to encode a wide range of order-independent, sequential, and temporal logic and memory 26 operations. Furthermore, we show that these operators can be used to perform both digital and 27 analog computation, and record signaling dynamics and cellular states in a long-term, autonomous, 28 and minimally disruptive fashion. Finally, we show that the platform can be functionalized with The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/263657 doi: bioRxiv preprint first posted online Feb. 15, 2018; 3 Main Text: 40 Robust and scalable molecular recording and computation platforms in living cells are key to 41 enabling a broad range of bioengineering and biomedical applications. Unlike their silicon-based 42 counterparts that have access to large capacities of addressable memory registers, synthetic genetic 43 circuits currently have very limited information storage capacities and existing methods for 44 encoding information into cellular memory, as well as strategies for integrating such memory with 45 logic operations, are challenging to scale. 46 Genomic DNA is an ideal medium for biological memory since it is ubiquitously present, 47 naturally replicated at high fidelity within cells, and compatible with natural biological operations. 48 In recent years, several strategies for encoding biological information into DNA and integrating 49 these memories with cellular computers have been described (Farzadfard and Lu, 2014; Kalhor et 50 al., 2017; McKenna et al., 2016; Perli et al., 2016; Roquet et al., 2016; Siuti et al., 2013). However, 51 these methods remain limited in their encoding capacity and scalability. For example, site-specific 52 recombinases that flip or excise targeted DNA segments have been used to create digital memory, 53 sequential logic, and biological state machines in living cells (Roquet et al., 2016; Siuti et al., 54 2013). However, a different recombinase is required for every unique event that one wishes to 55 record, thus limiting the number of potential states that can be encoded into DNA memory. 56 Furthermore, distances between recombinase-recognition sites usually need to be several hundred 57 base pairs to achieve efficient recombination, thus increasing circuit size (Coppoolse et al., 2005; 58 Stark, 2017). Furthermore, recombinase sites must be pre-engineered into desired target sites, 59 which is time-and labor-intensive, especially if they are to be used in the genomic context. 60 To address these limitations, we previously developed the SCRIBE DNA writing and 61 molecular recording system, which uses in vivo single-stranded DNA expression to generate 62 precise mutations that accumulate into target genomic loci as a function of the magnitude and 63 duration of exposure to an input (Farzadfard and Lu, 2014). However, this approach has been 64 limited to bacteria thus far due to the requirement for specific recombination mechanisms. 65Alternative molecular recording strategies based on Cas9 ...

Highlights d DOMINO operators enable analog recording and continuous monitoring of cellular events d Various forms of logic can be built by layering multiple DOMINO operators d DOMINO allows online monitoring of DNA memory states without need for sequencing d DOMINO can be coupled with gene regulation for advanced memory and computation operations

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SUMMARY The genome-wide perturbation of transcriptional networks with CRISPR-Cas technology has primarily involved systematic and targeted gene modulation. Here, we developed PRISM (Perturbing Regulatory Interactions by Synthetic Modulators), a screening platform that uses randomized CRISPR-Cas transcription factors (crisprTFs) to globally perturb transcriptional networks. By applying PRISM to a yeast model of Parkinson’s disease (PD), we identified guide RNAs (gRNAs) that modulate transcriptional networks and protect cells from alpha-synuclein (αSyn) toxicity. One gRNA identified in this screen outperformed the most protective suppressors of αSyn toxicity reported previously, highlighting PRISM’s ability to identify modulators of important phenotypes. Gene expression profiling revealed genes differentially modulated by this strong protective gRNA that rescued yeast from αSyn toxicity when overexpressed. Human homologs of top-ranked hits protected against αSyn-induced cell death in a human neuronal PD model. Thus, high-throughput and unbiased perturbation of transcriptional networks via randomized crisprTFs can reveal complex biological phenotypes and effective disease modulators.

Background Although, preliminary reports of Severe Acute Respiratory Syndrome (SARS)-CoV-2 infection suggest that the infection causes a less severe illness in children, there is now growing evidence of other rare or even serious complications of disease. Case presentation During the recent COVID-19 pandemic in Kerman, Iran, two children (an 8 year-old boy and a 6 year-old girl) were referred to outpatient Clinic of Pediatric Rheumatology with complaints of limping. Both children had experienced fever and mild respiratory tract infection. At the beginning of the second week of infection, they developed joint effusion. They both tested positive for coronavirus infection and were therefore diagnosed with post Coronavirus reactive arthritis. Both children were treated successfully with rest and Non-Steroidal Anti-Inflammatory Drugs (NSAID). They did not have any medical problems in the two months fallow up. Conclusions These two cases suggest that COVID-19 may be rheumatogenic. Highlighting the need for awareness of physicians, especially pediatricians, regarding the pathogenesis margins of this virus, as late presentations are of great importance.