Endosperm-Specific Chromatin Profiling by Fluorescence-Activated Nuclei Sorting and Chip-on-Chip

Author(s):  
Isabelle Weinhofer ◽  
Claudia Köhler
Keyword(s):  
On Chip ◽  
2015 ◽  
Vol 1 (1) ◽  
pp. 22 ◽  
Author(s):  
Giovanna Ambrosini ◽  
René Dreos ◽  
Philipp Bucher

Chromatin immunoprecipitation (ChIP) followed by highthroughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single ChIPseq experiment produces large amounts of highly reproducible data. The challenge is to extract knowledge from the data by thoughtful application of appropriate bioinformatics tools. Here we present a concise introduction into ChIP-seq data analysis in the form of a tutorial based on tools developed by our group. We expose biological questions, explain methods and provide guidelines for the interpretation of the results. While this article focuses on ChIP-seq, most of the algorithms and tools we present are applicable to other chromatin profiling assays based on next generation sequencing (NGS) technology as well.


2020 ◽  
Vol 477 (14) ◽  
pp. 2679-2696
Author(s):  
Riddhi Trivedi ◽  
Kalyani Barve

The intestinal microbial flora has risen to be one of the important etiological factors in the development of diseases like colorectal cancer, obesity, diabetes, inflammatory bowel disease, anxiety and Parkinson's. The emergence of the association between bacterial flora and lungs led to the discovery of the gut–lung axis. Dysbiosis of several species of colonic bacteria such as Firmicutes and Bacteroidetes and transfer of these bacteria from gut to lungs via lymphatic and systemic circulation are associated with several respiratory diseases such as lung cancer, asthma, tuberculosis, cystic fibrosis, etc. Current therapies for dysbiosis include use of probiotics, prebiotics and synbiotics to restore the balance between various species of beneficial bacteria. Various approaches like nanotechnology and microencapsulation have been explored to increase the permeability and viability of probiotics in the body. The need of the day is comprehensive study of mechanisms behind dysbiosis, translocation of microbiota from gut to lung through various channels and new technology for evaluating treatment to correct this dysbiosis which in turn can be used to manage various respiratory diseases. Microfluidics and organ on chip model are emerging technologies that can satisfy these needs. This review gives an overview of colonic commensals in lung pathology and novel systems that help in alleviating symptoms of lung diseases. We have also hypothesized new models to help in understanding bacterial pathways involved in the gut–lung axis as well as act as a futuristic approach in finding treatment of respiratory diseases caused by dysbiosis.


2016 ◽  
Vol 136 (6) ◽  
pp. 244-249
Author(s):  
Takahiro Watanabe ◽  
Fumihiro Sassa ◽  
Yoshitaka Yoshizumi ◽  
Hiroaki Suzuki

2012 ◽  
Vol E95.C (7) ◽  
pp. 1244-1251 ◽  
Author(s):  
Koji TAKEDA ◽  
Tomonari SATO ◽  
Takaaki KAKITSUKA ◽  
Akihiko SHINYA ◽  
Kengo NOZAKI ◽  
...  

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