Rescue of splicing-mediated intron loss maximizes expression in lentiviral vectors containing the human ubiquitin C promoter.

Lentiviral vectors almost universally use heterologous internal promoters to express transgenes. One of the most commonly used promoter fragments is a 1.2-kb sequence from the human ubiquitin C (UBC) gene, encompassing the promoter, some enhancers, first exon, first intron and a small part of the second exon of UBC. Because splicing can occur after transcription of the vector genome during vector production, we investigated whether the intron within the UBC promoter fragment is faithfully transmitted to target cells. Genetic analysis revealed that more than 80% of proviral forms lack the intron of the UBC promoter. The human elongation factor 1 alpha (EEF1A1) promoter fragment intron was not lost during lentiviral packaging, and this difference between the UBC and EEF1A1 promoter introns was conferred by promoter exonic sequences. UBC promoter intron loss caused a 4-fold reduction in transgene expression. Movement of the expression cassette to the opposite strand prevented intron loss and restored full expression. This increase in expression was mostly due to non-classical enhancer activity within the intron, and movement of putative intronic enhancer sequences to multiple promoter-proximal sites actually repressed expression. Reversal of the UBC promoter also prevented intron loss and restored full expression in bidirectional lentiviral vectors

The Origin of Double-peaked Narrow Lines in Active Galactic Nuclei. IV. Association with Galaxy Mergers

Double-peaked narrow emission lines in active galactic nucleus (AGN) spectra can be produced by AGN outflows, rotation, or dual AGNs, which are AGN pairs in ongoing galaxy mergers. Consequently, double-peaked narrow AGN emission lines are useful tracers of the coevolution of galaxies and their supermassive black holes, as driven by AGN feedback and AGN fueling. We investigate this concept further with follow-up optical longslit observations of a sample of 95 Sloan Digital Sky Survey (SDSS) galaxies that have double-peaked narrow AGN emission lines. Based on a kinematic analysis of the longslit spectra, we confirm previous work that finds that the majority of double-peaked narrow AGN emission lines are associated with outflows. We also find that eight of the galaxies have companion galaxies with line-of-sight velocity separations < 500 km/s and physical separations <30 kpc. Since we find evidence of AGNs in both galaxies, all eight of these systems are compelling dual AGN candidates. Galaxies with double-peaked narrow AGN emission lines occur in such galaxy mergers at least twice as often as typical active galaxies. Finally, we conclude that at least 3% of SDSS galaxies with double-peaked narrow AGN emission lines are found in galaxy mergers where both galaxies are resolved in SDSS imaging.Comment: 14 pages, 2 figures, ApJ in pres

Reliable and accurate diagnostics from highly multiplexed sequencing assays

Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, and clinical use of HMSAs requires overcoming several computational, statistical and engineering challenges. Using recently acquired experimental data, we present and validate a computational workflow based on kallisto and bustools, that utilizes robust statistical methods and fast, memory efficient algorithms, to quickly, accurately and reliably process high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSA

Reactivating Fetal Hemoglobin Expression in Human Adult Erythroblasts Through BCL11A Knockdown Using Targeted Endonucleases.

We examined the efficiency, specificity, and mutational signatures of zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 systems designed to target the gene encoding the transcriptional repressor BCL11A, in human K562 cells and human CD34+ progenitor cells. ZFNs and TALENs were delivered as in vitro transcribed mRNA through electroporation; CRISPR/Cas9 was codelivered by Cas9 mRNA with plasmid-encoded guideRNA (gRNA) (pU6.g1) or in vitro transcribed gRNA (gR.1). Analyses of efficacy revealed that for these specific reagents and the delivery methods used, the ZFNs gave rise to more allelic disruption in the targeted locus compared to the TALENs and CRISPR/Cas9, which was associated with increased levels of fetal hemoglobin in erythroid cells produced in vitro from nuclease-treated CD34+ cells. Genome-wide analysis to evaluate the specificity of the nucleases revealed high specificity of this specific ZFN to the target site, while specific TALENs and CRISPRs evaluated showed off-target cleavage activity. ZFN gene-edited CD34+ cells had the capacity to engraft in NOD-PrkdcSCID-IL2Rγnull mice, while retaining multi-lineage potential, in contrast to TALEN gene-edited CD34+ cells. CRISPR engraftment levels mirrored the increased relative plasmid-mediated toxicity of pU6.g1/Cas9 in hematopoietic stem/progenitor cells (HSPCs), highlighting the value for the further improvements of CRISPR/Cas9 delivery in primary human HSPCs

A Satellite-Based Multi-Pollutant Index of Global Air Quality

Air pollution is a major health hazard that is responsible formillions of annual excess deaths worldwide. Simpleindicators are useful for comparative studies and to asses strends over time. The development of global indicators hasbeen impeded by the lack of ground-based observations in vast regions of the world. Recognition is growing of the need for amultipollutant approach to air quality to better represent human exposure. Here we introduce the prospect of amultipollutant air quality indicator based on observations from satellite remote sensing

Van der Waals density functional: Self-consistent potential and the nature of the van der Waals bond

We derive the exchange-correlation potential corresponding to the nonlocal van der Waals density functional [M. Dion, H. Rydberg, E. Schroder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004)]. We use this potential for a self-consistent calculation of the ground state properties of a number of van der Waals complexes as well as crystalline silicon. For the latter, where little or no van der Waals interaction is expected, we find that the results are mostly determined by semilocal exchange and correlation as in standard generalized gradient approximations (GGA), with the fully nonlocal term giving little effect. On the other hand, our results for the van der Waals complexes show that the self-consistency has little effect at equilibrium separations. This finding validates previous calculations with the same functional that treated the fully nonlocal term as a post GGA perturbation. A comparison of our results with wave-function calculations demonstrates the usefulness of our approach. The exchange-correlation potential also allows us to calculate Hellmann-Feynman forces, hence providing the means for efficient geometry relaxations as well as unleashing the potential use of other standard techniques that depend on the self-consistent charge distribution. The nature of the van der Waals bond is discussed in terms of the self-consistent bonding charge.Comment: submitted to Phys. Rev.

Reliable and accurate diagnostics from highly multiplexed sequencing assays

Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, and clinical use of HMSAs requires overcoming several computational, statistical and engineering challenges. Using recently acquired experimental data, we present and validate a computational workflow based on kallisto and bustools, that utilizes robust statistical methods and fast, memory efficient algorithms, to quickly, accurately and reliably process high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSA

Cost-effectiveness of Implementing Low-Tidal Volume Ventilation in Patients With Acute Lung Injury

Background: Despite widespread guidelines recommending the use of lung-protective ventilation (LPV) in patients with acute lung injury (ALI), many patients do not receive this lifesaving therapy. We sought to estimate the incremental clinical and economic outcomes associated with LPV and determined the maximum cost of a hypothetical intervention to improve adherence with LPV that remained cost-effective. Methods: Adopting a societal perspective, we developed a theoretical decision model to determine the cost-effectiveness of LPV compared to non-LPV care. Model inputs were derived from the literature and a large population-based cohort of patients with ALI. Cost-effectiveness was determined as the cost per life saved and the cost per quality-adjusted life-years (QALYs) gained. Results: Application of LPV resulted in an increase in QALYs gained by 15% (4.21 years for non-LPV vs 4.83 years for LPV), and an increase in lifetime costs of $7,233 per patient with ALI ($99,588 for non-LPV vs $106,821 for LPV). The incremental cost-effectiveness ratios for LPV were$22,566 per life saved at hospital discharge and $11,690 per QALY gained. The maximum, cost-effective, per patient investment in a hypothetical program to improve LPV adherence from 50 to 90$9,482. Results were robust to a wide range of economic and patient parameter assumptions. Conclusions: Even a costly intervention to improve adherence with low-tidal volume ventilation in patients with ALI reduces death and is cost-effective by current societal standards.NIH F32HL090220.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/84154/1/Cooke - CEA LPV.pd

High Quality, Low Cost Egg Incubator for BIC Church in Choma, Zambia

The Egg Incubator team is partnering with the Brethren in Christ Church located in Choma, Zambia to design a high-quality, low-cost chicken egg incubator to supply the pastors and church members with a means of food and income. The design will need to take into account the accessibility and cost of the tools and materials. The current prototype features separate heating and humidity systems, a control system to maintain a set temperature and humidity, and tilting egg racks. The heating system consists of two stovetop coils to produce heat and a fan to transfer it to the air. The humidifier utilizes an atomizer in a pan of water to create a mist that mixes with the hot air to create humidity. The control system uses a proportional integral derivative controller (PID) to keep the temperature at 37 ± 1 °C and the humidity at 60–70%. The egg racks are tilted by a motor that runs every 6 hours to prevent the embryos from sticking to the shell. With a fully functioning prototype, the team has begun to incubate 60 real fertilized eggs. During the 21-day incubation process, a final prototype iteration is being designed and will be built on-site in Zambia in May 2022. Funding for this work provided by The Collaboratory for Strategic Partnerships and Applied Research.https://mosaic.messiah.edu/engr2022/1004/thumbnail.jp