The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Joining Policy Forums Together to Develop <i>Ki-no-Eki</i>, a Community Currency System for Forest Management in Japan: Dynamics of Policy Communication Networks

In some mountainous areas of Japan, the Ki-no-Eki system, in which wood is collected to thin the forest and is exchanged for community currency, has been specifically designed and implemented as a solution to current and emerging forest governance issues. This study aimed to capture the evolutionary processes of a complete communication network consisting of organizations that joined policy forums to help develop the Ki-no-Eki system. A total of 26 policy forums were held from 2011 to 2019 to discuss the adoption and implementation of the Ki-no-Eki system across Japan, and coattendance and the resultant policy discourses among 62 participating Ki-no-Eki organizations in these forums were regarded as dynamic communication network processes. We analyzed how policy communication networks formed and evolved to understand the underlying network dynamics driven by not only endogenous network processes—bonding and bridging social capital—but also exogenous effects defined by actors’ attributes. We employed the stochastic actor-oriented model for network dynamics to manage the collected longitudinal undirected network data. We found (i) the emergence of bonding social capital and (ii) homophilic and heterophilic connections in communication networks, which provided insightful explanations of the driving forces of social cohesion among Ki-no-Eki organizations engaged in forest management in Japan

Joining Policy Forums Together to Develop Ki-no-Eki, a Community Currency System for Forest Management in Japan: Dynamics of Policy Communication Networks

In some mountainous areas of Japan, the Ki-no-Eki system, in which wood is collected to thin the forest and is exchanged for community currency, has been specifically designed and implemented as a solution to current and emerging forest governance issues. This study aimed to capture the evolutionary processes of a complete communication network consisting of organizations that joined policy forums to help develop the Ki-no-Eki system. A total of 26 policy forums were held from 2011 to 2019 to discuss the adoption and implementation of the Ki-no-Eki system across Japan, and coattendance and the resultant policy discourses among 62 participating Ki-no-Eki organizations in these forums were regarded as dynamic communication network processes. We analyzed how policy communication networks formed and evolved to understand the underlying network dynamics driven by not only endogenous network processes&mdash;bonding and bridging social capital&mdash;but also exogenous effects defined by actors&rsquo; attributes. We employed the stochastic actor-oriented model for network dynamics to manage the collected longitudinal undirected network data. We found (i) the emergence of bonding social capital and (ii) homophilic and heterophilic connections in communication networks, which provided insightful explanations of the driving forces of social cohesion among Ki-no-Eki organizations engaged in forest management in Japan

Advantageous characteristics of the diatom Chaetoceros gracilis as a sustainable biofuel producer

[Background]Diatoms have attracted interest as biofuel producers. Here, the contents of lipids and photosynthetic pigments were analyzed in a marine centric diatom, Chaetoceros gracilis. This diatom can be genetically engineered using our previously reported transformation technique and has a potential to produce valuable materials photosynthetically. Sustainable culture conditions for cost-effective production of biological materials under autotrophic conditions with atmospheric carbon dioxide were investigated in the laboratory. A large-scale, open-air culture was also performed. [Results]Cell population doubling time was ~10 h under continuous illumination without CO2enrichment, and large amounts of triacylglycerols (TAG) and fucoxanthin accumulated under a wide range of salinity and nutrient conditions, reaching ~200 and 18.5 mg/L, respectively. It was also shown that C. gracilis produced high amounts of TAG without the need for nitrogen or silica deprivation, which is frequently imposed to induce lipid production in many other microalgae. Furthermore, C. gracilis was confirmed to be highly tolerant to changes in environmental conditions, such as salinity. The diatom grew well and produced abundant lipids when using sewage water or liquid fertilizer derived from cattle feces without augmented carbon dioxide. High growth rates (doubling time <20 h) were obtained in a large-scale, open-air culture, in which light irradiance and temperature fluctuated and were largely different from laboratory conditions. [Conclusions]The ability of this microalga to accumulate TAG without nutrient deprivation, which incurs added labor, high costs, and complicates scalability, is important for low-cost industrial applications. Furthermore, its high tolerance to changes in environmental conditions and high growth rates observed in large-scale, open-air culture implied scalability of this diatom for industrial applications. Therefore, C. gracilis would have great potential as a biofactory