Book Review: Jules Monchanin (1895-1957) as Seen from East and West, volumes 1 and 2

A review of Jules Monchanin (189501957) as Seen from East and West, volumes 1 and 2 edited by Thomas matus and Sister Sarananda

The Controversy and its Theological Implications

The controversy concerning evangelization and conversions in contemporary India may be productively interpreted as a conflict between stories, between what John Haught refers to as power-bestowing narratives, or between what Gerald Larson calls comprehensive interpretive frameworks. These Hindu stories and Christian stories are discordant, not only with each other, but with other stories within their own traditions, thus fostering the mutual mistrust that thoroughly colors the debate. My task is to sketch four such narrative frameworks, each centered upon an image of India and corresponding to one of four communities involved in the controversy: conservative Hindu nationalists, more secularist Hindus, Evangelical Christian missionaries, and Roman Catholic theologians in India

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

Thyroid hormone (TH) regulates diverse developmental events and can drive disparate cellular outcomes. In zebrafish, TH has opposite effects on neural crest derived pigment cells of the adult stripe pattern, limiting melanophore population expansion, yet increasing yellow/orange xanthophore numbers. To learn how TH elicits seemingly opposite responses in cells having a common embryological origin, we analyzed individual transcriptomes from thousands of neural crest-derived cells, reconstructed developmental trajectories, identified pigment cell-lineage specific responses to TH, and assessed roles for TH receptors. We show that TH promotes maturation of both cell types but in distinct ways. In melanophores, TH drives terminal differentiation, limiting final cell numbers. In xanthophores, TH promotes accumulation of orange carotenoids, making the cells visible. TH receptors act primarily to repress these programs when TH is limiting. Our findings show how a single endocrine factor integrates very different cellular activities during the generation of adult form

Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders

Nuclear factor κB (NF-κB) is a transcription factor that regulates various aspects of immune response, cell death, and differentiation as well as cancer. In this study we introduce the Py-Im polyamide 1 that binds preferentially to the sequences 5′-WGGWWW-3′ and 5′GGGWWW-3′. The compound is capable of binding to κB sites and reducing the expression of various NF-κB–driven genes including IL6 and IL8 by qRT-PCR. Chromatin immunoprecipitation experiments demonstrate a reduction of p65 occupancy within the proximal promoters of those genes. Genome-wide expression analysis by RNA-seq compares the DNA-binding polyamide with the well-characterized NF-κB inhibitor PS1145, identifies overlaps and differences in affected gene groups, and shows that both affect comparable numbers of TNF-α–inducible genes. Inhibition of NF-κB DNA binding via direct displacement of the transcription factor is a potential alternative to the existing antagonists

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

The sense of smell allows chemicals to be perceived as diverse scents. We used single neuron RNA-Sequencing (RNA-Seq) to explore developmental mechanisms that shape this ability as nasal olfactory neurons mature in mice. Most mature neurons expressed only one of the roughly 1000 odorant receptor genes (Olfrs) available, and that at high levels. However, many immature neurons expressed low levels of multiple Olfrs. Coexpressed Olfrs localized to overlapping zones of the nasal epithelium, suggesting regional biases, but not to single genomic loci. A single immature neuron could express Olfrs from up to seven different chromosomes. The mature state in which expression of Olfr genes is restricted to one per neuron emerges over a developmental progression that appears independent of neuronal activity requiring sensory transduction molecules

MGMR: leveraging RNA-Seq population data to optimize expression estimation

<p>Abstract</p> <p>Background</p> <p>RNA-Seq is a technique that uses Next Generation Sequencing to identify transcripts and estimate transcription levels. When applying this technique for quantification, one must contend with reads that align to multiple positions in the genome (multireads). Previous efforts to resolve multireads have shown that RNA-Seq expression estimation can be improved using probabilistic allocation of reads to genes. These methods use a probabilistic generative model for data generation and resolve ambiguity using likelihood-based approaches. In many instances, RNA-seq experiments are performed in the context of a population. The generative models of current methods do not take into account such population information, and it is an open question whether this information can improve quantification of the individual samples</p> <p>Results</p> <p>In order to explore the contribution of population level information in RNA-seq quantification, we apply a hierarchical probabilistic generative model, which assumes that expression levels of different individuals are sampled from a Dirichlet distribution with parameters specific to the population, and reads are sampled from the distribution of expression levels. We introduce an optimization procedure for the estimation of the model parameters, and use HapMap data and simulated data to demonstrate that the model yields a significant improvement in the accuracy of expression levels of paralogous genes.</p> <p>Conclusions</p> <p>We provide a proof of principal of the benefit of drawing on population commonalities to estimate expression. The results of our experiments demonstrate this approach can be beneficial, primarily for estimation at the gene level.</p

ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

RNA-Seq and microarray platforms have emerged as important tools for detecting changes in gene expression and RNA processing in biological samples. We present ExpressionPlot, a software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets. Download and installation instructions, a user's manual, discussion group, and a prototype are available at http://expressionplot.com/ webcite.ALS Therapy Allianc

Streaming fragment assignment for real-time analysis of sequencing experiments

We present eXpress, a software package for efficient probabilistic assignment of ambiguously mapping sequenced fragments. eXpress uses a streaming algorithm with linear run time and constant memory use. It can determine abundances of sequenced molecules in real time and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data. We demonstrate its use on RNA-seq data and show that eXpress achieves greater efficiency than other quantification methods

Nonrandom Gene Loss from the Drosophila miranda Neo-Y Chromosome

A lack of recombination leads to the degeneration of an evolving Y chromosome. However, it is not known whether gene loss is largely a random process and primarily driven by the order in which mutations occur or whether certain categories of genes are lost less quickly than others; the latter would imply that selection counteracts the degeneration of Y chromosomes to some extent. In this study, we investigate the relationship between putative ancestral expression levels of neo-Y–linked genes in Drosophila miranda and their rates of degeneration. We use RNA-Seq data from its close relative Drosophila pseudoobscura to show that genes that have become nonfunctional on the D. miranda neo-Y had, on average, lower ancestral transcript levels and were expressed in fewer tissues compared with genes with intact reading frames. We also show that genes with male-biased expression are retained for longer on the neo-Y compared with female-biased genes. Our results imply that gene loss on the neo-Y is not a purely random, mutation-driven process. Instead, selection is—at least to some extent—preserving the function of genes that are more costly to lose, despite the strongly reduced efficacy of selection on the neo-Y chromosome

Efficacy and safety of mavrilimumab in giant cell arteritis: a phase 2, randomised, double-blind, placebo-controlled trial

OBJECTIVES: Granulocyte-macrophage colony-stimulating factor (GM-CSF) is implicated in pathogenesis of giant cell arteritis. We evaluated the efficacy of the GM-CSF receptor antagonist mavrilimumab in maintaining disease remission. METHODS: This phase 2, double-blind, placebo-controlled trial enrolled patients with biopsy-confirmed or imaging-confirmed giant cell arteritis in 50 centres (North America, Europe, Australia). Active disease within 6 weeks of baseline was required for inclusion. Patients in glucocorticoid-induced remission were randomly assigned (3:2 ratio) to mavrilimumab 150 mg or placebo injected subcutaneously every 2 weeks. Both groups received a 26-week prednisone taper. The primary outcome was time to adjudicated flare by week 26. A prespecified secondary efficacy outcome was sustained remission at week 26 by Kaplan-Meier estimation. Safety was also assessed. RESULTS: Of 42 mavrilimumab recipients, flare occurred in 19% (n=8). Of 28 placebo recipients, flare occurred in 46% (n=13). Median time to flare (primary outcome) was 25.1 weeks in the placebo group, but the median was not reached in the mavrilimumab group (HR 0.38; 95% CI 0.15 to 0.92; p=0.026). Sustained remission at week 26 was 83% for mavrilimumab and 50% for placebo recipients (p=0.0038). Adverse events occurred in 78.6% (n=33) of mavrilimumab and 89.3% (n=25) of placebo recipients. No deaths or vision loss occurred in either group. CONCLUSIONS: Mavrilimumab plus 26 weeks of prednisone was superior to placebo plus 26 weeks of prednisone for time to flare by week 26 and sustained remission in patients with giant cell arteritis. Longer treatment is needed to determine response durability and quantify the glucocorticoid-sparing potential of mavrilimumab. TRIAL REGISTRATION NUMBER: ClinicalTrials.gov number: NCT03827018, Europe (EUdraCT number: 2018-001003-36), and Australia (CT-2018-CTN-01 865-1)