CCAR1 promotes DNA repair via alternative splicing.

DNA repair is directly performed by hundreds of core factors and indirectly regulated by thousands of others. We massively expanded a CRISPR inhibition and Cas9-editing screening system to discover factors indirectly modulating homology-directed repair (HDR) in the context of ∼18,000 individual gene knockdowns. We focused on CCAR1, a poorly understood gene that we found the depletion of reduced both HDR and interstrand crosslink repair, phenocopying the loss of the Fanconi anemia pathway. CCAR1 loss abrogated FANCA protein without substantial reduction in the level of its mRNA or that of other FA genes. We instead found that CCAR1 prevents inclusion of a poison exon in FANCA. Transcriptomic analysis revealed that the CCAR1 splicing modulatory activity is not limited to FANCA, and it instead regulates widespread changes in alternative splicing that would damage coding sequences in mouse and human cells. CCAR1 therefore has an unanticipated function as a splicing fidelity factor.

Single-nucleus sequencing reveals enriched expression of genetic risk factors in extratelencephalic neurons sensitive to degeneration in ALS.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by a progressive loss of motor function linked to degenerating extratelencephalic neurons/Betz cells (ETNs). The reasons why these neurons are selectively affected remain unclear. Here, to understand the unique molecular properties that may sensitize ETNs to ALS, we performed RNA sequencing of 79,169 single nuclei from cortices of patients and controls. In both patients and unaffected individuals, we found significantly higher expression of ALS risk genes in THY1+ ETNs, regardless of diagnosis. In patients, this was accompanied by the induction of genes involved in protein homeostasis and stress responses that were significantly induced in a wide collection of ETNs. Examination of oligodendroglial and microglial nuclei revealed patient-specific downregulation of myelinating genes in oligodendrocytes and upregulation of an endolysosomal reactive state in microglia. Our findings suggest that selective vulnerability of extratelencephalic neurons is partly connected to their intrinsic molecular properties sensitizing them to genetics and mechanisms of degeneration.

Application of environmental sampling to investigate a case of avian chlamydiosis in a pet store and breeding facility leading to mass bird exposures.

Chlamydia psittaci is a bacterium that causes chlamydiosis in birds and can cause zoonotic psittacosis in people. In November 2017, we received notification of a suspected case of avian chlamydiosis in a captive cockatiel (Nymphicus hollandicus) that was sold by an online pet bird retail and breeding facility in Washington State. We describe the investigation with emphasis on how environmental sampling was used to guide veterinary and public health interventions. Bird samples were collected either from pooled droppings, pooled plumage or individual nasal and choanal swabs. Environmental samples were obtained by swabbing cleaning mops, tables and cage structures. All samples were tested by polymerase chain reaction and positive samples underwent genotyping. Approximately 1000 birds representing four taxonomic orders were kept within an open-space warehouse. Eight of 14 environmental samples and one of two pooled faecal samples were positive for Chlamydia spp. The contaminating strain of Chlamydia spp. was identified as genotype A. The facility was closed for environmental disinfection, and all psittacines were treated with oral doxycycline for 45 days. Ten of 10 environmental and two of two pooled faecal samples were negative for C. psittaci 11 months after the completion of environmental disinfection and antimicrobial treatment. This investigation highlights the importance of preventing and mitigating pathogen incursion in an online pet retail and breeding facility. Environmental sampling is valuable to guide animal and public health interventions for control of C. psittaci, particularly when large numbers of birds are exposed to the pathogen.

Efficient generation of lower induced motor neurons by coupling Ngn2 expression with developmental cues.

Human pluripotent stem cells (hPSCs) are a powerful tool for disease modeling of hard-to-access tissues (such as the brain). Current protocols either direct neuronal differentiation with small molecules or use transcription-factor-mediated programming. In this study, we couple overexpression of transcription factor Neurogenin2 (Ngn2) with small molecule patterning to differentiate hPSCs into lower induced motor neurons (liMoNes/liMNs). This approach induces canonical MN markers including MN-specific Hb9/MNX1 in more than 95% of cells. liMNs resemble bona fide hPSC-derived MN, exhibit spontaneous electrical activity, express synaptic markers, and can contact muscle cells in vitro. Pooled, multiplexed single-cell RNA sequencing on 50 hPSC lines reveals reproducible populations of distinct subtypes of cervical and brachial MNs that resemble their in vivo, embryonic counterparts. Combining small molecule patterning with Ngn2 overexpression facilitates high-yield, reproducible production of disease-relevant MN subtypes, which is fundamental in propelling our knowledge of MN biology and its disruption in disease.

The Relative Importance of Vulnerability and Efficiency in COVID-19 Contact Tracing Programmes: A Discrete Choice Experiment.

Objectives: This study aims to assess the trade-offs between vulnerability and efficiency attributes of contact tracing programmes based on preferences of COVID-19 contact tracing practitioners, researchers and other relevant stakeholders at the global level. Methods: We conducted an online discrete choice experiment (DCE). Respondents were recruited globally to explore preferences according to country income level and the prevailing epidemiology of COVID-19 in the local setting. The DCE attributes represented efficiency (timeliness, completeness, number of contacts), vulnerability (vulnerable population), cooperation and privacy. A mixed-logit model and latent class analysis were used. Results: The number of respondents was 181. Timeliness was the most important attribute regardless of country income level and COVID-19 epidemiological condition. Vulnerability of contacts was the second most important attribute for low-to-lower-middle-income countries and third for upper-middle-to-high income countries. When normalised against conditional relative importance of timeliness, conditional relative importance of vulnerability ranged from 0.38 to 0.42. Conclusion: Vulnerability and efficiency criteria were both considered to be important attributes of contact tracing programmes. However, the relative values placed on these criteria varied significantly between epidemiological and economic context.

Loss of mouse Stmn2 function causes motor neuropathy.

Amyotrophic lateral sclerosis (ALS) is characterized by motor neuron degeneration accompanied by aberrant accumulation and loss of function of the RNA-binding protein TDP43. Thus far, it remains unresolved to what extent TDP43 loss of function directly contributes to motor system dysfunction. Here, we employed gene editing to find whether the mouse ortholog of the TDP43-regulated gene STMN2 has an important function in maintaining the motor system. Both mosaic founders and homozygous loss-of-function Stmn2 mice exhibited neuromuscular junction denervation and fragmentation, resulting in muscle atrophy and impaired motor behavior, accompanied by an imbalance in neuronal microtubule dynamics in the spinal cord. The introduction of human STMN2 through BAC transgenesis was sufficient to rescue the motor phenotypes observed in Stmn2 mutant mice. Collectively, our results demonstrate that disrupting the ortholog of a single TDP43-regulated RNA is sufficient to cause substantial motor dysfunction, indicating that disruption of TDP43 function is likely a contributor to ALS.

Molecular and genetic dissection of recursive splicing.

Intronic ratchet points (RPs) are abundant within long introns in the Drosophila genome and consist of juxtaposed splice acceptor and splice donor (SD) sites. Although they appear to encompass zero-nucleotide exons, we recently clarified that intronic recursive splicing (RS) requires a cryptic exon at the RP (an RS-exon), which is subsequently always skipped and thus absent from mRNA. In addition, Drosophila encodes a smaller set of expressed exons bearing features of RS. Here, we investigate mechanisms that regulate the choice between RP and RS-exon SDs. First, analysis of Drosophila RP SD mutants demonstrates that SD competition suppresses inclusion of cryptic exons in endogenous contexts. Second, characterization of RS-exon reporters implicates exonic sequences as influencing choice of RS-exon usage. Using RS-exon swap and mutagenesis assays, we show exonic sequences can determine RS-exon inclusion. Finally, we provide evidence that splicing can suppress utilization of RP SDs to enable RS-exon expression. Overall, multiple factors can influence splicing of Drosophila RS-exons, which usually result in their complete suppression as zero-nucleotide RPs, but occasionally yield translated RS-exons.

Evaluating the Addition of a Clinical Pharmacist Service to a Midlevel Provider-Driven Culture Follow-up Program in a Community Emergency Department.

Background: The impact that an antimicrobial stewardship program can have on an inpatient setting has been well documented, but there are limited data on the use of an antimicrobial stewardship program in the emergency department (ED). Objective: The objective of this study was to assess the impact of adding a pharmacist service to a midlevel provider-driven culture follow-up program in the ED on achieving optimal therapy. Methods: This was a quasi-experimental study with designations of pre- and post-interventions conducted at a large community hospital with the pre-intervention phase occurring from June 1, 2019, to August 31, 2019, and the post-intervention phase occurring from January 1, 2020, to March 31, 2020. The primary outcome was optimal antimicrobial therapy: a composite of optimal antibiotic, dose, and duration, prescribed after the culture resulted. Secondary outcomes included optimal antibiotic, dose, duration, and return to the ED within 30 days due to infection. Results: Optimal antimicrobial therapy received after the culture resulted occurred in 59 patients (26.81%) in the pre-implementation phase and 40 patients (43.96%) in the implementation phase (P = .003). For the secondary outcomes, optimal antibiotic choice occurred in 115 patients (52.27%) in the pre-implementation phase and 66 patients (72.53%) in the implementation phase (P = .001). Optimal antibiotic dose occurred in 113 patients (51.36%) in the pre-implementation phase and 65 patients (71.43%) in the implementation phase (P = .001). Optimal antibiotic duration occurred in 65 patients (29.55%) in the pre-implementation phase and 40 patients (43.96%) in the implementation phase (P = .014). Conclusions: The addition of a clinical pharmacist service in a midlevel provider-driven ED culture callback program resulted in an increased rate of achieving optimal antimicrobial therapy.

The Exon Junction Complex and intron removal prevent re-splicing of mRNA.

Accurate splice site selection is critical for fruitful gene expression. Recently, the mammalian EJC was shown to repress competing, cryptic, splice sites (SS). However, the evolutionary generality of this remains unclear. Here, we demonstrate the Drosophila EJC suppresses hundreds of functional cryptic SS, even though most bear weak splicing motifs and are seemingly incompetent. Mechanistically, the EJC directly conceals cryptic splicing elements by virtue of its position-specific recruitment, preventing aberrant SS definition. Unexpectedly, we discover the EJC inhibits scores of regenerated 5' and 3' recursive SS on segments that have already undergone splicing, and that loss of EJC regulation triggers faulty resplicing of mRNA. An important corollary is that certain intronless cDNA constructs yield unanticipated, truncated transcripts generated by resplicing. We conclude the EJC has conserved roles to defend transcriptome fidelity by (1) repressing illegitimate splice sites on pre-mRNAs, and (2) preventing inadvertent activation of such sites on spliced segments.

Miniaturized Fontan Circulation Assist Device: Chronic In Vivo Evaluation.

We have miniaturized and optimized our implantable rotary blood pump developed to provide long-term mechanical right heart support for patients who have failing Fontan circulation. The objective of this study was to evaluate the miniaturized Fontan circulation assist device (mini-FCAD) during 30-day sheep studies (n = 5). A complete right heart bypass was performed and all return flow was supported by the pump. Postoperatively, unfractionated heparin was given to maintain thromboelastography R times of 2× normal. The first two studies were terminated on day 0 and day 4 due to complications. In the final three studies, the animals remained healthy and were electively terminated at 30 ± 2 days. Pump flow was between 5 and 7 lpm, left atrial pressure remained normal, and inlet pressures were between 3 and 18 mm Hg with no incidents of suction. There was no evidence of hemolysis, end organ or pulmonary dysfunction, thromboembolic events, nor thermal damage to the surrounding tissue. Explanted devices from two studies were free of thrombi and in the third study there were unattached thrombi on the SVC inlet of the rotor. The mini-FCAD was successfully tested in vivo as a right heart replacement device demonstrating adequate circulatory support and normal physiologic pulmonary and venous pressures.

A neural m6A/Ythdf pathway is required for learning and memory in Drosophila.

Epitranscriptomic modifications can impact behavior. Here, we used Drosophila melanogaster to study N6-methyladenosine (m6A), the most abundant modification of mRNA. Proteomic and functional analyses confirm its nuclear (Ythdc1) and cytoplasmic (Ythdf) YTH domain proteins as major m6A binders. Assays of short term memory in m6A mutants reveal neural-autonomous requirements of m6A writers working via Ythdf, but not Ythdc1. Furthermore, m6A/Ythdf operate specifically via the mushroom body, the center for associative learning. We map m6A from wild-type and Mettl3 mutant heads, allowing robust discrimination of Mettl3-dependent m6A sites that are highly enriched in 5' UTRs. Genomic analyses indicate that Drosophila m6A is preferentially deposited on genes with low translational efficiency and that m6A does not affect RNA stability. Nevertheless, functional tests indicate a role for m6A/Ythdf in translational activation. Altogether, our molecular genetic analyses and tissue-specific m6A maps reveal selective behavioral and regulatory defects for the Drosophila Mettl3/Ythdf pathway.

Overlapping Activities of ELAV/Hu Family RNA Binding Proteins Specify the Extended Neuronal 3' UTR Landscape in Drosophila.

The tissue-specific deployment of highly extended neural 3' UTR isoforms, generated by alternative polyadenylation (APA), is a broad and conserved feature of metazoan genomes. However, the factors and mechanisms that control neural APA isoforms are not well understood. Here, we show that three ELAV/Hu RNA binding proteins (Elav, Rbp9, and Fne) have similar capacities to induce a lengthened 3' UTR landscape in an ectopic setting. These factors promote accumulation of chromatin-associated, 3' UTR-extended, nascent transcripts, through inhibition of proximal polyadenylation site (PAS) usage. Notably, Elav represses an unannotated splice isoform of fne, switching the normally cytoplasmic Fne toward the nucleus in elav mutants. We use genomic profiling to reveal strong and broad loss of neural APA in elav/fne double mutant CNS, the first genetic background to largely abrogate this distinct APA signature. Overall, we demonstrate how regulatory interplay and functionally overlapping activities of neural ELAV/Hu RBPs drives the neural APA landscape.

Test Process and Results of Potential Masking of Sterilizing-Grade Filters.

Pre-use/post-sterilization integrity testing (PUPSIT) has been a widely debated topic for the last several years. To a large extent, the debate is because of the fact that scientific data were not available to provide additional clarity that could inform appropriate risk-based judgements and commensurate actions. To gain clarity, the Parenteral Drug Association (PDA) and BioPhorum Organizations Group (BioPhorum) formed the Sterile Filtration Quality Risk Management (SFQRM) consortium in late 2017. The consortium goals have been to fill existing gaps in scientific data as adequately as possible with studies and industry guidance that would provide professionals and license holders with the ability to make informed decisions about appropriate risk-management strategies. This paper is one in a series of publications that are the result of the collaboration, and these should be considered together and viewed holistically in order to determine the best course of action with regard to PUPSIT. In total, the four papers cover the following areas: (1) data mining to determine the influence of fluid properties on integrity test values, (2) filter masking studies and results (this publication), (3) risk assessment and management from filter production to end use, and (4) points to consider in the best practice of the use of PUPSIT. In total, 25 manufacturers and filter suppliers have contributed to the work of the Consortium, deploying their filtration experts and pooling their collective knowledge and applied science experience to address these questions. This effort has also been supported by many independent experts currently available who have contributed to and driven the Filtration Interest Group in the PDA for many years. Both PDA and BioPhorum have prioritized this program and combined their approaches to deliver this comprehensive body of work. We hope that collectively the publications aid decision making and create greater certainty and confidence and above all alignment between suppliers, manufacturers, and regulators alike on these important questions.

Data Mining to Determine the Influence of Fluid Properties on the Integrity Test Values.

Eudralex volume 4, Annex 1, the European Union Good Manufacturing Practice for sterile products, requires that "The integrity of the sterilised filter should be verified before use" (1). Implicit in this requirement for a PUPSIT is the rationale that the sterilizing filter could sustain damage during sterilization or use (i.e., subsequent to any pre-use test conducted prior to sterilization), causing a defect which would not be detected by the post-use integrity ("masked" during filtration). To assess whether a filter defect could be masked by partial filter plugging, we evaluated the impact of the bacterial challenge test (BCT) on the bubble point (BP) of the test filters. The BP tests that are conducted before and after the BCT have been collected and compared for 2086 filters (1571 × test filters and 515 × control filters), representing 531 BCTs on 518 different pharmaceutical products, buffers, and in-process fluids. These tests comprise a cross section of fluids from multiple firms spanning the pharmaceutical and biotechnology industry. A posttest to pretest BP ratio was calculated for each filter and the distribution of these ratios examined to determine whether there were cases of elevation of the BP because of bacterial loading to the point where masking of a filter defect could occur; that is, if a defective filter could pass integrity testing due to apparent reduction in filter pore size because of the bacteria retained during the BCT. Ratios were averaged across all tests for the same test fluid. The mean average ratio was 1.00 ± 0.15, indicating that on the average, elevation of the BP does not occur. To assess the risk of masking a filter defect, observed BP ratios were compared to the ratio of the minimum BP specification of a 0.2 µm filter to that of a 0.45 µm filter of the same membrane type. The lowest such ratio for any membrane type was 1.33. A BP ratio equal to or higher than this ratio was considered a risk for masking, because a 0.45 µm filter could appear to meet the specifications of a 0.2 µm filter. Out of 518 average BP ratios, only eight fluids (1.5%) produced BP ratios meeting this criterion for a masking risk. Potential risk factors associated with these cases are discussed. We conclude that filtration processes producing BP changes sufficient to present a risk of masking defects are not common, and are detectable during the routine BCT. The BP ratios observed during routine BCT are one means to assess the potential of a given filtration process to mask defects and can be considered when determining whether a PUPSIT should be implemented.

Chronic In Vivo Test of a Right Heart Replacement Blood Pump for Failed Fontan Circulation.

An implantable rotary blood pump was developed to provide long-term mechanical right heart support for patients who have failing Fontan circulation. The objective of this study was to evaluate the pump in vivo in a 30 day sheep study. Pump speed was set at 3,900 rpm for the duration of the study, and pump power was between 4.3 and 4.6 W. The pump inlet pressures for the superior vena cava (SVC) and inferior vena cava (IVC) were 14 ± 15 and 11 ± 15 mm Hg, respectively, over the duration of the study. Hematocrit remained stable at 30% ± 4%. Partial thromboplastin time (PTT) steadily increased from 30 s preoperatively to a high of 59 s on postoperative day 20, while prothrombin time (PT) remained at 20 ± 2 s for the duration of the study. The implantation and postoperative recovery were successful, and the animal demonstrated normal physiologic pulmonary and venous pressures and cardiac output. On pump inspection, the IVC and SVC inlets were completely clear of any deposits, but there were small thrombi (approximately 0.5 mm diameter) between each of the three rotor blades and along 20% of the parting line of the two volute halves. A complete right heart bypass was performed, postoperative recovery was successful, and the pump demonstrated adequate circulatory support and normal physiologic pulmonary and venous pressures. This study was the first successful test of a right heart replacement device in a chronic animal study.

Vanishing spleen syndrome post right partial nephrectomy in a sicklemic patient.

Splenic infarction after contralateral laparoscopic renal surgery has not, to our knowledge, been reported. The spleen is the most affected organ in sickle cell disease and the mechanism of auto infarction is thought to result from the crystallization of abnormal hemoglobin during periods of hypoxia or acidosis resulting in parenchymal ischemia and ultimately tissue necrosis. We report a case of 45 year old female with sickle cell disease who had an unremarkable spleen at the time of a laparoscopic right partial nephrectomy and was subsequently found to have marked diminution in her splenic volume.

Rabies in a Dog Imported from Egypt - Connecticut, 2017.

In 2007, the United States successfully eliminated canine rabies virus variant. Globally, however, dogs remain the principal source of human rabies infections. Since 2007, three cases of canine rabies virus variant were reported in dogs imported into the United States, one each from India (2007), Iraq (2008), and Egypt (2015) (1-3). On December 20, 2017, a dog imported into the United States from Egypt was identified with rabies, representing the second case from Egypt in 3 years. An Egyptian-based animal rescue organization delivered four dogs from Cairo, Egypt, to a flight parent (a person solicited through social media, often not affiliated with the rescue organization, and usually compensated with an airline ticket), who transported the dogs to the United States. The flight parent arrived at John F. Kennedy International Airport (JFK) in New York City and, via transporters (persons who shuttle dogs from one state to another), transferred the dogs to foster families; the dogs ultimately were adopted in three states. The Connecticut Department of Public Health Laboratory (CDPHL) confirmed the presence of a canine rabies virus variant in one of the dogs, a male aged 6 months that was adopted by a Connecticut family. An investigation revealed the possibility of falsified rabies vaccination documentation presented on entry at JFK, allowing the unvaccinated dog entry to the United States. This report highlights the continuing risk posed by the importation of dogs inadequately vaccinated against rabies from high-risk countries and the difficulties in verifying any imported dog's health status and rabies vaccination history.