Site-specific regulation of RNA editing with ribose-modified nucleoside analogs in ADAR guide strands.

Adenosine Deaminases Acting on RNA (ADARs) are enzymes that catalyze the conversion of adenosine to inosine in RNA duplexes. These enzymes can be harnessed to correct disease-causing G-to-A mutations in the transcriptome because inosine is translated as guanosine. Guide RNAs (gRNAs) can be used to direct the ADAR reaction to specific sites. Chemical modification of ADAR guide strands is required to facilitate delivery, increase metabolic stability, and increase the efficiency and selectivity of the editing reaction. Here, we show the ADAR reaction is highly sensitive to ribose modifications (e.g. 4'-C-methylation and Locked Nucleic Acid (LNA) substitution) at specific positions within the guide strand. Our studies were enabled by the synthesis of RNA containing a new, ribose-modified nucleoside analog (4'-C-methyladenosine). Importantly, the ADAR reaction is potently inhibited by LNA or 4'-C-methylation at different positions in the ADAR guide. While LNA at guide strand positions -1 and -2 block the ADAR reaction, 4'-C-methylation only inhibits at the -2 position. These effects are rationalized using high-resolution structures of ADAR-RNA complexes. This work sheds additional light on the mechanism of ADAR deamination and aids in the design of highly selective ADAR guide strands for therapeutic editing using chemically modified RNA.

Complete genome sequence of Azrael100, a V cluster mycobacteriophage.

Azrael100, a cluster V siphoviral mycobacteriophage, was isolated from a garden in Johannesburg, South Africa. It can infect and lyse Mycobacterium smegmatis mc2155. The double-stranded DNA genome contains 78,063 base pairs with a GC content of 56.9%, with 141 predicted open reading frames, 23 tRNAs, and one tmRNA.

From Awareness to Action: Pathways to Equity in Pain Management.

This commentary calls for a shift in the identification, analysis, and treatment of disparities in pain management. We provide context and research that summarize social and structural determinants that contribute to disparities across multiple levels of the pain management continuum. Informed by the evidence, we provide guideposts for mitigating disparities in the assessment, diagnosis, and care provided to those experiencing pain, with a focus on highlighting the specific needs of marginalized communities and the importance of culturally appropriate and context-specific approaches to pain management. This commentary informs efforts to promote equity by identifying areas of concern, guiding interventions, and advocating for policies that aim to eliminate disparities in pain treatment. Researchers, health care providers, and organizations can collectively work to provide equitable culturally sensitive pain management and improve overall patient outcomes.

Complete Genome Sequence of Lopsy, a B1 Cluster Mycobacteriophage.

Lopsy is a siphovirus mycobacteriophage that is capable of lytic infection in Mycobacterium smegmatis. It is classified as a subcluster B1 mycobacteriophage and was isolated from soil in Estcourt, South Africa. The 68,542-bp double-stranded DNA genome is circularly permuted, has a GC content of 66.4%, and is predicted to contain 98 genes.

Complete Genome Sequence of Mycobacteriophage IgnatiusPatJac.

IgnatiusPatJac is a Siphoviridae mycobacteriophage capable of lytic infection in Mycobacterium smegmatis and Mycobacterium tuberculosis. It was isolated from damp soil in Johannesburg, South Africa. The 51,164-bp double-stranded DNA genome has a GC content of 63.6%, predicted to encode 93 genes. IgnatiusPatJac is classified as an A1 subcluster mycobacteriophage.

Detection of Mycobacterium tuberculosis Complex Bacilli and Nucleic Acids From Tongue Swabs in Young, Hospitalized Children.

Diagnosis of tuberculosis in pediatric patients remains challenging due to inherent difficulties associated with obtaining respiratory samples for molecular and culture-based testing. To address this, recent studies have highlighted the utility of tongue swabs to detect Mycobacterium tuberculosis genomic DNA in the oral epithelia of tuberculosis infected adults. It is unknown whether tongue swabs have similar utility for diagnosis of childhood tuberculosis and if the presence of DNA in these swabs was associated with whole bacilli. We therefore sought to conduct a preliminary assessment of the utility of tongue swabs to detect tubercle bacilli and their associated genetic material in young children. For this, we recruited hospitalized children with clinically diagnosed tuberculosis (n = 26) or lower respiratory tract infection (LRTI, n = 9). These categories were blinded for downstream laboratory tests, which included PCR, spoligotyping, smear microscopy, and culture. Mtb genomic DNA was detected by PCR only in clinically diagnosed TB cases [11/26 (31.4%)] and not in cases with LRTI. Of these, 5/11 [45.5%] were associated with a spoligotype. Spoligotyping also detected an additional six specimens that were negative by PCR. Using smear microscopy, 19/26 [73.1%] and 4/9 [44.4] were Mtb positive in the tuberculosis or LRTI categories respectively. We noted positive results on all three tests in 5/26 [19.2%] in the tuberculosis category and 0/9 in the LRTI category. All specimens were culture negative. Collectively, these preliminary data present a compelling case for broader testing of tongue swabs to diagnose tuberculosis in children where obtaining standard sputum specimens is not easy.

Occurrence of chlorinated volatile organic compounds (VOCs) in a sanitary sewer system: Implications for assessing vapor intrusion alternative pathways.

Sewer systems have been recently recognized as potentially important exposure pathways to consider during vapor intrusion assessments; however, this pathway has not been well-characterized and there is need for additional information about the occurrence of volatile organic compounds (VOCs) in sewer systems. This paper reports the results of sewer gas sampling conducted in a sanitary sewer over the years of 2014-2017. Sewer gas samples were collected and analyzed using several different techniques, including TO-15 (grab), TO-17 (passive), Radiello® (passive) and a novel continuous monitoring technique, the Autonomous Rugged Optical Multigas Analyzer (AROMA). The applicability of each of the different approaches used in this study is discussed in the context of investigating sanitary sewers as a vapor intrusion alternative pathway. The data confirmed that trichloroethylene (TCE) concentrations in sewer gas were detected adjacent to and extending hundreds of feet away from a previously defined vapor intrusion area, where TCE was a primary contaminant. TCE concentrations detected in sewer gas ranged from non-detect to 1600µg/m3. Temporal variability was observed in TCE concentrations over timescales that ranged from minutes to months to years at discrete sampling locations. Spatial variability in sewer gas concentrations was also observed throughout the study area. Temporal and spatial variability may be caused by groundwater contamination sources in the study area, as well as sewer gas transport mechanisms.