Human DNA Exonuclease TREX1 Is Also an Exoribonuclease That Acts on Single-Stranded RNA

3\u27 repair exonuclease 1 (TREX1) is a known DNA exonuclease involved in autoimmune disorders and the antiviral response. In this work, we show that TREX1 is also a RNA exonuclease. Purified TREX1 displays robust exoribonuclease activity that degrades single-stranded, but not double-stranded, RNA. TREX1-D200N, an Aicardi-Goutieres syndrome disease-causing mutant, is defective in degrading RNA. TREX1 activity is strongly inhibited by a stretch of pyrimidine residues as is a bacterial homolog, RNase T. Kinetic measurements indicate that the apparent Km of TREX1 for RNA is higher than that for DNA. Like RNase T, human TREX1 is active in degrading native tRNA substrates. Previously reported TREX1 crystal structures have revealed that the substrate binding sites are open enough to accommodate the extra hydroxyl group in RNA, further supporting our conclusion that TREX1 acts on RNA. These findings indicate that its RNase activity needs to be taken into account when evaluating the physiological role of TREX1

Secured Data Transmission Over Insecure Networks-on-Chip by Modulating Inter-Packet Delays

As the network-on-chip (NoC) integrated into an SoC design can come from an untrusted third party, there is a growing risk that data integrity and security get compromised when supposedly sensitive data flows through such an untrusted NoC. We thus introduce a new method that can ensure secure and secret data transmission over such an untrusted NoC. Essentially, the proposed scheme relies on encoding binary data as delays between packets travelling across the source and destination pair. The maximum data transmission rate of this inter-packet-delay (IPD)-based communication channel can be determined from the analytical model developed in this article. To further improve the undetectability and robustness of the proposed data transmission scheme, a new block coding method and communication protocol are also proposed. Experimental results show that the proposed IPD-based method can achieve a packet error rate (PER) of as low as 0.3% and an effective throughput of $\boldsymbol {2.3\times 10^{5}}$ b/s, outperforming the methods of thermal covert channel, cache covert channel, and circuit-based encryption and, thus, is suitable for secure data transmission in unsecure systems

Analytical methodology and pharmacokinetic study of elagolix in plasma of rats using a newly developed UPLC-MS/MS assay

Elagolix, as a competitive gonadotropin-releasing hormone (GnRH) receptor antagonist, has been recently approved by the US FDA for the management of moderate to severe pain due to endometriosis in women. In this study, we developed and verified an analysis assay to detect the concentration level of elagolix in plasma from rats after sample preparation based on a newly validated ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) technique in this study. The process of sample preparation used acetonitrile for a quick and easy protein precipitation method and diazepam was engaged as the internal standard (IS). Then, gradient elution was used to elute elagolix and IS. The mobile phase used in the present experiment was consisted of solvent A (acetonitrile) and solvent B (water having formic acid with the volume ratio of 0.1%), and the type of the C18 column used was named Acquity UPLC BEH C18 column with the specification of 2.1 mm × 100 mm, 1.7 μm. Multiple reaction monitoring (MRM) in positive ion mode for the experiment was engaged to detect the level of elagolix with electrospray ionization (ESI) source by m/z 632.4 → 529.5 transition for quantification and m/z 632.4 → 177.1 transition for qualification. It was found that the method in the scope of 1–2000 ng/mL indicated excellent linearity (r2 > 0.9983). The precision of this assay for intra-day was between 3.5 and 5.5%, and for inter-day was between 9.4 and 12.7%, respectively; the accuracy was 1.2–13.9% for the intra- and inter-day. The stability, extraction recovery, and matrix effect of the method were all in accordance with the rules of assay validation in biological medium proposed by FDA, whose application was also successfully used to determine the concentration of plasma elagolix from an experiment on pharmacokinetic investigation after oral administration of 15 mg/kg elagolix

Human DNA Exonuclease TREX1 Is Also an Exoribonuclease That Acts on Single-stranded RNA

3′ repair exonuclease 1 (TREX1) is a known DNA exonuclease involved in autoimmune disorders and the antiviral response. In this work, we show that TREX1 is also a RNA exonuclease. Purified TREX1 displays robust exoribonuclease activity that degrades single-stranded, but not double-stranded, RNA. TREX1-D200N, an Aicardi-Goutieres syndrome disease-causing mutant, is defective in degrading RNA. TREX1 activity is strongly inhibited by a stretch of pyrimidine residues as is a bacterial homolog, RNase T. Kinetic measurements indicate that the apparent Km of TREX1 for RNA is higher than that for DNA. Like RNase T, human TREX1 is active in degrading native tRNA substrates. Previously reported TREX1 crystal structures have revealed that the substrate binding sites are open enough to accommodate the extra hydroxyl group in RNA, further supporting our conclusion that TREX1 acts on RNA. These findings indicate that its RNase activity needs to be taken into account when evaluating the physiological role of TREX1. Background: 3′ repair exonuclease 1 (TREX1) is a DNase involved in autoimmune disorders and the antiviral response. Results: TREX1 also degrades single-stranded RNA or RNA in a RNA/DNA hybrid molecule. Conclusion: TREX1 is a human homolog of Escherichia coli RNase T. Significance: The novel RNase activity of TREX1 is crucial for understanding its physiological role

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field