Memory system and carbon trap

[git-cgalan]

DNA-based memory devices for recording cellular events

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6492567/

description

Description of all the existing measuring biological data across time and space using DNA (from detecting to interpreting) an their applications.

advantages of these recording system

• variety of signals can be taken as input
• possible to integrate information at the most relevant step of gene expression
• It can overcome the current problem of accessibility to the measurement
• It can overcome the current problem of generalized multiplexed measurements

The system has 3 major steps : sensing, writing and reading

      _signals_

• NATURE : mRNA, protein, metabolites, TFs an physical parameters (i.e. temperature, pH, oxidative stress, radiation levels, or electrochemical and electromagnetic gradient)
• SENSOR : specific biosensor (already big library), antigens, ligands

• TRANFORMATION : Crispr, tuning expression levels of recording machinery, protein engineering Can be optimized feedback loop, scaffold proteins, logic circuit,

    _writing_

• use nucleotides as bit of information
• addressing the location of the modification
• diversity of operation (i.e. insertion, substitution, deletion, one or several nucleotide)
• directional writing to scan the order of the recorded phenomenon

• site stochastic/flexible/specific writing exists depending application (the article cite some of them)

     _reading_

• using PCR to access the bases
• restriction digestion and PCR
• fluorescent reporters transcription (need to insert in the written record sequence)
• other optical in situ readout like FISH once the reading process has been done we have to think to a data processing process / making a model can also be useful

already existing systems

important point about the design

• anticipate the timescale/duration of the system
• capacity of storage
• accuracy and stability of the storage
• check the compatibility of the organism and the contruct otherwise it may impact cell growth rate and healthiness this will be possible by assessing the info collected from the first constructs

possible applications

• monitor populations and track cellular processes
• assess environment and record possible perturbations
• activate reporters or responses a concrete example can be to create a cellular sentinel which act as black blox to evaluate toxicity in the environment or pathogen attack cycle in the gut microbiota through recording inflammation.

main challenges for this range of techniques

• highly multiplexed recording
• fast reaction and low durability reaction recording
• quantifying variation
• stability of the recordings
• low cost, rapid and accurate data readout
• in vivo data processing

my opinion

This article is super interesting! there is many infos and the 4 systems that are presented seem to have a lot of applications. They are already really well designed but we can for sure improve them and find an great application of these DNA recording systems (diagnostic?, environment?). Following this 3 steps approach we can also easily design a new system where we choose the combiantion of the tools we want. Strong possibility to make a combo with biosensor and even associate a function.

[git-cgalan]

CO2-Fixation Strategies in Energy Extremophiles: What Can We Learn From Acetogens?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7146824/

description

Presentation of two different pathways present in extremophiles that represents a serious possible element of solution to solve the carbon trap problem. Focus on the main adaptations of those pathways and their efficiency.

the mechanisms

• each of the two pathways use a specific CO2 entry point and a common entry point, this process is called reductive acetyl-coA pathway
• the substrate are CO2 and H2
• the final products are acetone or methane and acetyl-coA
• this can occurs thanks to the use of low-potential electron and the associated membranous energy conserving enzymes

important enzymes

in methanogens:

• CO2 fixation complex = formyl-methanofuran dehydrogenase (Fwd) that transform CO2 to formate to formyl

in acetogens:

• CO2 fixation = formate dehydrogenase (Fdh, various form exists) that transform CO2 to formate + C1-carrier that transform formate to formyl

in both:

• formation of acetyl-coA = CO dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) that transform formyl in acetyl-coA

conclusion

these pathways are considered to be among the first, if not the first, biological energetic processes. The methanogenic one is sparing one ATP in the process so it seems more efficient. The acetonic one consume one ATP but produce one in through formation of the acetone. The two enzymes HDCR and Fdh are providing us a stable way to reversibly transform CO2 into formate and then into energy.