Hu ◽  
Ziyan Wen ◽  
Minjie Zhou ◽  
...  
Keyword(s):  
Oxygen Reduction Reaction ◽  
Oxygen Reduction ◽  
Rational Design ◽  
Clean Energy ◽  
Reduction Reaction ◽  
Hierarchical Porous Carbon ◽  
Hierarchical Porous ◽  
Carbon Nanoscrolls ◽  
Energy Conversion Devices

Rational design of oxygen reduction reaction (ORR) electrocatalysts is essential for promoting the development of clean energy conversion devices. Herein, we report an in–situ sacrificial template strategy combining with external...

scholarly journals In situ delivery of biobutyrate by probiotic Escherichia coli for cancer therapy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chung-Jen Chiang ◽  
Yan-Hong Hong
Keyword(s):  
Escherichia Coli ◽  
Cancer Therapy ◽  
Rational Design ◽  
Hypoxic Condition ◽  
Human Colorectal Cancer ◽  
Apoptosis Pathway ◽  
Mitochondrial Apoptosis Pathway ◽  
Cycle Arrest ◽  
Human Colorectal Cancer Cell

AbstractButyrate has a bioactive function to reduce carcinogenesis. To achieve targeted cancer therapy, this study developed bacterial cancer therapy (BCT) with butyrate as a payload. By metabolic engineering, Escherichia coli Nissle 1917 (EcN) was reprogrammed to synthesize butyrate (referred to as biobutyrate) and designated EcN-BUT. The adopted strategy includes construction of a synthetic pathway for biobutyrate and the rational design of central metabolism to increase the production of biobutyrate at the expense of acetate. With glucose, EcN-BUT produced primarily biobutyrate under the hypoxic condition. Furthermore, human colorectal cancer cell was administrated with the produced biobutyrate. It caused the cell cycle arrest at the G1 phase and induced the mitochondrial apoptosis pathway independent of p53. In the tumor-bearing mice, the injected EcN-BUT exhibited tumor-specific colonization and significantly reduced the tumor volume by 70%. Overall, this study opens a new avenue for BCT based on biobutyrate.

3D-IC Integration Using D2C or D2W Alignment Schemes Together with Local Oxide Reduction

2011 ◽  
Vol 2011 (DPC) ◽  
pp. 001291-001315
Author(s):  
Gilbert Lecarpentier ◽  
Jean-Stephane Mottet ◽  
Keith Cooper ◽  
Michael Stead
Keyword(s):  
Integrated Circuits ◽  
High Density ◽  
Oxide Reduction ◽  
3D Ic ◽  
3 Dimensional ◽  
Temperature Requirements

3-Dimensional interconnection of high density integrated circuits enables building devices with greater functionality with higher performances in a smaller space. This paper explores the chip-to-chip and chip-to-wafer alignment and the associated bonding techniques such as in-situ reflow or thermocompression with a local oxide reduction which contributes to higher yield together with reduction of the force or temperature requirements.

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