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1. DNA Retention, Human Rights, and the Landmark Decision That Underpinned the EU AI Act

   https://doi.org/10.1109/MTS.2024.3399248  

   Michael, Katina (June 2024, IEEE Technology and Society Magazine)

   Have You Ever wondered what governments that collect deoxyribonucleic acid (DNA), do with the data? In 2009, I completed a Masters in the Faculty of Law at the University of Wollongong Australia, exploring the impact of DNA storage in all its forms ( Figure 1 ). Encouraged by my thesis supervisor, Associate Professor Clive Harfield, formerly of the Center for Transnational Crime Prevention (CTCP) at UOW, I investigated the S and Marper case [1] , [4] 

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2. Engineered Acinetobacter baylyi ADP1-ISx Cells Are Sensitive DNA Biosensors for Antibiotic Resistance Genes and a Fungal Pathogen of Bats

   https://doi.org/10.1021/acssynbio.5c00360  

   Chuong, Jeffrey; Brown, Keaton W; Gifford, Isaac; Mishler, Dennis M; Barrick, Jeffrey E (July 2025, ACS Synthetic Biology)

   Naturally competent bacteria can be engineered into platforms for detecting environmental DNA. This capability could be used to monitor the spread of pathogens, invasive species, and resistance genes, among other applications. Here, we create Acinetobacter baylyi ADP1-ISx biosensors that detect specific target DNA sequences through natural transformation. We tested strains with DNA sensors that consisted of either a mutated antibiotic resistance gene (TEM-1 bla or nptII) or a counterselectable gene flanked by sequences from the fungus Pseudogymnoascus destructans, which causes white-nose syndrome in bats. Upon uptake of homologous DNA, recombination restored antibiotic resistance gene function or removed the counterselectable gene, enabling selection of cells that sensed the target DNA. The antibiotic resistance gene and P. destructans biosensors could detect as few as 3,000 or 5,000,000 molecules of their DNA targets, respectively, and their sensitivity was not affected by excess off-target DNA. These results demonstrate how A. baylyi can be reprogrammed into a modular platform for monitoring environmental DNA. 

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3. Early-Phase Drive to the Precursor Pool: Chloroviruses Dive into the Deep End of Nucleotide Metabolism

   https://doi.org/10.3390/v15040911  

   Dunigan, David D.; Agarkova, Irina V.; Esmael, Ahmed; Alvarez, Sophie; Van Etten, James L. (April 2023, Viruses)

   Viruses face many challenges on their road to successful replication, and they meet those challenges by reprogramming the intracellular environment. Two major issues challenging Paramecium bursaria chlorella virus 1 (PBCV-1, genus Chlorovirus, family Phycodnaviridae) at the level of DNA replication are (i) the host cell has a DNA G+C content of 66%, while the virus is 40%; and (ii) the initial quantity of DNA in the haploid host cell is approximately 50 fg, yet the virus will make approximately 350 fg of DNA within hours of infection to produce approximately 1000 virions per cell. Thus, the quality and quantity of DNA (and RNA) would seem to restrict replication efficiency, with the looming problem of viral DNA synthesis beginning in only 60–90 min. Our analysis includes (i) genomics and functional annotation to determine gene augmentation and complementation of the nucleotide biosynthesis pathway by the virus, (ii) transcriptional profiling of these genes, and (iii) metabolomics of nucleotide intermediates. The studies indicate that PBCV-1 reprograms the pyrimidine biosynthesis pathway to rebalance the intracellular nucleotide pools both qualitatively and quantitatively, prior to viral DNA amplification, and reflects the genomes of the progeny virus, providing a successful road to virus infection. 

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4. Downstream sequence-dependent RNA cleavage and pausing by RNA polymerase I

   https://doi.org/10.1074/jbc.RA119.011354  

   Scull, Catherine E.; Clarke, Andrew M.; Lucius, Aaron L.; Schneider, David Alan (January 2020, Journal of Biological Chemistry)

   null (Ed.)

   The sequence of the DNA template has long been thought to influence the rate of transcription by DNA-dependent RNA polymerases, but the influence of DNA sequence on transcription elongation properties of eukaryotic RNA polymerase I (Pol I) from Saccharomyces cerevisiae has not been defined. In this study, we observe changes in dinucleotide production, transcription elongation complex stability, and Pol I pausing in vitro in response to downstream DNA. In vitro studies demonstrate that AT-rich downstream DNA enhances pausing by Pol I and inhibits Pol I nucleolytic cleavage activity. Analysis of Pol I native elongating transcript sequencing data in Saccharomyces cerevisiae suggests that these downstream sequence elements influence Pol I in vivo . Native elongating transcript sequencing studies reveal that Pol I occupancy increases as downstream AT content increases and decreases as downstream GC content increases. Collectively, these data demonstrate that the downstream DNA sequence directly impacts the kinetics of transcription elongation prior to the sequence entering the active site of Pol I both in vivo and in vitro . 

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5. Cu( ii )-based DNA labeling identifies the structural link between transcriptional activation and termination in a metalloregulator

   https://doi.org/10.1039/d1sc06563g  

   Casto, Joshua; Mandato, Alysia; Hofmann, Lukas; Yakobov, Idan; Ghosh, Shreya; Ruthstein, Sharon; Saxena, Sunil (February 2022, Chemical Science)

   Understanding the structural and mechanistic details of protein-DNA interactions that lead to cellular defence against toxic metal ions in pathogenic bacteria can lead to new ways of combating their virulence. Herein, we examine the Copper Efflux Regulator (CueR) protein, a transcription factor which interacts with DNA to generate proteins that ameliorate excess free Cu( i ). We exploit site directed Cu( ii ) labeling to measure the conformational changes in DNA as a function of protein and Cu( i ) concentration. Unexpectedly, the EPR data indicate that the protein can bend the DNA at high protein concentrations even in the Cu( i )-free state. On the other hand, the bent state of the DNA is accessed at a low protein concentration in the presence of Cu( i ). Such bending enables the coordination of the DNA with RNA polymerase. Taken together, the results lead to a structural understanding of how transcription is activated in response to Cu( i ) stress and how Cu( i )-free CueR can replace Cu( i )-bound CueR in the protein-DNA complex to terminate transcription. This work also highlights the utility of EPR to measure structural data under conditions that are difficult to access in order to shed light on protein function. 

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