Quantifying Whole Transcriptome Size, a Prerequisite for Understanding Transcriptome Evolution Across Species: An Example from a Plant Allopolyploid

Evolutionary biologists are increasingly comparing gene expression patterns across species. Due to the way in which expression assays are normalized, such studies provide no direct information about expression per gene copy (dosage responses) or per cell and can give a misleading picture of genes that are differentially expressed. We describe an assay for estimating relative expression per cell. When used in conjunction with transcript profiling data, it is possible to compare the sizes of whole transcriptomes, which in turn makes it possible to compare expression per cell for each gene in the transcript profiling data set. We applied this approach, using quantitative reverse transcriptase-polymerase chain reaction and high throughput RNA sequencing, to a recently formed allopolyploid and showed that its leaf transcriptome was approximately 1.4-fold larger than either progenitor transcriptome (70% of the sum of the progenitor transcriptomes). In contrast, the allopolyploid genome is 94.3% as large as the sum of its progenitor genomes and retains ≥93.5% of the sum of its progenitor gene complements. Thus, “transcriptome downsizing” is greater than genome downsizing. Using this transcriptome size estimate, we inferred dosage responses for several thousand genes and showed that the majority exhibit partial dosage compensation. Homoeologue silencing is nonrandomly distributed across dosage responses, with genes showing extreme responses in either direction significantly more likely to have a silent homoeologue. This experimental approach will add value to transcript profiling experiments involving interspecies and interploidy comparisons by converting expression per transcriptome to expression per genome, eliminating the need for assumptions about transcriptome size

Long-standing nonkin relationships of older adults in the Netherlands and the United States

The main research questions of this study were (1) How long have adults in the Netherlands and the United States known members of their nonkin networks? (2) What are the predictors of long-standing nonkin relationships? and (3) Which predictors are recognizable in both societies? The data came from the NESTOR-LSN survey (3,229 adults aged 55 to 89 years in the Netherlands) and from the Northern California Community Study (n = 1,050, with 225 respondents aged 55 to 91 years in the United States). In both countries, the duration of nonkin relationships was related to the absence of network-disturbing variables (e.g., the number of years since the last move), network-sustaining variables (e.g., distance to nonkin), and other network properties (e.g., homogeneity). Nationally based differences were also observed (e.g., having a car was related to stable relationships only in the United States, and the special integrative functions of exclusive friendships were elicited only in Europe)

Mapping deliberation: calculation, articulation and intervention in the politics of organ transplantation

This paper reflects on the aims and outcomes of an innovative methodology of participatory technology appraisal, called Deliberative Mapping, which seeks to contribute to theoretical debates and practical experimentation around what it might mean to bring the technosciences into democracy. Deliberative Mapping is a hybrid methodology, involving both calculative and deliberative processes, which seeks to map the entanglements of biotechnological imbroglios, and translate these connections into the contexts of decision-making. Through application to the case study of organ transplantation, these procedures of calculation and articulation are critically examined, exploring their aim to reduce asymmetries between scientific, political, economic and other framings of the issue and their operation in contexts already complexly structured through existing power relations, which indicate the challenge of co-fabricating these experimental forms of intervention into political facts