Scalable single-photon detection on a photonic chip

We developed a scalable method for integrating sub-70-ps-timing-jitter superconducting nanowire single-photon detectors with photonic integrated circuits. We assembled a photonic chip with four integrated detectors and performed the first on-chip g[superscript (2)](τ)-measurements of an entangled-photon source

Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae

Background: Rates of synonymous nucleotide substitutions are, in general, exceptionally low in plant mitochondrial genomes, several times lower than in chloroplast genomes, 10-20 times lower than in plant nuclear genomes, and 50-100 times lower than in many animal mitochondrial genomes. Several cases of moderate variation in mitochondrial substitution rates have been reported in plants, but these mostly involve correlated changes in chloroplast and/or nuclear substitution rates and are therefore thought to reflect whole-organism forces rather than ones impinging directly on the mitochondrial mutation rate. Only a single case of extensive, mitochondrial-specific rate changes has been described, in the angiosperm genus Plantago. Results: We explored a second potential case of highly accelerated mitochondrial sequence evolution in plants. This case was first suggested by relatively poor hybridization of mitochondrial gene probes to DNA of Pelargonium hortorum (the common geranium). We found that all eight mitochondrial genes sequenced from P. hortorum are exceptionally divergent, whereas chloroplast and nuclear divergence is unexceptional in P. hortorum. Two mitochondrial genes were sequenced from a broad range of taxa of variable relatedness to P. hortorum, and absolute rates of mitochondrial synonymous substitutions were calculated on each branch of a phylogenetic tree of these taxa. We infer one major, similar to 10-fold increase in the mitochondrial synonymous substitution rate at the base of the Pelargonium family Geraniaceae, and a subsequent similar to 10-fold rate increase early in the evolution of Pelargonium. We also infer several moderate to major rate decreases following these initial rate increases, such that the mitochondrial substitution rate has returned to normally low levels in many members of the Geraniaceae. Finally, we find unusually little RNA editing of Geraniaceae mitochondrial genes, suggesting high levels of retroprocessing in their history. Conclusion: The existence of major, mitochondrial-specific changes in rates of synonymous substitutions in the Geraniaceae implies major and reversible underlying changes in the mitochondrial mutation rate in this family. Together with the recent report of a similar pattern of rate heterogeneity in Plantago, these findings indicate that the mitochondrial mutation rate is a more plastic character in plants than previously realized. Many molecular factors could be responsible for these dramatic changes in the mitochondrial mutation rate, including nuclear gene mutations affecting the fidelity and efficacy of mitochondrial DNA replication and/or repair and consistent with the lack of RNA editing - exceptionally high levels of mutagenic retroprocessing. That the mitochondrial mutation rate has returned to normally low levels in many Geraniaceae raises the possibility that, akin to the ephemerality of mutator strains in bacteria, selection favors a low mutation rate in plant mitochondria

Membrane-integrated superconducting nanowire single-photon detectors

CLEO: QELS--Fundamental Science, San Jose, California United States, June 9-14, 2013We integrated superconducting nanowire single-photon detectors on sub-400-nm-thick silicon nitride membranes, which can then be transferred and aligned to photonic structures on a secondary chip with sub-micron placement accuracy

On-Chip Detection of Entangled Photons by Scalable Integration of Single-Photon Detectors

Photonic integrated circuits (PICs) have emerged as a scalable platform for complex quantum technologies using photonic and atomic systems. A central goal has been to integrate photon-resolving detectors to reduce optical losses, latency, and wiring complexity associated with off-chip detectors. Superconducting nanowire single-photon detectors (SNSPDs) are particularly attractive because of high detection efficiency, sub-50-ps timing jitter, nanosecond-scale reset time, and sensitivity from the visible to the mid-infrared spectrum. However, while single SNSPDs have been incorporated into individual waveguides, the system efficiency of multiple SNSPDs in one photonic circuit has been limited below 0.2% due to low device yield. Here we introduce a micrometer-scale flip-chip process that enables scalable integration of SNSPDs on a range of PICs. Ten low-jitter detectors were integrated on one PIC with 100% device yield. With an average system efficiency beyond 10% for multiple SNSPDs on one PIC, we demonstrate high-fidelity on-chip photon correlation measurements of non-classical light.Comment: 27 pages, manuscript including supporting informatio

Origin and evolution of the octoploid strawberry genome.

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry

Properties of bio-based insulation materials and their potential impact on indoor air quality

Significantly decreasing energy consumption in buildings requires more air-tight construction combined with much higher insulation levels. A potential unintended consequence of this approach has been deterioration in the indoor air quality, resulting from significantly reduced ventilation rates and the accumulation of airborne pollutants, and this has proven to be a bottleneck to successful implementation of legislation. The use of natural bio-based insulation materials has increased in recent years, largely driven by concerns over the embodied energy and whole-life environmental impact of insulation materials. This has led to their increased use, typically within breathable wall constructions. A breathable wall construction allows the insulation material to directly contribute to the indoor air quality.Volatile Organic Compounds (VOCs) having boiling points within the range 60-280 °C contribute to the indoor air contamination in buildings, and at certain concentrations can contribute to building-related illnesses. This paper presents some findings from the early stages of a phased experimental study to explore use of bio-based insulation materials, including hemp-lime and sheep’s wool, to reduce VOCs from the room atmosphere. There are many different volatile organic compounds and this study will consider the Total Volatile Organic Compound (TVOC) emissions expressed as toluene, as well as the formaldehyde emissions separately.Insulation specimens with nominal dimensions 200 x 60 x 50 mm were prepared and placed in horizontally mounted cylindrical chambers. Air maintained at 23 °C (±2 °C) and 50 % (±5 %) RH was fed in coaxially to one end of the cylinder. The exhaust air was sampled for VOCs and for formaldehyde following 3 and 28 day of exposure. The results of this paper will help inform the design of holistic indoor environments that consider more than just the hygrothermal properties of insulation materials

Bio-based plaster for improved indoor air quality

People in industrialised countries spend approximately 80% of their time indoors. As such, the internal environment quality can have a significant impact on occupant health and wellbeing. Additionally, the demand for increased building energy efficiency has the potential to degrade Indoor Air Quality (IAQ) through a reduction of air exchange rates. In many forms of construction, the walls and ceilings are plastered, providing a large surface area exposed to the indoor environment. There is a growing recognition of the important role this surface may have on IAQ through regulation of relative humidity. Another, less well known, impact is that porous coatings have the potential to adsorb Volatile Organic Compounds (VOCs) from the air, which offers further potential to improve IAQ.This paper presents work from the development of a novel bio-based plaster with improved hygrothermal performance and VOC sorption characteristics. Cellulose flakes, used for blown insulation, were added into a cement-lime substrate in three different proportions. A range of mechanical, hygrothermal, VOC emission and VOC adsorption properties were investigated to evaluate the potential of the bio-based cement-lime plaster to improve IAQ. The bio-based cement-lime plaster resulted in an improved thermal conductivity and an improvement in the material’s moisture buffering capacity and VOC adsorption capacity. With 5% addition of cellulose flakes, the hygrothermal performance increased by over 25%. This material also showed the ability to capture VOCs and formaldehyde from the air, reducing the concentrations of these compounds by up to 22% and 70 % respectively. Therefore, the impact of the implementation of this plaster includes potential benefits regarding better operational performance of the building and improved occupant health and wellbeing.<br/

The Mitochondrial Genome of the Legume Vigna radiata and the Analysis of Recombination across Short Mitochondrial Repeats

The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean), and show that despite its unexceptional size (401,262 nt), the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38–297 nt) repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes

Recent Acceleration of Plastid Sequence and Structural Evolution Coincides with Extreme Mitochondrial Divergence in the Angiosperm Genus Silene

The angiosperm genus Silene exhibits some of the most extreme and rapid divergence ever identified in mitochondrial genome architecture and nucleotide substitution rates. These patterns have been considered mitochondrial specific based on the absence of correlated changes in the small number of available nuclear and plastid gene sequences. To better assess the relationship between mitochondrial and plastid evolution, we sequenced the plastid genomes from four Silene species with fully sequenced mitochondrial genomes. We found that two species with fast-evolving mitochondrial genomes, S. noctiflora and S. conica, also exhibit accelerated rates of sequence and structural evolution in their plastid genomes. The nature of these changes, however, is markedly different from those in the mitochondrial genome. For example, in contrast to the mitochondrial pattern, which appears to be genome wide and mutationally driven, the plastid substitution rate accelerations are restricted to a subset of genes and preferentially affect nonsynonymous sites, indicating that altered selection pressures are acting on specific plastid-encoded functions in these species. Indeed, some plastid genes in S. noctiflora and S. conica show strong evidence of positive selection. In contrast, two species with more slowly evolving mitochondrial genomes, S. latifolia and S. vulgaris, have correspondingly low rates of nucleotide substitution in plastid genes as well as a plastid genome structure that has remained essentially unchanged since the origin of angiosperms. These results raise the possibility that common evolutionary forces could be shaping the extreme but distinct patterns of divergence in both organelle genomes within this genus