Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters.

The inability to scalably and precisely measure the activity of developmental cis-regulatory elements (CREs) in multicellular systems is a bottleneck in genomics. Here we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode stabilization via circularization, these scalable single-cell quantitative expression reporters provide high-contrast readouts, analogous to classic in situ assays but entirely from sequencing. Screening >200 regions of accessible chromatin in a multicellular in vitro model of early mammalian development, we identify 13 (8 previously uncharacterized) autonomous and cell-type-specific developmental CREs. We further demonstrate that chimeric CRE pairs generate cognate two-cell-type activity profiles and assess gain- and loss-of-function multicellular expression phenotypes from CRE variants with perturbed transcription factor binding sites. Single-cell quantitative expression reporters can be applied in developmental and multicellular systems to quantitatively characterize native, perturbed and synthetic CREs at scale, with high sensitivity and at single-cell resolution.

Protein kinase C activity modulates nuclear Lamin A/C dynamics in HeLa cells.

The nuclear lamina serves important functions in the nucleus, providing structural support to the nuclear envelope and contributing to chromatin organization. The primary proteins that constitute the lamina are nuclear lamins whose functions are impacted by post-translational modifications, including phosphorylation by protein kinase C (PKC). While PKC-mediated lamin phosphorylation is important for nuclear envelope breakdown during mitosis, less is known about interphase roles for PKC in regulating nuclear structure. Here we show that overexpression of PKC ß, but not PKC α, increases the Lamin A/C mobile fraction in the nuclear envelope in HeLa cells without changing the overall structure of Lamin A/C and Lamin B1 within the nuclear lamina. Conversely, knockdown of PKC ß, but not PKC α, reduces the Lamin A/C mobile fraction. Thus, we demonstrate an isoform-specific role for PKC in regulating interphase Lamin A/C dynamics outside of mitosis.

Support for management actions to protect night sky quality: Insights from visitors to state and national park units in the U.S.

Light pollution is a global phenomenon where anthropogenic light sources continue to grow unabated, affecting both social and ecological systems. This is leaving parks and protected areas as some of the last vestiges of naturally dark environments for protecting views of the night sky. Yet, even parks and protected areas have outdoor lighting. Alternative lighting practices are needed to reduce or prevent light pollution from within parks. However, making parks darker may not be desirable for some visitors if they believe it will reduce navigability, safety, or restrict how they recreate (e.g., requiring the use of red-light flashlights after dark and before dawn). How visitors will respond to alternative lighting practices that park managers can implement is still unknown. We used an on-site intercept survey at nine state and national park units in Utah, U.S., to investigate nighttime visitors' support or opposition to management actions to protect night sky quality and their interest in learning about topics related to night skies. Further, this study also segmented visitors into two groups: those 'dependent' on the dark sky as a resource and those whose activities did not depend on a dark sky. Defining what a 'dark sky dependent' visitor is, which has yet to be done in the literature, is a fundamental step to furthering night sky research and management efforts. Across nine parks and protected areas, 62% of nighttime visitors participated in dark sky dependent activities. Findings indicate broad support for management actions designed to improve night sky quality, with between 74% and 89% of all visitors supporting seven different management actions. There was stronger support from dark sky dependent visitors for some elements of alternative lighting practices, but there was still strong support for those who do not participate in dark sky dependent outdoor recreation. Additionally, between 57% and 75% of visitors were interested in learning more about topics related to night skies. This research indicates most visitors would welcome actions to preserve the quality of the rapidly dwindling naturally dark experiences offered by parks and protected areas.

Differential Eye Expression of Xenopus Acyltransferase Gnpat and Its Biochemical Characterization Shed Light on Lipid-Associated Ocular Pathologies.

Purpose: Plasmalogens (Plgs) are highly abundant lipids in the retina, and their deficiency leads to severe abnormalities during eye development. The first acylation step in the synthesis of Plgs is catalyzed by the enzyme glyceronephosphate O-acyltransferase (GNPAT), which is also known as dihydroxyacetone phosphate-acyltransferase (EC 2.3.1.42). GNPAT deficiency produces rhizomelic chondrodysplasia punctata type 2, a genetic disorder associated with developmental ocular defects. Despite the relevance of retinal Plgs, our knowledge of the mechanisms that regulate their synthesis, and the role of GNPAT during eye development is limited. Methods: Using the Xenopus laevis model organism, we characterized by in situ hybridization the expression pattern of gnpat and compared it to glycerol 3-phosphate acyltransferase mitochondrial (gpam or gpat1) during eye neurogenesis, lamination, and morphogenesis. The Xenopus Gnpat was biochemically characterized in a heterologous expression system in yeast. Results: During development, gnpat is expressed in proliferative cells of the retina and lens, and post-embryogenesis in proliferative cells of the ciliary marginal zone and lens epithelium. In contrast, gpam expression is mainly restricted to photoreceptors. Xenopus Gnpat expressed in yeast is present in both soluble and membrane fractions, but only the membrane-bound enzyme displays activity. The amino terminal of Gnpat, conserved in humans, shows lipid binding capacity that is enhanced by phosphatidic acid. Conclusions: Enzymes involved in the Plgs and glycerophospholipid biosynthetic pathways are differentially expressed during eye morphogenesis. The gnpat expression pattern and the molecular determinants regulating Gnpat activity advance our knowledge of this enzyme, contributing to our understanding of the retinal pathophysiology associated with GNPAT deficiency.

The social-ecological system of the Kenai River Fishery (Alaska, USA).

We present a collaboratively developed social-ecological model of the Kenai River Fishery. We developed the model through iterative interviews with stakeholders throughout the Kenai Peninsula using a novel participatory Fuzzy Cognitive Mapping process grounded in Ostrom's social-ecological systems framework. Individual social-ecological models, developed one-on-one with stakeholders, were combined into a single aggregated model representing the system's structure and function. We validated this aggregated model through subsequent interviews with stakeholders and focused literature reviews. The result is a model that can: 1) illustrate the breadth and interconnectedness of the Kenai River Fishery's social-ecological system; 2) be used to facilitate discussions around management of the fishery; and 3) be used to explore the components and interactions that move the system toward or away from sustainability. Using the model, we identify how the nature of salmon (migratory) and their habitat (large and unpredictable) leads to uncertainty about effective management strategies. This uncertainty, in addition to a large and diverse set of resource users, creates conflicting management goals that ultimately limit the governance system in making decisions that might increase the sustainability of the fishery.

Differentiation-dependent changes in lamin B1 dynamics and lamin B receptor localization.

The nuclear lamina serves important roles in chromatin organization and structural support, and lamina mutations can result in laminopathies. Less is known about how nuclear lamina structure changes during cellular differentiation-changes that may influence gene regulation. We examined the structure and dynamics of the nuclear lamina in human-induced pluripotent stem cells (iPSCs) and differentiated germ layer cells, focusing on lamin B1. We report that lamin B1 dynamics generally increase as iPSCs differentiate, especially in mesoderm and ectoderm, and that lamin B receptor (LBR) partially redistributes from the nucleus to cytoplasm in mesoderm. Knocking down LBR in iPSCs led to an increase in lamin B1 dynamics, a change that was not observed for ELYS, emerin, or lamin B2 knockdown. LBR knockdown also affected expression of differentiation markers. These data suggest that differentiation-dependent tethering of lamin B1 either directly by LBR or indirectly via LBR-chromatin associations impacts gene expression.

Do Prophylactic Inferior Vena Cava Filters Affect the Rates of Venous Thromboembolism and Pulmonary Embolism in Patients Undergoing Major Spine Surgery?

STUDY DESIGN: Retrospective Analysis. BACKGROUND: Venous thromboembolism (VTE) represents a significant cause of morbidity and mortality in major spine surgery. Placement of prophylactic inferior vena cava filters (IVCF) in patients undergoing major spine surgery was previously adopted at our institution. This study reports our experience and compares VTE rates between patients with and without preoperative IVCF placement. METHODS: A Retrospective comparative study was conducted on adult patients who underwent IVCF placement and those who did not prior to their spinal fusion procedure, between 2013 and 2016. Thoracolumbar fusions (anterior and/or posterior) of 7 or more levels, spinal osteotomies, and a minimum of a 3-month follow-up were included. Traumatic, oncologic, and cervical pathology were excluded. Primary outcomes measured included the incidence of overall VTE (DVT/PE), death, IVCF related complications, and IVCF retrieval. RESULTS: 386 patients who underwent major spine surgery, 258 met the eligibility criteria. Of those patients, 105 patients (40.7%) had prophylactic IVCF placement. All patients had postoperative SCDs and chemoprophylaxis. The presence of an IVCF was associated with an increased rate of overall VTE (14.3% vs 6.5%, P ≤ .05) and DVT episodes (8.6% vs 2.6%, P = .04). The rate of PE for the IVCF group and non-IVCF group was 8.6% and 4.6%, respectively, which was not statistically significant (P = .32). The all-cause mortality rate overall of 2.3% was statistically similar between both groups (P = 1.0). The IVCF group had higher rates of hematoma/seroma vs the non-IVCF group (12.4% vs 3.9%, P ≤ .05). 99 IVCFs were retrievable designs, and 85% were successfully retrieved. Overall IVCF-related complication rate was 11%. CONCLUSIONS: No statistical difference in PE or mortality rates existed between the IVCF and the control group. Patients with IVCF placement experienced approximately twice the rate of VTE and three times the rate of DVT compared to those without IVCF. The IVCF-related complication rate was 11%. Based on the results of this study, the authors recommend against the routine use of prophylactic IVCFs in adults undergoing major spine surgery. LEVEL OF EVIDENCE: III.

Persistent craniopharyngeal canal with an associated sphenoid sinus fistula.

Persistent craniopharyngeal canal (PCC) is a rare congenital anomaly that appears as a linear well-corticated canal running from the sella through the clivus and into the nasopharynx. Case reports of this anomaly have shown it is associated with a range of craniofacial defects, pituitary abnormalities, and meningoencephaloceles. It predisposes patients to bacterial meningitis. In this case a 46-year-old gentleman presenting for preoperative planning for surgical drainage of Potts Puffy tumor was found to have a PCC on CT and MRI. Imaging also demonstrated the presence of chronic inflammation and a fistula extending from the tract into the sphenoid sinus. This unusual presentation of a PCC with a sphenoid sinus fistula broadens the potential clinical presentations of PCC and further emphasizes the ability of this anomaly to serve as a conduit for CNS infection.

Antibiofilm Activity of PEGylated Branched Polyethylenimine.

Biofilm formation is an adaptive resistance mechanism that pathogens employ to survive in the presence of antimicrobials. Pseudomonas aeruginosa is an infectious Gram-negative bacterium whose biofilm allows it to withstand antimicrobial attack and threaten human health. Chronic wound healing is often impeded by P. aeruginosa infections and the associated biofilms. Previous findings demonstrate that 600 Da branched polyethylenimine (BPEI) can restore ß-lactam potency against P. aeruginosa and disrupt its biofilms. Toxicity concerns of 600 Da BPEI are mitigated by covalent linkage with low-molecular-weight polyethylene glycol (PEG), and, in this study, PEGylated BPEI (PEG350-BPEI) was found exhibit superior antibiofilm activity against P. aeruginosa. The antibiofilm activity of both 600 Da BPEI and its PEG derivative was characterized with fluorescence studies and microscopy imaging. We also describe a variation of the colony biofilm model that was employed to evaluate the biofilm disruption activity of BPEI and PEG-BPEI.

Refractory Ventricular Tachycardia and Seizures With Lacosamide Overdose.

We describe a 60-year-old female patient who suffered an apparently intentional overdose of lacosamide and who developed status epilepticus secondary to its toxicity, complicated by refractory ventricular arrhythmia necessitating advanced cardiac life support and percutaneous stellate ganglion blockade. Extracorporeal membrane oxygenation was considered, and arterial and venous small-bore sheaths were placed in order to allow for extracorporeal cardiopulmonary resuscitation if cardiac arrest recurred, but they were not ultimately used. She suffered an embolic left middle cerebral artery stroke but otherwise recovered from the episode. This eventful clinical course highlights the dangers of lacosamide in high doses.

A time-resolved, multi-symbol molecular recorder via sequential genome editing.

DNA is naturally well suited to serve as a digital medium for in vivo molecular recording. However, contemporary DNA-based memory devices are constrained in terms of the number of distinct 'symbols' that can be concurrently recorded and/or by a failure to capture the order in which events occur1. Here we describe DNA Typewriter, a general system for in vivo molecular recording that overcomes these and other limitations. For DNA Typewriter, the blank recording medium ('DNA Tape') consists of a tandem array of partial CRISPR-Cas9 target sites, with all but the first site truncated at their 5' ends and therefore inactive. Short insertional edits serve as symbols that record the identity of the prime editing guide RNA2 mediating the edit while also shifting the position of the 'type guide' by one unit along the DNA Tape, that is, sequential genome editing. In this proof of concept of DNA Typewriter, we demonstrate recording and decoding of thousands of symbols, complex event histories and short text messages; evaluate the performance of dozens of orthogonal tapes; and construct 'long tape' potentially capable of recording as many as 20 serial events. Finally, we leverage DNA Typewriter in conjunction with single-cell RNA-seq to reconstruct a monophyletic lineage of 3,257 cells and find that the Poisson-like accumulation of sequential edits to multicopy DNA tape can be maintained across at least 20 generations and 25 days of in vitro clonal expansion.

Medicine in Motion: Addressing Physician Burnout Through Fitness, Philanthropy, and Interdisciplinary Community Building.

Physician burnout is a public health crisis. Although recent studies underscore its prevalence, there are few rigorous studies examining its prevention, especially among medical students and residents. Prior interventions have centered on mindfulness techniques and flexible workload scheduling, yielding limited success. However, interventions that combine fitness with philanthropy and community building may be more effective. The purpose of this report is 2-fold: first, to provide a review of physician burnout and potential prevention mechanisms and, second, to present a case study of how Medicine in Motion (MiM) addresses these issues. MiM facilitates various athletic workouts, competitions, and other events for students and professionals in medicine, dentistry, nursing, and physical therapy to support wellness and charitable initiatives. This analysis identifies 4 barriers to physicians and those in the health care profession from participating in wellness activities: (1) insufficient awareness, (2) logistical challenges, (3) lack of purpose, and (4) absence of perceived support. To overcome these barriers, MiM provides a model toolkit for starting a grassroots movement against physician burnout that other health care institutions may emulate. Institutions should provide financial support for these wellness programs. Future research is needed to evaluate these combined exercise, philanthropic, and community building efforts.

Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region.

The ecological and oceanographic processes that drive the response of pelagic ocean microbiomes to environmental changes remain poorly understood, particularly in coastal upwelling ecosystems. Here we show that seasonal and interannual variability in coastal upwelling predicts pelagic ocean microbiome diversity and community structure in the Southern California Current region. Ribosomal RNA gene sequencing, targeting prokaryotic and eukaryotic microbes, from samples collected seasonally during 2014-2020 indicate that nitracline depth is the most robust predictor of spatial microbial community structure and biodiversity in this region. Striking ecological changes occurred due to the transition from a warm anomaly during 2014-2016, characterized by intense stratification, to cooler conditions in 2017-2018, representative of more typical upwelling conditions, with photosynthetic eukaryotes, especially diatoms, changing most strongly. The regional slope of nitracline depth exerts strong control on the relative proportion of highly diverse offshore communities and low biodiversity, but highly productive nearshore communities.

GABAB receptors in prelimbic cortex and basolateral amygdala differentially influence intertemporal decision making and decline with age.

The ability to decide adaptively between immediate vs. delayed gratification (intertemporal choice) is critical for well-being and is associated with a range of factors that influence quality of life. In contrast to young adults, many older adults show enhanced preference for delayed gratification; however, the neural mechanisms underlying this age difference in intertemporal choice are largely un-studied. Changes in signaling through GABAB receptors (GABABRs) mediate several age-associated differences in cognitive processes linked to intertemporal choice. The current study used a rat model to determine how GABABRs in two brain regions known to regulate intertemporal choice (prelimbic cortex; PrL and basolateral amygdala; BLA) contribute to age differences in this form of decision making in male rats. As in humans, aged rats showed enhanced preference for large, delayed over small, immediate rewards during performance in an intertemporal choice task in operant test chambers. Activation of PrL GABABRs via microinfusion of the agonist baclofen increased choice of large, delayed rewards in young adult rats but did not influence choice in aged rats. Conversely, infusion of baclofen into the BLA strongly reduced choice of large, delayed rewards in both young adult and aged rats. Aged rats further showed a significant reduction in expression of GABABR1 subunit isoforms in the prefrontal cortex, a discovery that is consonant with the null effect of intra-PrL baclofen on intertemporal choice in aged rats. In contrast, expression of GABABR subunits was generally conserved with age in the BLA. Jointly, these findings elucidate a role for GABABRs in intertemporal choice and identify fundamental features of brain maturation and aging that mediate an improved ability to delay gratification.

An Analysis of the Evidence Underpinning the American Urologic Association Clinical Practice Guidelines.

OBJECTIVE: To evaluate the reporting quality of systematic reviews (SRs) underpinning the American Urologic Association (AUA) clinical practice guidelines (CPGs). METHODS: We searched the AUA for CPGs from 2015-2021. We extracted all SRs from the reference sections and two independent investigators evaluated eligible SR/meta-analysis using the PRISMA (Preferred Reporting Instrument for Systematic Reviews and Meta-Analyses) and AMSTAR-2 (A Measurement Tool to Assess Systematic Reviews 2) instruments. We compared SRs conducted by the Cochrane group to non-Cochrane SRs using a Mann-Whitney test. A multivariate regression was used to compare study characteristics. RESULTS: Eighteen CPG's met inclusion criteria. We extracted 120 unique SRs, which accounted for 5.1% (n = 120/2346) of all citations. Mean percent adherence to PRISMA and AMSTAR-2 was 65.4% -d 55.2% respectively. SRs conducted by the Cochrane Collaboration scored higher on AMSTAR-2 compared to non-Cochrane (z = -4.41, P <.01) and a positive correlation between PRISMA and AMSTAR-2 scores (r = 0.56, P <.001) was determined. CONCLUSION: Our study indicated the quality of SRs used to develop AUA CPGs across both PRISMA and AMSTAR-2 was variable. Despite higher evaluations, Cochrane SRs accounted for less than 15% of SRs underpinning CPG recommendations. Given the importance placed on CPGs within clinical practice, we recommended a synergistic relationship between the AUA and the Cochrane Collaboration to increase the number of quality urologic SRs.

Early Prostate-Specific Antigen Kinetics for Low- and Intermediate-Risk Prostate Cancer Treated With Definitive Radiation Therapy.

PURPOSE: This study used a patient-specific model to characterize and compare ideal prostate-specific antigen (PSA) kinetics for low- and intermediate-risk prostate cancer after definitive radiation treatment with conventionally fractionated, hypofractionated, stereotactic body radiation therapy, or brachytherapy, both high-dose and low-dose rate. METHODS AND MATERIALS: This retrospective analysis includes low- and intermediate-risk patients with prostate cancer treated between 1998 and 2018 at an National Cancer Institute-designated comprehensive cancer center. Demographics and treatment characteristics were prospectively collected. Patients had at least 2 PSA measurements within 24 months of treatment and were free from biochemical recurrence. The incidence of, time to, and risk factors for PSA nadir (nPSA) and bounce (bPSA) were analyzed at 24 months after radiation therapy. Ideal PSA kinetics were characterized for each modality and compared. RESULTS: Of 1042 patients, 45% had low-risk cancer, 37% favorable intermediate risk, and 19% unfavorable intermediate risk. nPSAs were higher for ablative modalities, both as absolute nPSA and relative to initial PSA. Median time to nPSA ranged from 14.8 to 17.1 months. Over 50% treated with nonablative therapy (conventionally fractionated, hypofractionated, and low-dose rate) reached an nPSA threshold of ≤0.5 ng/mL compared with 23% of stereotactic body radiation therapy and 33% of high-dose rate cohorts. The incidence of bPSA was 13.3% and not affected by treatment modality, Gleason score, or prostate volume. PSA decay rate was faster for ablative therapies in the 6- to 24-month period. CONCLUSIONS: Analysis of PSA within 24 months after radiation therapy revealed ablative therapies are associated with a latent PSA response and higher nPSA. Multivariable logistics modeling revealed younger age, initial PSA above the median, presence of bPSA, and ablative therapy as predictors for not achieving nPSA ≤0.5 ng/mL. PSA decay rate appears to be faster in ablative therapies after a latent period. Understanding the different PSA kinetic profiles is necessary to assess treatment response and survey for disease recurrence.

Precise genomic deletions using paired prime editing.

Current methods to delete genomic sequences are based on clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 and pairs of single-guide RNAs (sgRNAs), but can be inefficient and imprecise, with errors including small indels as well as unintended large deletions and more complex rearrangements. In the present study, we describe a prime editing-based method, PRIME-Del, which induces a deletion using a pair of prime editing sgRNAs (pegRNAs) that target opposite DNA strands, programming not only the sites that are nicked but also the outcome of the repair. PRIME-Del achieves markedly higher precision than CRISPR-Cas9 and sgRNA pairs in programming deletions up to 10 kb, with 1-30% editing efficiency. PRIME-Del can also be used to couple genomic deletions with short insertions, enabling deletions with junctions that do not fall at protospacer-adjacent motif sites. Finally, extended expression of prime editing components can substantially enhance efficiency without compromising precision. We anticipate that PRIME-Del will be broadly useful for precise, flexible programming of genomic deletions, epitope tagging and, potentially, programming genomic rearrangements.

Systematic review: investigating the added diagnostic value of gadolinium contrast agents for osteomyelitis in the appendicular skeleton.

OBJECTIVE: Osteomyelitis is an infection of the bone marrow. MRI with gadolinium-based contrast is frequently performed for cases of suspected osteomyelitis. The objective of this systematic review is to examine the diagnostic accuracy of contrast-enhanced vs non-contrast-enhanced MRI for osteomyelitis in the appendicular skeleton. MATERIALS AND METHODS: We conducted a systematic review of MRI in the diagnosis of osteomyelitis by searching MEDLINE and EMBASE from January 2000 to March 2020. There were 21 studies that met the inclusion criteria for the systematic review for a total of 1095 patients. Analytic methods were based on Preferred Reporting Items for Systematic Reviews and Meta-Analyses. Evidence was evaluated using the STARD criteria for evaluation of completeness and transparency of reporting. RESULTS: For diagnosing osteomyelitis in the appendicular skeleton, MRI with gadolinium-based contrast has 89% sensitivity (95% CI, 86-92%), 79% specificity (95% CI, 75-83%), and 90% overall diagnostic accuracy ([SE] = 0.03). For diagnosing osteomyelitis in the appendicular skeleton, MRI without gadolinium-based contrast has a 92% sensitivity (95% CI, 87-96%), 89% specificity (95% CI, 84-93%), and 96% overall diagnostic accuracy ([SE] = 0.03). The median score of included studies was 85% utilizing the STARD criteria with excellent interobserver agreement of 83.4%. Limitations included small sample size of studies, with retrospective designs. CONCLUSION: No evidence was found to suggest an added diagnostic value of gadolinium contrast for the diagnosis of osteomyelitis in the appendicular skeleton. For routine cases of suspected non-spinal osteomyelitis, non-contrast MRI of the area of interest is the next most appropriate study after radiographs.

Intraseasonal predictability of natural phytoplankton population dynamics.

It is difficult to make skillful predictions about the future dynamics of marine phytoplankton populations. Here, we use a 22-year time series of monthly average abundances for 198 phytoplankton taxa from Station L4 in the Western English Channel (1992-2014) to test whether and how aggregating phytoplankton into multi-species assemblages can improve predictability of their temporal dynamics. Using a non-parametric framework to assess predictability, we demonstrate that the prediction skill is significantly affected by how species data are grouped into assemblages, the presence of noise, and stochastic behavior within species. Overall, we find that predictability one month into the future increases when species are aggregated together into assemblages with more species, compared with the predictability of individual taxa. However, predictability within dinoflagellates and larger phytoplankton (>12 µm cell radius) is low overall and does not increase by aggregating similar species together. High variability in the data, due to observational error (noise) or stochasticity in population growth rates, reduces the predictability of individual species more than the predictability of assemblages. These findings show that there is greater potential for univariate prediction of species assemblages or whole-community metrics, such as total chlorophyll or biomass, than for the individual dynamics of phytoplankton species.