genomation: a toolkit to summarize, annotate and visualize genomic intervals

Summary: Biological insights can be obtained through computational integration of genomics data sets consisting of diverse types of information. The integration is often hampered by a large variety of existing file formats, often containing similar information, and the necessity to use complicated tools to achieve the desired results. We have built an R package, genomation, to expedite the extraction of biological information from high throughput data. The package works with a variety of genomic interval file types and enables easy summarization and annotation of high throughput data sets with given genomic annotations. Availability and implementation: The software is currently distributed under MIT artistic license and freely available at http://bioinformatics.mdc-berlin.de/genomation, and through the Bioconductor framework. Contact: [email protected], [email protected], [email protected], or [email protected]

The nature and persistence of the effects of posthypnotic suggestions on food preferences: The final report of an online study

The persistence of food preferences, which are crucial for diet-related decisions, is a significant obstacle to changing unhealthy eating behavior. To overcome this obstacle, the current study investigates whether posthypnotic suggestions (PHSs) can enhance food-related decisions by measuring food choices and subjective ratings. After assessing hypnotic susceptibility in Session 1, at the beginning of Session 2, a PHS was delivered aiming to increase the desirability of healthy food items (e.g., vegetables and fruit). After the termination of hypnosis, a set of two tasks was administrated twice, once when the PHS was activated and once deactivated in counterbalanced order. The task set consisted of rating 170 pictures of food items, followed by an online supermarket where participants were instructed to select enough food from the same item pool for a fictitious week of quarantine. After 1 week, Session 3 mimicked Session 2 without renewed hypnosis induction to assess the persistence of the PHS effects. The Bayesian hierarchical modeling results indicate that the PHS increased preferences and choices of healthy food items without altering the influence of preferences in choices. In contrast, for unhealthy food items, not only both preferences and choices were decreased due to the PHS, but also their relationship was modified. That is, although choices became negatively biased against unhealthy items, preferences played a more dominant role in unhealthy choices when the PHS was activated. Importantly, all effects persisted over 1 week, qualitatively and quantitatively. Our results indicate that although the PHS affected healthy choices through resolve, i.e., preferred more and chosen more, unhealthy items were probably chosen less impulsively through effortful suppression. Together, besides the translational importance of the current results for helping the obesity epidemic in modern societies, our results contribute theoretically to the understanding of hypnosis and food choices.Peer Reviewe

Soil ecosystem services of the under different uses in the Colombian Amazonia

Agroforestry systems (AFs), where agricultural and livestock crops are associated with woody plants, are known as sustainable systems, that conserve biodiversity and improve the provision of ecosystem services without compromising productivity. This work focuses mainly on cacao AFs, which have been related to different ecosystem services in tropical regions. Especially, our study focuses on the ability of the cacao AFs to improve soil ecosystem services in the Colombian Amazon region. We focused on soil ecosystems ecosystem services in the Colombian Amazonia because: of the social importance of cacao production system in the study region, specifically within the post conflict context; the lack of knowledge on the capacity of cacao AFs to offer soil ecosystem services in the study zone and its capacity in restoring ecosystem services in degraded soils. Aim The objective of our work was to evaluate the soil quality in different cacao agroforestry systems in the Colombian Amazonia, and to compare these evaluated soil quality of soil quality in Forest and Pasture. Material and methods The study was conducted at the Macagual Amazon Research Center, located west of the Colombian Amazon. We evaluated soil quality in four types of AFs Cacao, presenting different establishment, composition and structural characteristics; but also in a plot of native forest composed of characteristic species of the area, and in a plot of pasture composed of grasses. In the different plot of each land use, we evaluated the diversity of macrofauna, the morphology of aggregate, the physical properties and the soil chemistry. We summarized these variables in a General Indicator of Soil Quality GISQ, characterizing soil quality in the different land uses. Major results and Conclusion It was found that the level of intensification among land uses (Bosque>AFs>Pasture) affects the decrease of the macrofauna populations, which was related to soil compaction (physical properties). Chemical fertility improved with the establishment of AFs influenced by the application of amendments and organic fertilizers. When establishing agroforestry systems from pasture areas at a certain level of degradation, the GISQ scale was found to increase by 42%. Our results indicate that AFs practices can definitely be used as a restoration strategy, for the recovery of degraded areas

Cancer of the Esophagus

This chapter in Cancer Concepts: A Guidebook for the Non-Oncologist presents an overview of esophageal cancer, including etiology, epidemiology, screening, pathology, staging, and treatment.https://escholarship.umassmed.edu/cancer_concepts/1027/thumbnail.jp

Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program

Herpesvirus infection initiates a range of perturbations in the host cell, which remain poorly understood at the level of individual cells. Here, we quantify the transcriptome of single human primary fibroblasts during the first hours of lytic infection with HSV-1. By applying a generalizable analysis scheme, we define a precise temporal order of early viral gene expression and propose a set-wise emergence of viral genes. We identify host cell genes and pathways relevant for infection by combining three different computational approaches: gene and pathway overdispersion analysis, prediction of cell-state transition probabilities, as well as future cell states. One transcriptional program, which correlates with increased resistance to infection, implicates the transcription factor NRF2. Consequently, Bardoxolone methyl and Sulforaphane, two known NRF2 agonists, impair virus production, suggesting that NRF2 activation restricts viral infection. Our study provides insights into early stages of HSV-1 infection and serves as a general blueprint for the investigation of heterogeneous cell states in virus infection

FACT sets a barrier for cell fate reprogramming in Caenorhabditis elegans and human cells

The chromatin regulator FACT (facilitates chromatin transcription) is essential for ensuring stable gene expression by promoting transcription. In a genetic screen using Caenorhabditis elegans, we identified that FACT maintains cell identities and acts as a barrier for transcription factor-mediated cell fate reprogramming. Strikingly, FACT's role as a barrier to cell fate conversion is conserved in humans as we show that FACT depletion enhances reprogramming of fibroblasts. Such activity is unexpected because FACT is known as a positive regulator of gene expression, and previously described reprogramming barriers typically repress gene expression. While FACT depletion in human fibroblasts results in decreased expression of many genes, a number of FACT-occupied genes, including reprogramming-promoting factors, show increased expression upon FACT depletion, suggesting a repressive function of FACT. Our findings identify FACT as a cellular reprogramming barrier in C. elegans and humans, revealing an evolutionarily conserved mechanism for cell fate protection

RNA localization is a key determinant of neurite-enriched proteome

Protein subcellular localization is fundamental to the establishment of the body axis, cell migration, synaptic plasticity, and a vast range of other biological processes. Protein localization occurs through three mechanisms: protein transport, mRNA localization, and local translation. However, the relative contribution of each process to neuronal polarity remains unknown. Using neurons differentiated from mouse embryonic stem cells, we analyze protein and RNA expression and translation rates in isolated cell bodies and neurites genome-wide. We quantify 7323 proteins and the entire transcriptome, and identify hundreds of neurite-localized proteins and locally translated mRNAs. Our results demonstrate that mRNA localization is the primary mechanism for protein localization in neurites that may account for half of the neurite-localized proteome. Moreover, we identify multiple neurite-targeted non-coding RNAs and RNA-binding proteins with potential regulatory roles. These results provide further insight into the mechanisms underlying the establishment of neuronal polarity. Subcellular localization of RNAs and proteins is important for polarized cells such as neurons. Here the authors differentiate mouse embryonic stem cells into neurons, and analyze the local transcriptome, proteome, and translated transcriptome in their cell bodies and neurites, providing a unique resource for future studies on neuronal polarity

Investigation of optimal parameters for finite element solution of the forward problem in magnetic field tomography based on magnetoencephalography

This paper presents an investigation of optimal parameters for finite element (FE) solution of the forward problem in magnetic field tomography (MFT) brain imaging based on magnetoencephalography (MEG). It highlights detailed analyses of the main parameters involved and evaluates their optimal values for various cases of FE model solutions (e.g., steady-state, transient, etc.). In each case, a detail study of some of the main parameters and their effects on FE solution and its accuracy are carefully tested and evaluated. These parameters include: total number and size of 3D FE elements used, number and size of elements used in surface discretisation (of both white and grey matters of the brain), number and size of elements used for approximation of current sources, number of anisotropic properties used in steady-state and transient solutions, and the time steps used in transient analyses. The optimal values of these parameters in relation to solution accuracy and mesh convergence criteria have been found and presented