Development and analysis of a multi-module peristaltic simulator for gastrointestinal research.

Many existing in vitro digestion systems do not accurately represent the peristaltic contractions of the gastrointestinal system; most of the systems that have physiologically-relevant peristaltic contractions have low throughput and can only test one sample at a time. A device has been developed that provides simulated peristaltic contractions for up to 12 digestion modules simultaneously using rollers of varying width to modulate the dynamics of the peristaltic motion. The force applied to a simulated food bolus varied from 2.61 ± 0.03 N to 4.51 ± 0.16 N (p < 0.05) depending on roller width. Video analysis showed that the degree of occlusion of the digestion module varied from 72.1 ± 0.4% to 84.6 ± 1.2% (p < 0.05). A multiphysics, computational fluid dynamics model was created to understand the fluid flow. The fluid flow was also examined experimentally using video analysis of tracer particles. The model-predicted maximum fluid velocity in the peristaltic simulator incorporating the thin rollers was 0.016 m/s, and the corresponding value measured using tracer particles was 0.015 m/s. The occlusion, pressure, and fluid velocity in the new peristaltic simulator fell within physiologically representative ranges. Although no in vitro device perfectly recreates the conditions of the gastrointestinal system, this novel device is a flexible platform for future gastrointestinal research and could allow for high-throughput screening of food materials for health-promoting properties under conditions representative of human gastrointestinal motility.

Cell Cycle Synchrony Methods for Fission Yeast, Schizosaccharomyces pombe.

The fission yeast, Schizosaccharomyces pombe, is a genetically tractable model organism for cell cycle and molecular genetics research. We describe methods to synchronize S. pombe cultures, and the benefits and limitations of each. Drug-induced synchrony is a convenient method to arrest the cell cycle. An example of the drug hydroxyurea is shown, which arrests cells in S-phase. Environmental modulation through media composition or growth conditions may also be used to synchronize cultures, most commonly with nitrogen depletion to arrest in G1-phase. Finally, examples of temperature-sensitive conditional alleles are shown which arrest the cell cycle at key transition points. Each of these methods must be assessed relative to the desired effect and the process being studied, providing the best synchrony with the fewest off-target effects.

Detecting Cell Cycle Stage and Progression in Fission Yeast, Schizosaccharomyces pombe.

We have previously described methods to synchronize cultures of fission yeast, Schizosaccharomyces pombe. In this chapter, we provide methods to detect cell cycle stage in cells and populations of S. pombe. These protocols used fixed samples. First, we describe sample preparation for flow cytometry of bulk DNA content. This technique allows users to monitor progression of DNA replication and detect any perturbation during the synthesis (S) phase of the cell cycle. Second, we describe methods to stain nuclei and septa of fixed yeast cells, and monitor proportions of cell cycle stages within cultures. Together, these methods provide the ability to compare cell cycle progression or delay between cultures, making use of the powerful molecular genetics tool that is S. pombe.

Trends and outcomes of mechanically ventilated cirrhotic patients in the United States from 2005-2014.

Purpose: Cirrhotic patients in organ failure are frequently admitted to intensive care units (ICUs) to receive invasive mechanical ventilation (IMV). We evaluated the trends of hospitalizations, in-hospital mortality, hospital costs, and hospital length of stay (LOS) of IMV patients with cirrhosis. Methods: We analyzed the United States National Inpatient Sample from 2005-2014. We selected discharges of IMV adult (≥18 years) patients with cirrhosis using the International Classification of Diseases, 9th Edition, Clinical Modification codes. Trends were assessed using linear regression and joinpoint regression. Results: Between 2005 and 2014, there were approximately 9,441,605 hospitalizations of IMV adult patients, of which 4.7% had cirrhosis. There was an increasing trend in the total number of IMV cirrhotic patient hospitalizations (annual percent change [APC] 7.0%, 95% confidence interval [CI] 6.4%; 7.6%, Ptrend < 0.001). The in-hospital case-fatality ratio declined between 2005-2011 (APC -2.9%, 95% CI, -3.4%; -2.4%, Ptrend < 0.001); however, it remained similar between 2011-2014 (Ptrend = 0.58). The total annual hospital costs of all IMV cirrhotic patients increased from approximately $1.2 billion USD in 2005 to $2.7 billion USD in 2014 (Ptrend < 0.001). The mean hospital costs per patient and mean LOS declined between 2005 and 2014 (Ptrend < 0.001 and Ptrend = 0.01 respectively). Conclusions: The total number of hospitalizations and total annual costs of IMV patients with cirrhosis have been increasing over time. However, past hesitancy around admitting cirrhotic patients to the ICU may need to be tempered by the improving mortality trends in this patient population.

Mitochondrial Sirtuin-3 (SIRT3) Prevents Doxorubicin-Induced Dilated Cardiomyopathy by Modulating Protein Acetylation and Oxidative Stress.

BACKGROUND: High doses of doxorubicin put cancer patients at risk for developing dilated cardiomyopathy. Previously, we showed that doxorubicin treatment decreases SIRT3 (sirtuin 3), the main mitochondrial deacetylase and increases protein acetylation in rat cardiomyocytes. Here, we hypothesize that SIRT3 expression can attenuate doxorubicin induced dilated cardiomyopathy in vivo by preventing the acetylation of mitochondrial proteins. METHODS: Nontransgenic, M3-SIRT3 (truncated SIRT3; short isoform), and M1-SIRT3 (full-length SIRT3; mitochondrial localized) transgenic mice were treated with doxorubicin for 4 weeks (8 mg/kg body weight per week). Echocardiography was performed to assess cardiac structure and function and validated by immunohistochemistry and immunofluorescence (n=4-10). Mass spectrometry was performed on cardiac mitochondrial peptides in saline (n=6) and doxorubicin (n=5) treated hearts. Validation was performed in doxorubicin treated primary rat and human induced stem cell derived cardiomyocytes transduced with adenoviruses for M3-SIRT3 and M1-SIRT3 and deacetylase deficient mutants (n=4-10). RESULTS: Echocardiography revealed that M3-SIRT3 transgenic mice were partially resistant to doxorubicin induced changes to cardiac structure and function whereas M1-SIRT3 expression prevented cardiac remodeling and dysfunction. In doxorubicin hearts, 37 unique acetylation sites on mitochondrial proteins were altered. Pathway analysis revealed these proteins are involved in energy production, fatty acid metabolism, and oxidative stress resistance. Increased M1-SIRT3 expression in primary rat and human cardiomyocytes attenuated doxorubicin-induced superoxide formation, whereas deacetylase deficient mutants were unable to prevent oxidative stress. CONCLUSIONS: Doxorubicin reduced SIRT3 expression and markedly affected the cardiac mitochondrial acetylome. Increased M1-SIRT3 expression in vivo prevented doxorubicin-induced cardiac dysfunction, suggesting that SIRT3 could be a potential therapeutic target for mitigating doxorubicin-induced dilated cardiomyopathy.

Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease.

The COVID-19 pandemic has highlighted the urgent need for the identification of new antiviral drug therapies for a variety of diseases. COVID-19 is caused by infection with the human coronavirus SARS-CoV-2, while other related human coronaviruses cause diseases ranging from severe respiratory infections to the common cold. We developed a computational approach to identify new antiviral drug targets and repurpose clinically-relevant drug compounds for the treatment of a range of human coronavirus diseases. Our approach is based on graph convolutional networks (GCN) and involves multiscale host-virus interactome analysis coupled to off-target drug predictions. Cell-based experimental assessment reveals several clinically-relevant drug repurposing candidates predicted by the in silico analyses to have antiviral activity against human coronavirus infection. In particular, we identify the MET inhibitor capmatinib as having potent and broad antiviral activity against several coronaviruses in a MET-independent manner, as well as novel roles for host cell proteins such as IRAK1/4 in supporting human coronavirus infection, which can inform further drug discovery studies.

Estimation of Fractional Photosynthetically Active Radiation From a Canopy 3D Model; Case Study: Almond Yield Prediction.

Canopy-intercepted light, or photosynthetically active radiation, is fundamentally crucial for quantifying crop biomass development and yield potential. Fractional photosynthetically active radiation (PAR) (fPAR) is conventionally obtained by measuring the PAR both below and above the canopy using a mobile lightbar platform to predict the potential yield of nut crops. This study proposed a feasible and low-cost method for accurately estimating the canopy fPAR using aerial photogrammetry-based canopy three-dimensional models. We tested up to eight different varieties in three experimental almond orchards, including California's leading variety of 'Nonpareil'. To extract various canopy profile features, such as canopy cover and canopy volume index, we developed a complete data collection and processing pipeline called Virtual Orchard (VO) in Python environment. Canopy fPAR estimated by VO throughout the season was compared against midday canopy fPAR measured by a mobile lightbar platform in midseason, achieving a strong correlation (R 2) of 0.96. A low root mean square error (RMSE) of 2% for 'Nonpareil'. Furthermore, we developed regression models for predicting actual almond yield using both measures, where VO estimation of canopy fPAR, as a stronger indicator, achieved a much better prediction (R 2 = 0.84 and RMSE = 195 lb acre-1) than the lightbar (R 2 = 0.70 and RMSE = 266 lb acre-1) for 'Nonpareil'. Eight different new models for estimating potential yield were also developed using temporal analysis from May to August in 2019 by adjusting the ratio between fPAR and dry kernel yield previously found using a lightbar. Finally, we compared the two measures at two different spatial precision levels: per-row and per-block. fPAR estimated by VO at the per-tree level was also assessed. Results showed that VO estimated canopy fPAR performed better at each precision level than lightbar with up to 0.13 higher R 2. The findings in this study serve as a fundamental link between aerial-based canopy fPAR and the actual yield of almonds.

Case Report: Visual Rehabilitation in Hemianopia Patients. Home-Based Visual Rehabilitation in Patients With Hemianopia Consecutive to Brain Tumor Treatment: Feasibility and Potential Effectiveness.

Background/Objectives: Visual field loss is frequent in patients with brain tumors, worsening their daily life and exacerbating the burden of disease, and no supportive care strategies exist. In this case series, we sought to characterize the feasibility and potential effectiveness of a home-based visual rehabilitation program in hemianopia patients using immersive virtual-reality stimulation. Subjects/Methods: Two patients, one with homonymous hemianopia and the other with bitemporal hemianopia, consecutive to pediatric brain tumors, with no prior visual rehabilitation performed 15 min of home-based audiovisual stimulation every 2 days for 6 weeks (case 2) and 7 weeks (case 1) between February and August 2020. Patients used a virtual-reality, stand-alone, and remotely controlled device loaded with a non-commercial audiovisual stimulation program managed in real time from the laboratory. Standard visual outcomes assessed in usual care in visual rehabilitation were measured at the clinic. Following a mixed method approach in this pragmatic study of two cases, we collected quantitative and qualitative data on feasibility and potential effectiveness and compared the results pre- and post-treatment. Results: Implementation and wireless delivery of the audiovisual stimulation, remote data collection, and analysis for cases 1 and 2 who completed 19/20 and 20/20 audiovisual stimulation sessions at home, respectively, altogether indicated feasibility. Contrast sensitivity increased in both eyes for cases 1 and 2. Visual fields, measured by binocular Esterman and monocular Humphrey full-field analyses, improved in case 1. A minor increase was observed in case 2. Cases 1 and 2 enhanced reading speed. Case 2 strongly improved quality of life scores. Conclusion: This is the first report of a home-based virtual-reality visual rehabilitation program for adult patients with hemianopia consecutive to a pediatric brain tumor. We show the feasibility in real-world conditions and potential effectiveness of such technology on visual perception and quality of life.

An Audiovisual 3D-Immersive Stimulation Program in Hemianopia Using a Connected Device.

BACKGROUND Homonymous hemianopia is a loss of conscious vision in one hemifield, strongly affecting everyday life. Audiovisual stimulation programs improve visual perception in the blind hemifield; however, they use large equipment operated in clinical settings. Such treatments require frequent visits at the clinic, hampering the patient's adherence and compliance. In one hemianopia patient, we tested a 4-week dynamic audiovisual rehabilitation program in the stand-alone, remotely controlled, virtual-reality, head-mounted display Oculus Go and measured the effect on visual perception. CASE REPORT A 15-year-old Caucasian male was diagnosed with a right homonymous hemianopia with splitting of central fixation after a traumatic occipital contusion at age 7 months. Visual assessment showed impaired binocular contrast sensitivity and retinal sensitivity. Fixation stability and visual fields were strongly affected. After a 4-week audiovisual rehabilitation program, including 3 hours 20 minutes of stimulation, the contrast sensitivity, fixation stability, and paracentral visual perception were significantly enhanced, improving quality of life. CONCLUSIONS This pioneering work reports the use of virtual-reality in a head-mounted display to provide an audiovisual stimulation protocol for low-vision rehabilitation in a hemianopia patient. Real-time data recording and remote control of the stimulation program demonstrate that such rehabilitation treatment can be performed by the patient at home without interruption of care, decreasing the burden of disease. Beneficial effects on visual function were measured according to clinical guidelines of low-vision assessment. Improvement in visual function and quality of life challenge the prevailing belief that post-acute vision loss is both permanent and unchangeable.

New insights on the modeling of the molecular mechanisms underlying neural maps alignment in the midbrain.

We previously identified and modeled a principle of visual map alignment in the midbrain involving the mapping of the retinal projections and concurrent transposition of retinal guidance cues into the superior colliculus providing positional information for the organization of cortical V1 projections onto the retinal map (Savier et al., 2017). This principle relies on mechanisms involving Epha/Efna signaling, correlated neuronal activity and axon competition. Here, using the 3-step map alignment computational model, we predict and validate in vivo the visual mapping defects in a well-characterized mouse model. Our results challenge previous hypotheses and provide an alternative, although complementary, explanation for the phenotype observed. In addition, we propose a new quantification method to assess the degree of alignment and organization between maps, allowing inter-model comparisons. This work generalizes the validity and robustness of the 3-step map alignment algorithm as a predictive tool and confirms the basic mechanisms of visual map organization.

Nonnutritive sweetener consumption during pregnancy, adiposity, and adipocyte differentiation in offspring: evidence from humans, mice, and cells.

BACKGROUND: Obesity often originates in early life, and is linked to excess sugar intake. Nonnutritive sweeteners (NNS) are widely consumed as "healthier" alternatives to sugar, yet recent evidence suggests NNS may adversely influence weight gain and metabolic health. The impact of NNS during critical periods of early development has rarely been studied. We investigated the effect of prenatal NNS exposure on postnatal adiposity and adipocyte development. METHODS: In the CHILD birth cohort (N = 2298), we assessed maternal NNS beverage intake during pregnancy and child body composition at 3 years, controlling for maternal BMI and other potential confounders. To investigate causal mechanisms, we fed NNS to pregnant C57BL6J mice at doses relevant to human consumption (42 mg/kg/day aspartame or 6.3 mg/kg/day sucralose), and assessed offspring until 12 weeks of age for: body weight, adiposity, adipose tissue morphology and gene expression, glucose and insulin tolerance. We also studied the effect of sucralose on lipid accumulation and gene expression in cultured 3T3-L1 pre-adipocyte cells. RESULTS: In the CHILD cohort, children born to mothers who regularly consumed NNS beverages had elevated body mass index (mean z-score difference +0.23, 95% CI 0.05-0.42 for daily vs. no consumption, adjusted for maternal BMI). In mice, maternal NNS caused elevated body weight, adiposity, and insulin resistance in offspring, especially in males (e.g., 47% and 15% increase in body fat for aspartame and sucralose vs. controls, p < 0.001). In cultured adipocytes, sucralose exposure at early stages of differentiation caused increased lipid accumulation and expression of adipocyte differentiation genes (e.g., C/EBP-α, FABP4, and FASN). These genes were also upregulated in adipose tissue of male mouse offspring born to sucralose-fed dams. CONCLUSION: By triangulating evidence from humans, mice, and cultured adipocytes, this study provides new evidence that maternal NNS consumption during pregnancy may program obesity risk in offspring through effects on adiposity and adipocyte differentiation.

Correction to: Myocardin regulates mitochondrial calcium homeostasis and prevents permeability transition.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Myocardin regulates mitochondrial calcium homeostasis and prevents permeability transition.

Myocardin is a transcriptional co-activator required for cardiovascular development, but also promotes cardiomyocyte survival through an unclear molecular mechanism. Mitochondrial permeability transition is implicated in necrosis, while pore closure is required for mitochondrial maturation during cardiac development. We show that loss of myocardin function leads to subendocardial necrosis at E9.5, concurrent with elevated expression of the death gene Nix. Mechanistically, we demonstrate that myocardin knockdown reduces microRNA-133a levels to allow Nix accumulation, leading to mitochondrial permeability transition, reduced mitochondrial respiration, and necrosis. Myocardin knockdown elicits calcium release from the endo/sarcoplasmic reticulum with mitochondrial calcium accumulation, while restoration of microRNA-133a function, or knockdown of Nix rescues calcium perturbations. We observed reduced myocardin and elevated Nix expression within the infarct border-zone following coronary ligation. These findings identify a myocardin-regulated pathway that maintains calcium homeostasis and mitochondrial function during development, and is attenuated during ischemic heart disease. Given the diverse role of Nix and microRNA-133a, these findings may have broader implications to metabolic disease and cancer.

Sirtuin-3 (SIRT3) Protein Attenuates Doxorubicin-induced Oxidative Stress and Improves Mitochondrial Respiration in H9c2 Cardiomyocytes.

Doxorubicin (DOX) is a chemotherapeutic agent effective in the treatment of many cancers. However, cardiac dysfunction caused by DOX limits its clinical use. DOX is believed to be harmful to cardiomyocytes by interfering with the mitochondrial phospholipid cardiolipin and causing inefficient electron transfer resulting in the production of reactive oxygen species (ROS). Sirtuin-3 (SIRT3) is a class III lysine deacetylase that is localized to the mitochondria and regulates mitochondrial respiration and oxidative stress resistance enzymes such as superoxide dismutase-2 (SOD2). The purpose of this study was to determine whether SIRT3 prevents DOX-induced mitochondrial ROS production. Administration of DOX to mice suppressed cardiac SIRT3 expression, and DOX induced a dose-dependent decrease in SIRT3 and SOD2 expression in H9c2 cardiomyocytes. SIRT3-null mouse embryonic fibroblasts produced significantly more ROS in the presence of DOX compared with wild-type cells. Overexpression of wild-type SIRT3 increased cardiolipin levels and rescued mitochondrial respiration and SOD2 expression in DOX-treated H9c2 cardiomyocytes and attenuated the amount of ROS produced following DOX treatment. These effects were absent when a deacetylase-deficient SIRT3 was expressed in H9c2 cells. Our results suggest that overexpression of SIRT3 attenuates DOX-induced ROS production, and this may involve increased SOD2 expression and improved mitochondrial bioenergetics. SIRT3 activation could be a potential therapy for DOX-induced cardiac dysfunction.

Bidirectional but asymmetrical sexual hybridization between Brassica carinata and Sinapis arvensis (Brassicaceae).

With transgenic crop development it is important to evaluate the potential for transgenes to escape into populations of wild, weedy relatives. Ethiopian mustard (Brassica carinata, BBCC) is easily transformed and is being investigated for uses from biodiesel fuels to biopharmaceuticals. However, little work has been done evaluating its ability to cross with relatives such as wild mustard (Sinapsis arvensis, SrSr), an abundant, cosmopolitan weedy relative. Here we conducted bidirectional crosses with Ethiopian mustard as a maternal parent in 997 crosses and paternal parent in 1,109 crosses. Hybrids were confirmed using flow cytometry and species-specific ITS molecular markers and indicate a high hybridization rate of 6.43 % between Ethiopian mustard (♀) and wild mustard (♂) and a lower, but not insignificant, hybridization rate of 0.01 % in the reverse direction. The majority of the hybrids were homoploid (BCSr) with less than 1 % of pollen production of their parents and low seed production (0.26 seeds/pollination) in crosses and backcrosses indicating a potential for advanced generation hybrids. The accession used had a significant effect on hybrid seed production with different accessions of Ethopian mustard varying in their production of hybrid offspring from 2.69 to 16.34 % and one accession of wild mustard siring almost twice as many hybrid offspring per flower as the other. One pentaploid (BBCCSr) and one hexaploid (BBCCSrSr) hybrid were produced and had higher pollen viability, though no and low seed production, respectively. As wild mustard is self-incompatible and the outcrossing rate of Ethiopian mustard has been estimated as 30 % potential for hybrid production in the wild appears to be high, though the hybridization rate found here represents a worst case scenario as it does not incorporate pre-pollination barriers. Hybridization in the wild needs to be directly evaluated as does the propensity of Ethiopian mustard to volunteer.