Discovery and Validation of Context-Dependent Synthetic Mammalian Promoters.

Cellular transcription enables cells to adapt to various stimuli and maintain homeostasis. Transcription factors bind to transcription response elements (TREs) in gene promoters, initiating transcription. Synthetic promoters, derived from natural TREs, can be engineered to control exogenous gene expression using endogenous transcription machinery. This technology has found extensive use in biological research for applications including reporter gene assays, biomarker development, and programming synthetic circuits in living cells. However, a reliable and precise method for selecting minimally-sized synthetic promoters with desired background, amplitude, and stimulation response profiles has been elusive. In this study, we introduce a massively parallel reporter assay library containing 6184 synthetic promoters, each less than 250 bp in length. This comprehensive library allows for rapid identification of promoters with optimal transcriptional output parameters across multiple cell lines and stimuli. We showcase this library's utility to identify promoters activated in unique cell types, and in response to metabolites, mitogens, cellular toxins, and agonism of both aminergic and non-aminergic GPCRs. We further show these promoters can be used in luciferase reporter assays, eliciting 50-100 fold dynamic ranges in response to stimuli. Our platform is effective, easily implemented, and provides a solution for selecting short-length promoters with precise performance for a multitude of applications.

Characterization of Altered Gene Expression and Histone Methylation in Peripheral Blood Mononuclear Cells Regulating Inflammation in COVID-19 Patients.

The pandemic of COVID-19 has caused >5 million deaths in the world. One of the leading causes of the severe form of COVID-19 is the production of massive amounts of proinflammatory cytokines. Epigenetic mechanisms, such as histone/DNA methylation, miRNA, and long noncoding RNA, are known to play important roles in the regulation of inflammation. In this study, we investigated if hospitalized COVID-19 patients exhibit alterations in epigenetic pathways in their PBMCs. We also compared gene expression profiles between healthy controls and COVID-19 patients. Despite individual variations, the expressions of many inflammation-related genes, such as arginase 1 and IL-1 receptor 2, were significantly upregulated in COVID-19 patients. We also found the expressions of coagulation-related genes Von Willebrand factor and protein S were altered in COVID-19 patients. The expression patterns of some genes, such as IL-1 receptor 2, correlated with their histone methylation marks. Pathway analysis indicated that most of those dysregulated genes were in the TGF-ß, IL-1b, IL-6, and IL-17 pathways. A targeting pathway revealed that the majority of those altered genes were targets of dexamethasone, which is an approved drug for COVID-19 treatment. We also found that the expression of bone marrow kinase on chromosome X, a member of TEC family kinases, was increased in the PBMCs of COVID-19 patients. Interestingly, some inhibitors of TEC family kinases have been used to treat COVID-19. Overall, this study provides important information toward identifying potential biomarkers and therapeutic targets for COVID-19 disease.

An interesting case of giant fusiform right coronary artery aneurysm.

Coronary artery aneurysm is an uncommon cardiovascular disease and a standard surgical approach is still not recognized. A 58-year-old man was referred to our department, after being investigated for worsening shortness of breath and tiredness, with a diagnosis of a 70 mm right coronary artery aneurysm. Surgical excision of the aneurysm and single vein graft on the posterior descending artery was performed, with satisfactory results.

Usefulness of extracorporeal membrane oxygenation in status asthmaticus with severe tracheal stenosis.

Extracorporeal membrane oxygenation, traditionally used to treat refractory hypoxemic respiratory failure due to acute respiratory distress syndrome, is being used to treat other etiologies of severe respiratory failure refractory to conventional mechanical ventilation. We present a 30-year-old woman with concomitant life-threatening airway obstruction due to severe tracheal stenosis and status asthmaticus treated effectively with veno-venous extracorporeal membrane oxygenation.

The Genesis of Pain Medicine as a Subspecialty in Anesthesiology.

Certification in pain medicine as a subspecialty in Anesthesiology was conceived in 1989 and first discussed by the American Board of Anesthesiology in 1990. Shortly thereafter, the ABA submitted an application to the American Board of Medical Specialties for recognition to certify in pain management. That was approved in 1991. The Accreditation Council of Graduate Medical Education approved an application from the Anesthesiology Residency Review Committee to accredit programs in pain management education and training in 1992. The first examination for Pain Management certification was given in 1993. The certificate was modified in 2002 to Pain Medicine rather than Pain Management. Five member boards of ABMS are now approved for certification in pain medicine and all use the ABA Pain Medicine examination.

Derivation of a quick Pitt bacteremia score to predict mortality in patients with Gram-negative bloodstream infection.

PURPOSE: This retrospective cohort study derived a "quick" version of the Pitt bacteremia score (qPitt) using binary variables in patients with Gram-negative bloodstream infections (BSI). The qPitt discrimination was then compared to quick sepsis-related organ failure assessment (qSOFA) and systemic inflammatory response syndrome (SIRS). METHODS: Hospitalized adults with Gram-negative BSI at Palmetto Health hospitals in Columbia, SC, USA from 2010 to 2013 were identified. Multivariate Cox proportional hazards regression was used to determine variables associated with 14-day mortality. RESULTS: Among 832 patients with Gram-negative BSI, median age was 65 years and 449 (54%) were women. After adjustments for age and Charleston comorbidity score, all five components of qPitt were independently associated with mortality: temperature < 36 °C [hazard ratio (HR) 3.02, 95% confidence interval (CI) 1.95-4.62], systolic blood pressure < 90 mmHg or vasopressor use (HR 2.40, 95% CI 1.37-4.13), respiratory rate ≥ 25/min or mechanical ventilation (HR 3.01, 95% CI 1.81-5.14), cardiac arrest (HR 5.35, 95% CI 2.81-9.43), and altered mental status (HR 3.99, 95% CI 2.44-6.80). The qPitt had higher discrimination to predict mortality [area under receiver operating characteristic curve (AUROC) 0.85] than both qSOFA (AUROC 0.77, p < 0.001) and SIRS (AUROC 0.63, p < 0.001). There was a significant difference in mortality between appropriate and inappropriate empirical antimicrobial therapy in patients with qPitt ≥ 2 (24% vs. 49%, p < 0.001), but not in those with qPitt < 2 (3% vs. 5%, p = 0.36). CONCLUSIONS: The qPitt had good discrimination in predicting mortality following Gram-negative BSI and identifying opportunities for improved survival with appropriate empirical antimicrobial therapy.

PICK1-Deficient Mice Exhibit Impaired Response to Cocaine and Dysregulated Dopamine Homeostasis.

Protein interacting with C-kinase 1 (PICK1) is a widely expressed scaffold protein known to interact via its PSD-95/discs-large/ZO-1 (PDZ)-domain with several membrane proteins including the dopamine (DA) transporter (DAT), the primary target for cocaine's reinforcing actions. Here, we establish the importance of PICK1 for behavioral effects observed after both acute and repeated administration of cocaine. In PICK1 knock-out (KO) mice, the acute locomotor response to a single injection of cocaine was markedly attenuated. Moreover, in support of a role for PICK1 in neuroadaptive changes induced by cocaine, we observed diminished cocaine intake in a self-administration paradigm. Reduced behavioral effects of cocaine were not associated with decreased striatal DAT distribution and most likely not caused by the ∼30% reduction in synaptosomal DA uptake observed in PICK1 KO mice. The PICK1 KO mice demonstrated preserved behavioral responses to DA receptor agonists supporting intact downstream DA receptor signaling. Unexpectedly, we found a prominent increase in striatal DA content and levels of striatal tyrosine hydroxylase (TH) in PICK1 KO mice. Chronoamperometric recordings showed enhanced DA release in PICK1 KO mice, consistent with increased striatal DA pools. Viral-mediated knock-down (KD) of PICK1 in cultured dopaminergic neurons increased TH expression, supporting a direct cellular effect of PICK1. In summary, in addition to demonstrating a key role of PICK1 in mediating behavioral effects of cocaine, our data reveal a so far unappreciated role of PICK1 in DA homeostasis that possibly involves negative regulation of striatal TH levels.

Risk factors for pneumonia due to beta-lactam-susceptible and beta-lactam-resistant Pseudomonas aeruginosa: a case-case-control study.

PURPOSE: This case-case-control study aims to identify clinical predictors for pneumonia due to Pseudomonas aeruginosa (PA) which is (1) susceptible to all routinely tested antipseudomonal beta-lactams (APBL-S) and (2) resistant to at least one antipseudomonal beta-lactam (APBL-R). METHODS: Hospitalized adults with acute bacterial pneumonia at Palmetto Health hospitals in Columbia, SC, USA from January 1, 2012 to April 15, 2014 were identified. Multivariate logistic regression was used to determine risk factors for pneumonia due to APBL-S PA and APBL-R PA. RESULTS: Among 326 unique patients, 119 had pneumonia due to APBL-S PA (cases), 44 due to APBL-R PA (cases) and 163 due to ceftriaxone-susceptible bacteria (controls). Bronchiectasis [odds ratio (OR) 5.7, 95% confidence intervals (CI) 1.3-39.2], interstitial lung disease (OR 6.2, 95% CI 1.5-42.6), prior airway colonization with APBL-S PA (OR 7.2, 95% CI 1.1-139.4) and recent exposure to both antipseudomonal beta-lactam (APBL; OR 2.2, 95% CI 1.1-4.5) and nonpseudomonal beta-lactams (OR 2.6, 95% CI 1.0-6.8) were independently associated with increased risk of APBL-S PA pneumonia. Bronchiectasis (OR 8.3, 95% CI 1.7-46.6), prior airway colonization with APBL-R PA (OR 14.9, 95% CI 2.0-312.9) and recent use of only APBL (OR 7.7, 95% CI 3.4-17.9) were predictors for APBL-R PA pneumonia. CONCLUSIONS: Stratification of hospitalized patients with pneumonia based on structural lung disease, prior airway colonization and recent antimicrobial exposure may improve empirical antimicrobial selection. Expansion of antimicrobial regimen from ceftriaxone to APBL or combination therapy is suggested in patients with risk factors for APBL-S or APBL-R PA, respectively.

Iron pill pneumonitis with reactive lymph nodes.

Iron pill pneumonitis can result from accidental aspiration. It usually presents as a triad of airway inflammation, aspiration, and hemosiderin deposition. We report a case of an elderly woman with chronic cough, infiltrates, and lymphadenopathy on imaging alongside nonnecrotizing granulomas on biopsy diagnosed with iron pill pneumonitis.

Intervertebral disc detection in X-ray images using faster R-CNN.

Automatic identification of specific osseous landmarks on the spinal radiograph can be used to automate calculations for correcting ligament instability and injury, which affect 75% of patients injured in motor vehicle accidents. In this work, we propose to use deep learning based object detection method as the first step towards identifying landmark points in lateral lumbar X-ray images. The significant breakthrough of deep learning technology has made it a prevailing choice for perception based applications, however, the lack of large annotated training dataset has brought challenges to utilizing the technology in medical image processing field. In this work, we propose to fine tune a deep network, Faster-RCNN, a state-of-the-art deep detection network in natural image domain, using small annotated clinical datasets. In the experiment we show that, by using only 81 lateral lumbar X-Ray training images, one can achieve much better performance compared to traditional sliding window detection method on hand crafted features. Furthermore, we fine-tuned the network using 974 training images and tested on 108 images, which achieved average precision of 0.905 with average computation time of 3 second per image, which greatly outperformed traditional methods in terms of accuracy and efficiency.

Ca2+ dependent surface trafficking of norepinephrine transporters depends on threonine 30 and Ca2+ calmodulin kinases.

The antidepressant-sensitive norepinephrine (NE) transporter (NET) inactivates NE released during central and peripheral neuronal activity by transport into presynaptic cells. Altered NE clearance due to dysfunction of NET has been associated with the development of mental illness and cardiovascular diseases. NET activity in vivo is influenced by stress, neuronal activity, hormones and drugs. We investigated the mechanisms of Ca2+ regulation of NET and found that Ca2+ influenced both Vmax and Km for NE transport into cortical synaptosomes. Changes in extracellular Ca2+ triggered rapid and bidirectional surface trafficking of NET expressed in cultured cells. Deletion of residues 28-47 in the NET NH2-terminus abolished the Ca2+ effect on surface trafficking. Mutagenesis studies identified Thr30 in this region as the essential residue for both Ca2+- dependent phosphorylation and trafficking of NET. Depolarization of excitable cells increased surface NET in a Thr30 dependent manner. A proteomic analysis, RNA interference, and pharmacological inhibition supported roles of CaMKI and CaMKII in Ca2+-modulated NE transport and NET trafficking. Depolarization of primary noradrenergic neurons in culture with elevated K+ increased NET surface expression in a process that required external Ca2+ and depended on CaMK activity. Hippocampal NE clearance in vivo was also stimulated by depolarization, and inhibitors of CaMK signaling prevented this stimulation. In summary, Ca2+ signaling influenced surface trafficking of NET through a CaMK-dependent mechanism requiring Thr30.

Fast scale-invariant lateral lumbar vertebrae detection and segmentation in X-ray images.

Fully automatic localization of lumbar vertebrae from clinical X-ray images is very challenging due to the variation of X-ray quality, scale, contrast, number of visible vertebrae, etc. To overcome these challenges, we present a novel framework, where we accelerate a scale-invariant object detection method using Support Vector Machines (SVM) trained on Histogram of Oriented Gradients (HOG) features and segmenting a fine vertebra contour using Gradient Vector Flow (GVF) based snake model. Support Vector Machines trained on HOG features are now an object detection standard in many perception fields and have demonstrated good performance on medical images as well. However, the computational complexity and lack of robustness brought by rescaling the original images have prevented its applicability. The proposed multistage detection framework uses lower-level detection result to determine the rescaling regions to reduce the region of interest, thereby decreasing the execution time. We further refine the detection result by segmenting the contour of vertebra using GVF snake, where we use edge detection techniques to increase the robustness of the GVF snake. Finally, we experimentally demonstrate the effectiveness of this framework using a large set of clinical X-ray images.

The evolution of an integrated ultrasound curriculum (iUSC) for medical students: 9-year experience.

Interest in ultrasound education in medical schools has increased dramatically in recent years as reflected in a marked increase in publications on the topic and growing attendance at international meetings on ultrasound education. In 2006, the University of South Carolina School of Medicine introduced an integrated ultrasound curriculum (iUSC) across all years of medical school. That curriculum has evolved significantly over the 9 years. A review of the curriculum is presented, including curricular content, methods of delivery of the content, student assessment, and program assessment. Lessons learned in implementing and expanding an integrated ultrasound curriculum are also presented as are thoughts on future directions of undergraduate ultrasound education. Ultrasound has proven to be a valuable active learning tool that can serve as a platform for integrating the medical student curriculum across many disciplines and clinical settings. It is also well-suited for a competency-based model of medical education. Students learn ultrasound well and have embraced it as an important component of their education and future practice of medicine. An international consensus conference on ultrasound education is recommended to help define the essential elements of ultrasound education globally to ensure ultrasound is taught and ultimately practiced to its full potential. Ultrasound has the potential to fundamentally change how we teach and practice medicine to the benefit of learners and patients across the globe.

Cardiomyocyte Regeneration in the mdx Mouse Model of Nonischemic Cardiomyopathy.

Endogenous regeneration has been demonstrated in the mammalian heart after ischemic injury. However, approximately one-third of cases of heart failure are secondary to nonischemic heart disease and cardiac regeneration in these cases remains relatively unexplored. We, therefore, aimed at quantifying the rate of new cardiomyocyte formation at different stages of nonischemic cardiomyopathy. Six-, 12-, 29-, and 44-week-old mdx mice received a 7 day pulse of BrdU. Quantification of isolated cardiomyocyte nuclei was undertaken using cytometric analysis to exclude nondiploid nuclei. Between 6-7 and 12-13 weeks, there was a statistically significant increase in the number of BrdU-labeled nuclei in the mdx hearts compared with wild-type controls. This difference was lost by the 29-30 week time point, and a significant decrease in cardiomyocyte generation was observed in both the control and mdx hearts by 44-45 weeks. Immunohistochemical analysis demonstrated BrdU-labeled nuclei exclusively in mononucleated cardiomyocytes. This study demonstrates cardiomyocyte regeneration in a nonischemic model of mammalian cardiomyopathy, controlling for changes in nuclear ploidy, which is lost with age, and confirms a decrease in baseline rates of cardiomyocyte regeneration with aging. While not attempting to address the cellular source of regeneration, it confirms the potential utility of innate regeneration as a therapeutic target.

Eating high fat chow decreases dopamine clearance in adolescent and adult male rats but selectively enhances the locomotor stimulating effects of cocaine in adolescents.

BACKGROUND: Feeding conditions can influence dopamine neurotransmission and impact behavioral and neurochemical effects of drugs acting on dopamine systems. This study examined whether eating high fat chow alters the locomotor effects of cocaine and dopamine transporter activity in adolescent (postnatal day 25) and adult (postnatal day 75) male Sprague-Dawley rats. METHODS: Dose-response curves for cocaine-induced locomotor activity were generated in rats with free access to either standard or high fat chow or restricted access to high fat chow (body weight matched to rats eating standard chow). RESULTS: Compared with eating standard chow, eating high fat chow increased the sensitivity of adolescent, but not adult, rats to the acute effects of cocaine. When tested once per week, sensitization to the locomotor effects of cocaine was enhanced in adolescent rats eating high fat chow compared with adolescent rats eating standard chow. Sensitization to cocaine was not different among feeding conditions in adults. When adolescent rats that previously ate high fat chow ate standard chow, sensitivity to cocaine returned to normal. As measured by chronoamperometry, dopamine clearance rate in striatum was decreased in both adolescent and adult rats eating high fat chow compared with age-matched rats eating standard chow. CONCLUSIONS: These results suggest that high fat diet-induced reductions in dopamine clearance rate do not always correspond to increased sensitivity to the locomotor effects of cocaine, suggesting that mechanisms other than dopamine transporter might play a role. Moreover, in adolescent but not adult rats, eating high fat chow increases sensitivity to cocaine and enhances the sensitization that develops to cocaine.

Dysregulation in microRNA expression in peripheral blood mononuclear cells of sepsis patients is associated with immunopathology.

Sepsis is a major cause of death worldwide. It triggers systemic inflammation, the role of which remains unclear. In the current study, we investigated the induction of microRNA (miRNA) during sepsis and their role in the regulation of inflammation. Patients, on days 1 and 5 following sepsis diagnosis, had reduced T cells but elevated monocytes. Plasma levels of IL-6, IL-8, IL-10 and MCP-1 dramatically increased in sepsis patients on day 1. T cells from sepsis patients differentiated primarily into Th2 cells, whereas regulatory T cells decreased. Analysis of 1163 miRNAs from PBMCs revealed that miR-182, miR-143, miR-145, miR-146a, miR-150, and miR-155 were dysregulated in sepsis patients. miR-146a downregulation correlated with increased IL-6 expression and monocyte proliferation. Bioinformatics analysis uncovered the immunological associations of dysregulated miRNAs with clinical disease. The current study demonstrates that miRNA dysregulation correlates with clinical manifestations and inflammation, and therefore remains a potential therapeutic target against sepsis.

Membrane-permeable C-terminal dopamine transporter peptides attenuate amphetamine-evoked dopamine release.

The dopamine transporter (DAT) is responsible for sequestration of extracellular dopamine (DA). The psychostimulant amphetamine (AMPH) is a DAT substrate, which is actively transported into the nerve terminal, eliciting vesicular depletion and reversal of DA transport via DAT. Here, we investigate the role of the DAT C terminus in AMPH-evoked DA efflux using cell-permeant dominant-negative peptides. A peptide, which corresponded to the last 24 C-terminal residues of DAT (TAT-C24 DAT) and thereby contained the Ca(2+)-calmodulin-dependent protein kinase IIα (CaMKIIα) binding domain and the PSD-95/Discs-large/ZO-1 (PDZ)-binding sequence of DAT, was made membrane-permeable by fusing it to the cell membrane transduction domain of the HIV-1 Tat protein (TAT-C24WT). The ability of TAT-C24WT but not a scrambled peptide (TAT-C24Scr) to block the CaMKIIα-DAT interaction was supported by co-immunoprecipitation experiments in heterologous cells. In heterologous cells, we also found that TAT-C24WT, but not TAT-C24Scr, decreased AMPH-evoked 1-methyl-4-phenylpyridinium efflux. Moreover, chronoamperometric recordings in striatum revealed diminished AMPH-evoked DA efflux in mice preinjected with TAT-C24WT. Both in heterologous cells and in striatum, the peptide did not further inhibit efflux upon KN-93-mediated inhibition of CaMKIIα activity, consistent with a dominant-negative action preventing binding of CaMKIIα to the DAT C terminus. This was further supported by the ability of a peptide with perturbed PDZ-binding sequence, but preserved CaMKIIα binding (TAT-C24AAA), to diminish AMPH-evoked DA efflux in vivo to the same extent as TAT-C24WT. Finally, AMPH-induced locomotor hyperactivity was attenuated following systemic administration of TAT-C24WT but not TAT-C24Scr. Summarized, our findings substantiate that DAT C-terminal protein-protein interactions are critical for AMPH-evoked DA efflux and suggest that it may be possible to target protein-protein interactions to modulate transporter function and interfere with psychostimulant effects.

Inhibition of dopamine transporter activity by G protein ßγ subunits.

Uptake through the Dopamine Transporter (DAT) is the primary mechanism of terminating dopamine signaling within the brain, thus playing an essential role in neuronal homeostasis. Deregulation of DAT function has been linked to several neurological and psychiatric disorders including ADHD, schizophrenia, Parkinson's disease, and drug addiction. Over the last 15 years, several studies have revealed a plethora of mechanisms influencing the activity and cellular distribution of DAT; suggesting that fine-tuning of dopamine homeostasis occurs via an elaborate interplay of multiple pathways. Here, we show for the first time that the ßγ subunits of G proteins regulate DAT activity. In heterologous cells and brain tissue, a physical association between Gßγ subunits and DAT was demonstrated by co-immunoprecipitation. Furthermore, in vitro pull-down assays using purified proteins established that this association occurs via a direct interaction between the intracellular carboxy-terminus of DAT and Gßγ. Functional assays performed in the presence of the non-hydrolyzable GTP analog GTP-γ-S, Gßγ subunit overexpression, or the Gßγ activator mSIRK all resulted in rapid inhibition of DAT activity in heterologous systems. Gßγ activation by mSIRK also inhibited dopamine uptake in brain synaptosomes and dopamine clearance from mouse striatum as measured by high-speed chronoamperometry in vivo. Gßγ subunits are intracellular signaling molecules that regulate a multitude of physiological processes through interactions with enzymes and ion channels. Our findings add neurotransmitter transporters to the growing list of molecules regulated by G-proteins and suggest a novel role for Gßγ signaling in the control of dopamine homeostasis.