scholarly journals The role of high-throughput transcriptome analysis in metabolic engineering

2005 ◽  
Vol 10 (5) ◽  
pp. 385-399 ◽  
Author(s):  
Michael C. Jewett ◽  
Ana Paula Oliveira ◽  
Kiran Raosaheb Patil ◽  
Jens Nielsen
Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 466
Author(s):  
Marie-Christine Carpentier ◽  
Cécile Bousquet-Antonelli ◽  
Rémy Merret

The recent development of high-throughput technologies based on RNA sequencing has allowed a better description of the role of post-transcriptional regulation in gene expression. In particular, the development of degradome approaches based on the capture of 5′monophosphate decay intermediates allows the discovery of a new decay pathway called co-translational mRNA decay. Thanks to these approaches, ribosome dynamics could now be revealed by analysis of 5′P reads accumulation. However, library preparation could be difficult to set-up for non-specialists. Here, we present a fast and efficient 5′P degradome library preparation for Arabidopsis samples. Our protocol was designed without commercial kit and gel purification and can be easily done in one working day. We demonstrated the robustness and the reproducibility of our protocol. Finally, we present the bioinformatic reads-outs necessary to assess library quality control.


2021 ◽  
Vol 22 (6) ◽  
pp. 3010
Author(s):  
Michal Szeremeta ◽  
Karolina Pietrowska ◽  
Anna Niemcunowicz-Janica ◽  
Adam Kretowski ◽  
Michal Ciborowski

Forensic toxicology and forensic medicine are unique among all other medical fields because of their essential legal impact, especially in civil and criminal cases. New high-throughput technologies, borrowed from chemistry and physics, have proven that metabolomics, the youngest of the “omics sciences”, could be one of the most powerful tools for monitoring changes in forensic disciplines. Metabolomics is a particular method that allows for the measurement of metabolic changes in a multicellular system using two different approaches: targeted and untargeted. Targeted studies are focused on a known number of defined metabolites. Untargeted metabolomics aims to capture all metabolites present in a sample. Different statistical approaches (e.g., uni- or multivariate statistics, machine learning) can be applied to extract useful and important information in both cases. This review aims to describe the role of metabolomics in forensic toxicology and in forensic medicine.


2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Pankaj Kumar ◽  
Ankita Mishra ◽  
Himanshu Sharma ◽  
Dixit Sharma ◽  
Mohammed Saba Rahim ◽  
...  

Author(s):  
Aleksandra Pekowska ◽  
Joaquin Zacarias-Cabeza ◽  
Jinsong Jia ◽  
Pierre Ferrier ◽  
Salvatore Spicuglia

2021 ◽  
Vol 118 (48) ◽  
pp. e2112107118
Author(s):  
Eduardo M. Bruch ◽  
Pierre Vilela ◽  
Lu Yang ◽  
Alexandra Boyko ◽  
Norik Lexa-Sapart ◽  
...  

α-oxoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have been, so far, all considered to be structured around a high–molecular weight hollow core, consisting of up to 60 subunits of the acyltransferase component. We provide here evidence that Actinobacteria break the rule by possessing an acetyltranferase component reduced to its minimally active, trimeric unit, characterized by a unique C-terminal helix bearing an actinobacterial specific insertion that precludes larger protein oligomerization. This particular feature, together with the presence of an odhA gene coding for both the decarboxylase and the acyltransferase domains on the same polypetide, is spread over Actinobacteria and reflects the association of PDH and ODH into a single physical complex. Considering the central role of the pyruvate and 2-oxoglutarate nodes in central metabolism, our findings pave the way to both therapeutic and metabolic engineering applications.


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