SummarySymbiosis between unicellular dinoflagellates (genus Symbiodinium) and their cnidarian hosts (e.g. corals, sea anemones) is the foundation of coral reef ecosystems. Dysfunction of this symbiosis under changing environmental conditions has led to global reef decline. Little information is known about Symbiodinium gene expression and mechanisms by which light impacts host–symbiont associations. To address these issues, we generated a transcriptome from axenic Symbiodinium strain SSB01. Here we report features of the transcriptome, including occurrence and length distribution of spliced leader sequences, the functional landscape of encoded proteins and the impact of light on gene expression. Expression of many Symbiodinium genes appears to be significantly impacted by light. Transcript encoding cryptochrome 2 declined in high light while some transcripts for Regulators of Chromatin Condensation (RCC1) declined in the dark. We also identified a transcript encoding a light harvesting AcpPC protein with homology to Chlamydomonas LHCSR2. The level of this transcript increased in high light autotrophic conditions, suggesting that it is involved in photo‐protection and the dissipation of excess absorbed light energy. The most extensive changes in transcript abundances occurred when the algae were transferred from low light to darkness. Interestingly, transcripts encoding several cell adhesion proteins rapidly declined following movement of cultures to the dark, which correlated with a dramatic change in cell surface morphology, likely reflecting the complexity of the extracellular matrix. Thus, light‐sensitive cell adhesion proteins may play a role in establishing surface architecture, which may in turn alter interactions between the endosymbiont and its host.

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To investigate the epigenetic landscape at the interface between mother and fetus, we provide a comprehensive analysis of parent-of-origin bias in the mouse placenta. Using F1 interspecies hybrids between mus musculus (C57BL/6J) and mus musculus castaneus, we sequenced RNA from 23 individual midgestation placentas, five late stage placentas, and two yolk sac samples and then used SNPs to determine whether transcripts were preferentially generated from the maternal or paternal allele. In the placenta, we find 103 genes that show significant and reproducible parent-of-origin bias, of which 78 are novel candidates. Most (96%) show a strong maternal bias which we demonstrate, via multiple mathematical models, pyrosequencing, and FISH, is not due to maternal decidual contamination. Analysis of the X chromosome also reveals paternal expression of Xist and several genes that escape inactivation, most significantly Alas2, Fhl1, and Slc38a5. Finally, sequencing individual placentas allowed us to reveal notable expression similarity between littermates. In all, we observe a striking preference for maternal transcription in the midgestation mouse placenta and a dynamic imprinting landscape in extraembryonic tissues, reflecting the complex nature of epigenetic pathways in the placenta.

A 3D woodpile structure tunable plasma photonic crystal is designed, simulated, and experimentally characterized over the S -X band of the electromagnetic spectrum. The measurements confirm that the electromagnetic response is rich in dynamics. The photonic crystal's reconfigurability, achieved through individual discharge control of the properties of the woodpile plasma columns, offers an unprecedented opportunity to better resolve the interactions between both the Bragg and localized surface plasmon modes which dominate the spectrum at lower frequencies.Both the experiments and simulations reveal evidence for the coupling of Bragg and surface plasmon modes through a Fano resonance. arXiv:1810.02000v1 [physics.app-ph] 3 Oct 2018 3D woodpile structure tunable plasma photonic crystal

Identity-by-descent (IBD) inference is the problem of establishing a genetic connection between two individuals through a genomic segment that is inherited by both individuals from a recent common ancestor. IBD inference is an important preceding step in a variety of population genomic studies, ranging from demographic studies to linking genomic variation with phenotype and disease. The problem of accurate IBD detection has become increasingly challenging with the availability of large collections of human genotypes and genomes: Given a cohort's size, a quadratic number of pairwise genome comparisons must be performed. Therefore, computation time and the false discovery rate can also scale quadratically. To enable accurate and efficient large-scale IBD detection, we present Parente2, a novel method for detecting IBD segments. Parente2 is based on an embedded log-likelihood ratio and uses a model that accounts for linkage disequilibrium by explicitly modeling haplotype frequencies. Parente2 operates directly on genotype data without the need to phase data prior to IBD inference. We evaluate Parente2's performance through extensive simulations using real data, and we show that it provides substantially higher accuracy compared to previous state-of-the-art methods while maintaining high computational efficiency.[Supplemental material is available for this article.]When two individuals co-inherit a genomic segment from a common ancestor, the shared haplotypes are identical to each other except for occasional lineage-specific de novo mutations. Such shared segments are called identical-by-descent (IBD).Computational detection of IBD segments from genotyping or sequencing data serves as the foundation for many downstream applications . IBD detection is the prevalent method for finding familial relatives in direct-to-consumer genomics companies such as 23andMe (23andme.com) and AncestryDNA (ancestry.com) and is a key step in analyzing relatedness within a population and across populations; for example, IBD analysis was applied to study the demographic history across Ashkenazi Jewish and Masai populations (Palamara et al. 2012), to demonstrate increased sharing across Welsh individuals as compared to individuals from other regions in the United Kingdom (Browning and Browning 2011), and to compare relatedness across hunting-gathering, agricultural, and pastoralist African populations (Soi et al. 2011). IBD detection was also shown to be useful in estimating narrow-sense (additive) heritability Extensive previous work has focused on developing methods for IBD segment detection. One of the earlier methods, PLINK (Purcell et al. 2007), uses a three-state hidden Markov model (HMM) with states corresponding to zero, one or two co-inherited copies of the genome, and assumes that all markers are in linkage equilibrium. BEAGLE IBD (Browning and Browning 2010) uses a model of haplotype frequencies that simultaneously phases and infers the particular shared haplotype by a pair of individuals. BEAGLE IBD is based on a factorial HMM...