Mariner: explore the Hi-Cs.

MOTIVATION: 3D chromatin structure plays an important role in regulating gene expression and alterations to this structure can result in developmental abnormalities and disease. While genomic approaches like Hi-C and Micro-C can provide valuable insights in 3D chromatin architecture, the resulting datasets are extremely large and difficult to manipulate. RESULTS: Here, we present mariner, a rapid and memory efficient tool to extract, aggregate, and plot data from Hi-C matrices within the R/Bioconductor environment. Mariner simplifies the process of querying and extracting contacts from multiple Hi-C files using a parallel and block-processing approach. Modular functions allow complete workflow customization for advanced users, yet all-in-one functions are available for running the most common types of analyses. Finally, tight integration with existing Bioconductor infrastructure enables complete analysis and visualization of Hi-C data in R. AVAILABILITY AND IMPLEMENTATION: Available on GitHub at https://github.com/EricSDavis/mariner and on Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/mariner.html.

Plotgardener: cultivating precise multi-panel figures in R.

MOTIVATION: The R programming language is one of the most widely used programming languages for transforming raw genomic datasets into meaningful biological conclusions through analysis and visualization, which has been largely facilitated by infrastructure and tools developed by the Bioconductor project. However, existing plotting packages rely on relative positioning and sizing of plots, which is often sufficient for exploratory analysis but is poorly suited for the creation of publication-quality multi-panel images inherent to scientific manuscript preparation. RESULTS: We present plotgardener, a coordinate-based genomic data visualization package that offers a new paradigm for multi-plot figure generation in R. Plotgardener allows precise, programmatic control over the placement, esthetics and arrangements of plots while maximizing user experience through fast and memory-efficient data access, support for a wide variety of data and file types, and tight integration with the Bioconductor environment. Plotgardener also allows precise placement and sizing of ggplot2 plots, making it an invaluable tool for R users and data scientists from virtually any discipline. AVAILABILITY AND IMPLEMENTATION: Package: https://bioconductor.org/packages/plotgardener, Code: https://github.com/PhanstielLab/plotgardener, Documentation: https://phanstiellab.github.io/plotgardener/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The effect of prolonged light intensity exercise in the heat on executive function.

OBJECTIVE: When people are involved in outdoor activities, it is important to be able to assess a situation and make rational decisions. The goal of this study is to determine the effects of 90 minutes of light-intensity exercise in a hot environment on executive functioning capabilities of healthy individuals. METHODS: In this prospective laboratory study, 40 healthy male and female subjects 18 to 45 years of age performed treadmill exercise while wearing athletic clothing and a backpack in either a hot or temperate environment. Vital signs, core and skin temperature, and perceptual measures (thermal sensation, sweating, comfort, and perceived exertion) were measured before, during, and after the treadmill test. Cognitive function was measured before and after the treadmill test using the Wisconsin Card Sorting Test (WCST) and a Psychomotor Vigilance Test (PVT). RESULTS: Subjects in the hot condition reached a similar core temp of 38.2° ± 0.5°C vs 37.7° ± 0.3°C (P = .325) in the temperate group but had a higher heart rate (P < .001) and skin temperature (P < .001). Hot and normal temperature groups did not differ in their PVT performance. There were more correct responses (P < .001), fewer errors (P < .001), and more conceptual responses (P = .001) on the WCST after exertion in both the hot room and normal temperature room conditions. Perseverations and perseverative errors (P = .002) decreased in both groups after exertion. CONCLUSIONS: Conditions of mild heat stress coupled with modest rehydration and short hiking treks do not appear to negatively affect executive function or vigilance.

Guiding the design of well-powered Hi-C experiments to detect differential loops.

3D chromatin structure plays an important role in gene regulation by connecting regulatory regions and gene promoters. The ability to detect the formation and loss of these loops in various cell types and conditions provides valuable information on the mechanisms driving these cell states and is critical for understanding how long-range gene regulation works. Hi-C is a powerful technique used to characterize three-dimensional chromatin structure; however, Hi-C can quickly become a costly and labor-intensive endeavor, and proper planning is required to determine how to best use time and resources while maintaining experimental rigor and well-powered results. To facilitate better planning and interpretation of Hi-C experiments, we have conducted a detailed evaluation of statistical power using publicly available Hi-C datasets paying particular attention to the impact of loop size on Hi-C contacts and fold change compression. In addition, we have developed Hi-C Poweraid, a publicly-hosted web application to investigate these findings (http://phanstiel-lab.med.unc.edu/poweraid/). For experiments involving well-replicated cell lines, we recommend a total sequencing depth of at least 6 billion contacts per condition, split between at least 2 replicates in order to achieve the power to detect the majority of differential loops. For experiments with higher variation, more replicates and deeper sequencing depths are required. Exact values and recommendations for specific cases can be determined through the use of Hi-C Poweraid. This tool simplifies the complexities behind calculating power for Hi-C data and will provide useful information on the amount of well-powered loops an experiment will be able to detect given a specific set of experimental parameters, such as sequencing depth, replicates, and the sizes of the loops of interest. This will allow for more efficient use of time and resources and more accurate interpretation of experimental results.

Guiding the design of well-powered Hi-C experiments to detect differential loops.

Motivation: Three-dimensional chromatin structure plays an important role in gene regulation by connecting regulatory regions and gene promoters. The ability to detect the formation and loss of these loops in various cell types and conditions provides valuable information on the mechanisms driving these cell states and is critical for understanding long-range gene regulation. Hi-C is a powerful technique for characterizing 3D chromatin structure; however, Hi-C can quickly become costly and labor-intensive, and proper planning is required to ensure efficient use of time and resources while maintaining experimental rigor and well-powered results. Results: To facilitate better planning and interpretation of human Hi-C experiments, we conducted a detailed evaluation of statistical power using publicly available Hi-C datasets, paying particular attention to the impact of loop size on Hi-C contacts and fold change compression. In addition, we have developed Hi-C Poweraid, a publicly hosted web application to investigate these findings. For experiments involving well-replicated cell lines, we recommend a total sequencing depth of at least 6 billion contacts per condition, split between at least two replicates to achieve the power to detect differences in the majority of loops. For experiments with higher variation, more replicates and deeper sequencing depths are required. Values for specific cases can be determined by using Hi-C Poweraid. This tool simplifies Hi-C power calculations, allowing for more efficient use of time and resources and more accurate interpretation of experimental results. Availability and implementation: Hi-C Poweraid is available as an R Shiny application deployed at http://phanstiel-lab.med.unc.edu/poweraid/, with code available at https://github.com/sarmapar/poweraid.

Unsupervised invariance learning of transformation sequences in a model of object recognition yields selectivity for non-accidental properties.

Non-accidental properties (NAPs) correspond to image properties that are invariant to changes in viewpoint (e.g., straight vs. curved contours) and are distinguished from metric properties (MPs) that can change continuously with in-depth object rotation (e.g., aspect ratio, degree of curvature, etc.). Behavioral and electrophysiological studies of shape processing have demonstrated greater sensitivity to differences in NAPs than in MPs. However, previous work has shown that such sensitivity is lacking in multiple-views models of object recognition such as Hmax. These models typically assume that object processing is based on populations of view-tuned neurons with distributed symmetrical bell-shaped tuning that are modulated at least as much by differences in MPs as in NAPs. Here, we test the hypothesis that unsupervised learning of invariances to object transformations may increase the sensitivity to differences in NAPs vs. MPs in Hmax. We collected a database of video sequences with objects slowly rotating in-depth in an attempt to mimic sequences viewed during object manipulation by young children during early developmental stages. We show that unsupervised learning yields shape-tuning in higher stages with greater sensitivity to differences in NAPs vs. MPs in agreement with monkey IT data. Together, these results suggest that greater NAP sensitivity may arise from experiencing different in-depth rotations of objects.

Optically responsive gold nanorod-polypeptide assemblies.

Environmentally responsive nanoassemblies based on polypeptides and nanoparticles can have a number of promising biological/biomedical applications. We report the generation of gold nanorod (GNR)-elastin-like polypeptide (ELP) nanoassemblies whose optical response can be manipulated based on exposure to near-infrared (NIR) light. Cysteine-containing ELPs were self-assembled on GNRs mediated by gold-thiol bonds, leading to the generation of GNR-ELP nanoassemblies. Exposure of GNR-ELP assemblies to NIR light resulted in the heating of GNRs due to surface plasmon resonance. Heat transfer from the GNRs resulted in an increase in temperature of the self-assembled ELP above its transition temperature (Tt), which led to a phase transition and aggregation of the GNR-ELP assemblies. This phase transition was detected using an optical readout (increase in optical density); no change in optical behavior was observed in the case of either ELP alone or GNR alone. The optical response was reproducibele and reversible across a number of cycles following exposure to or removal of the laser excitation. Our results indicate that polypeptides may be interfaced with GNRs resulting in optically responsive nanoasssemblies for sensing and drug delivery applications.

Adenoviral overexpression of the glutamylcysteine ligase catalytic subunit protects pancreatic islets against oxidative stress.

The catalytic subunit of glutamylcysteine ligase (GCLC) primarily regulates de novo synthesis of glutathione (GSH) in mammalian cells and is central to the antioxidant capacity of the cell. However, GCLC expression in pancreatic islets has not been previously examined. We designed experiments to ascertain whether GCLC is normally expressed in islets and whether it is up-regulated by interleukin-1 beta (IL-1 beta). GCLC expression levels were intermediate compared with other metabolic tissues (kidney, liver, muscle, fat, and lung). IL-1 beta up-regulated GCLC expression (10 ng/ml IL-1 beta, 3.76 +/- 0.86; 100 ng/ml IL-1 beta, 4.22 +/- 0.68-fold control) via the p38 form of mitogen-activated protein kinase and NF kappa B and also increased reactive oxygen species levels (10 ng/ml IL-1 beta, 5.41 +/- 1.8-fold control). This was accompanied by an increase in intraislet GSH/GSSG ratio (control, 7.1 +/- 0.1; 10 ng/ml IL-1 beta, 8.0 +/- 0.5; 100 ng/ml IL-1 beta, 8.2 +/- 0.5-fold control; p < 0.05). To determine whether overexpression of GCLC increases the antioxidant capacity of the islet and prevents the adverse effects of IL-1 beta on glucose-induced insulin secretion, islets were infected with an adenovirus encoding GCLC. IL-1 beta significantly decreased glucose-stimulated insulin secretion (control, 123.8 +/- 17.7; IL-1 beta, 40.2 +/- 3.9 microunits/ml insulin/islet). GCLC overexpression increased intraislet GSH levels and partially prevented the decrease in glucose-stimulated insulin secretion caused by IL-1 beta. These data provide the first report of GCLC expression in the islet and demonstrate that adenoviral overexpression of GCLC increases intracellular GSH levels and protects the beta cell from the adverse effects of IL-1 beta.