High-speed 4 ×{\times} 4 silicon photonic electro-optic switch, operating at the 2 {\mu}m waveband

The escalating need for expansive data bandwidth, and the resulting capacity constraints of the single mode fiber (SMF) have positioned the 2-${\mu}$m waveband as a prospective window for emerging applications in optical communication. This has initiated an ecosystem of silicon photonic components in the region driven by CMOS compatibility, low cost, high efficiency and potential for large-scale integration. In this study, we demonstrate a plasma dispersive, 4 ${\times}$ 4 electro-optic switch operating at the 2-${\mu}$m waveband with the shortest switching times. The demonstrated switch operates across a 45-nm bandwidth, with 10-90% rise and 90-10% fall time of 1.78 ns and 3.02 ns respectively. In a 4 ${\times}$ 4 implementation, crosstalk below -15 dB and power consumption below 19.15 mW across all 16 ports are indicated. The result brings high-speed optical switching to the portfolio of devices at the promising waveband

Crown ether decorated silicon photonics for safeguarding against lead poisoning

Lead (Pb2+) toxification in society is one of the most concerning public health crisis that remains unaddressed. The exposure to Pb2+ poisoning leads to a multitude of enduring health issues, even at the part-per-billion scale (ppb). Yet, public action dwarfs its impact. Pb2+ poisoning is estimated to account for 1 million deaths per year globally, which is in addition to its chronic impact on children. With their ring-shaped cavities, crown ethers are uniquely capable of selectively binding to specific ions. In this work, for the first time, the synergistic integration of highly-scalable silicon photonics, with crown ether amine conjugation via Fischer esterification in an environmentally-friendly fashion is demonstrated. This realises a photonic platform that enables the in-situ, highly-selective and quantitative detection of various ions. The development dispels the existing notion that Fischer esterification is restricted to organic compounds, laying the ground for subsequent amine conjugation for various crown ethers. In this work, the platform is engineered for Pb2+ detection, demonstrating a large dynamic detection range of 1 - 262000 ppb with high selectivity against a wide range of relevant ions. These results indicate the potential for the pervasive implementation of the technology to safeguard against ubiquitous lead poisoning in our society

Dense sampling of bird diversity increases power of comparative genomics

© 2020, The Author(s). Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian (\u27marsupial\u27) species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation. ©2007 Nature Publishing Group

Functional EPAS1/ HIF2A Missense Variant Is Associated With Hematocrit in Andean Highlanders

Hypoxia-inducible factor pathway genes are linked to adaptation in both human and nonhuman highland species. EPAS1, a notable target of hypoxia adaptation, is associated with relatively lower hemoglobin concentration in Tibetans. We provide evidence for an association between an adaptive EPAS1 variant (rs570553380) and the same phenotype of relatively low hematocrit in Andean highlanders. This Andean-specific missense variant is present at a modest frequency in Andeans and absent in other human populations and vertebrate species except the coelacanth. CRISPR-base-edited human cells with this variant exhibit shifts in hypoxia-regulated gene expression, while metabolomic analyses reveal both genotype and phenotype associations and validation in a lowland population. Although this genocopy of relatively lower hematocrit in Andean highlanders parallels well-replicated findings in Tibetans, it likely involves distinct pathway responses based on a protein-coding versus noncoding variants, respectively. These findings illuminate how unique variants at EPAS1 contribute to the same phenotype in Tibetans and a subset of Andean highlanders despite distinct evolutionary trajectories

A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes

Recent studies have suggested that the thermodynamic stability of mRNA secondary structure near the start codon can regulate translation efficiency in Escherichia coli, and that translation is more efficient the less stable the secondary structure. We survey the complete genomes of 340 species for signals of reduced mRNA secondary structure near the start codon. Our analysis includes bacteria, archaea, fungi, plants, insects, fishes, birds, and mammals. We find that nearly all species show evidence for reduced mRNA stability near the start codon. The reduction in stability generally increases with increasing genomic GC content. In prokaryotes, the reduction also increases with decreasing optimal growth temperature. Within genomes, there is variation in the stability among genes, and this variation correlates with gene GC content, codon bias, and gene expression level. For birds and mammals, however, we do not find a genome-wide trend of reduced mRNA stability near the start codon. Yet the most GC rich genes in these organisms do show such a signal. We conclude that reduced stability of the mRNA secondary structure near the start codon is a universal feature of all cellular life. We suggest that the origin of this reduction is selection for efficient recognition of the start codon by initiator-tRNA

Late nitrogen application enhances spikelet number in indica hybrid rice (Oryza sativa L.)

ABSTRACT To increase rice yield potential, field experiments were conducted in farmers’ paddies in 2011 and 2012 to evaluate the effects of different nitrogen applications on the yield and panicle components of three typical indica hybrid rice varieties in Sichuan Province. The number of grains per panicle resulting from late nitrogen application (LA) was 12 % greater than that obtained from traditional nitrogen application (TA); this increase was the main source of improvements in yield. The number of surviving and differentiated spikelets (NSS and NDiS) resulting from LA was significantly higher than that measured under TA, especially for the Fyou498 cultivar, where the NSS and NDiS increased by 15 % and 14 %, respectively. Compared with TA, the number of degenerated secondary branches and the percentage of degenerated secondary branches (NDeSB and PDeSB) were significantly reduced by 9 % and 11 %, respectively, by LA. This is the first study to demonstrate that an increase in NSS and a decrease in NDeSB lead to yield-improving effects attributable to LA. The grain yields of different varieties ranged from 9225.6 to 9408.7 kg ha−1, the PDeSB was as high as 31 %, and the number of surviving secondary branches (NSSB) was significantly and positively correlated with NSS. These data indicate that the yield of indica hybrid rice has considerable potential for being improved, and increasing NSSB is key to increasing NSS and improving the grain yield. These improvements should be pursued so as to increase the yield of hybrid rice to ensure both food security and sustainable agricultural development