Low-coherence interferometric measurement of the spectral dependence of the light field backscattered by optical interfaces

In this paper, we show how the combined use of low coherence interferometry, balanced detection and data processing comparable to that used in Fourier transform spectrometry allows us to characterize with ultimate resolutions (sub-ppm in level, 0.2 nm in wavelength and 5 mdeg in angle) the retro-reflection and retro-scattering response of both sides of a 2 mm thick silica wafer

Refractive index determination of SiO2 layer in the UV/Vis/NIR range: spectrophotometric reverse engineering on single and bi-layer designs

In this paper we use spectrophotometric measurements and a Clustering Global Optimization procedure to determine the complex refractive index of SiO2 layer from 250 nm to 1250 nm. A special commercial optical module allows the reflection and transmission measurements to be made under exactly the same illumination and measurement conditions. We compare the index determination results obtained from two different single layer SiO2 samples, with high and low index glass substrates, respectively. We then determine the refractive index of SiO2 for a bi-layer design in which the first deposited layer is Ta2O5. The corresponding solutions are discussed and we show that the real part of the complex refractive index obtained for a bi-layer is slightly different to that found for a single layer investigation. When SiO2 is included inside a thin film stack, we propose the use of an index determination method in which a bi-layer is used for the real part of the complex refractive index, and single layer determination is used for the imaginary part of the refractive index in the UV range

The Viral Susceptibility of the Haloferax Species

Viruses can infect members of all three domains of life. However, little is known about viruses infecting archaea and the mechanisms that determine their host interactions are poorly understood. Investigations of molecular mechanisms of viral infection rely on genetically accessible virus–host model systems. Euryarchaea belonging to the genus Haloferax are interesting models, as a reliable genetic system and versatile microscopy methods are available. However, only one virus infecting the Haloferax species is currently available. In this study, we tested ~100 haloarchaeal virus isolates for their infectivity on 14 Haloferax strains. From this, we identified 10 virus isolates in total capable of infecting Haloferax strains, which represented myovirus or siphovirus morphotypes. Surprisingly, the only susceptible strain of all 14 tested was Haloferax gibbonsii LR2-5, which serves as an auspicious host for all of these 10 viruses. By applying comparative genomics, we shed light on factors determining the host range of haloarchaeal viruses on Haloferax. We anticipate our study to be a starting point in the study of haloarchaeal virus–host interactions

The viral susceptibility of the <i>Haloferax</i> species

Viruses can infect members of all three domains of life. However, little is known about viruses infecting archaea and the mechanisms that determine their host interactions are poorly understood. Investigations of molecular mechanisms of viral infection rely on genetically accessible virus–host model systems. Euryarchaea belonging to the genus Haloferax are interesting models, as a reliable genetic system and versatile microscopy methods are available. However, only one virus infecting the Haloferax species is currently available. In this study, we tested ~100 haloarchaeal virus isolates for their infectivity on 14 Haloferax strains. From this, we identified 10 virus isolates in total capable of infecting Haloferax strains, which represented myovirus or siphovirus morphotypes. Surprisingly, the only susceptible strain of all 14 tested was Haloferax gibbonsii LR2-5, which serves as an auspicious host for all of these 10 viruses. By applying comparative genomics, we shed light on factors determining the host range of haloarchaeal viruses on Haloferax. We anticipate our study to be a starting point in the study of haloarchaeal virus–host interaction

The Viral Susceptibility of the Haloferax Species

Viruses can infect members of all three domains of life. However, little is known about viruses infecting archaea and the mechanisms that determine their host interactions are poorly understood. Investigations of molecular mechanisms of viral infection rely on genetically accessible virus–host model systems. Euryarchaea belonging to the genus Haloferax are interesting models, as a reliable genetic system and versatile microscopy methods are available. However, only one virus infecting the Haloferax species is currently available. In this study, we tested ~100 haloarchaeal virus isolates for their infectivity on 14 Haloferax strains. From this, we identified 10 virus isolates in total capable of infecting Haloferax strains, which represented myovirus or siphovirus morphotypes. Surprisingly, the only susceptible strain of all 14 tested was Haloferax gibbonsii LR2-5, which serves as an auspicious host for all of these 10 viruses. By applying comparative genomics, we shed light on factors determining the host range of haloarchaeal viruses on Haloferax. We anticipate our study to be a starting point in the study of haloarchaeal virus–host interactions

Electrohydrodynamic Jet Printing of 1D Photonic Crystals: Part II—Optical Design and Reflectance Characteristics

Additive manufacturing systems that can arbitrarily deposit multiple materials into precise, 3D spaces spanning the micro‐ to nanoscale are enabling novel structures with useful thermal, electrical, and optical properties. In this companion paper set, electrohydrodynamic jet (e‐jet) printing is investigated for its ability in depositing multimaterial, multilayer films with microscale spatial resolution and nanoscale thickness control, with a demonstration of this capability in creating 1D photonic crystals (1DPCs) with response near the visible regime. Transfer matrix simulations are used to evaluate different material classes for use in a printed 1DPC, and commercially available photopolymers with varying refractive indices (n = 1.35 to 1.70) are selected based on their relative high index contrast and fast curing times. E‐jet printing is then used to experimentally demonstrate pixelated 1DPCs with individual layer thicknesses between 80 and 200 nm, square pixels smaller than 40 µm across, with surface roughness less than 20 nm. The reflectance characteristics of the printed 1DPCs are measured using spatially selective microspectroscopy and correlated to the transfer matrix simulations. These results are an important step toward enabling cost‐effective, custom‐fabrication of advanced imaging devices or photonic crystal sensing platforms.Electrohydrodynamic jet printing is used to create patterned arrays of multimaterial photopolymer 1D photonic crystals. Patterns are demonstrated with in‐plane dimensions below 40 µm, layer thicknesses less than 100 nm, and surface root mean square roughness below 20 nm. This novel fabrication method can enable rapid, reconfigurable manufacturing of custom photonic sensing arrays.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163389/2/admt202000431-sup-0001-SuppMat.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163389/1/admt202000431.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163389/3/admt202000431_am.pd

Highly divergent CRESS DNA and picorna-like viruses associated with bleached thalli of the green seaweed <i>Ulva</i>

Marine macroalgae (seaweeds) are important primary producers and foundation species in coastal ecosystems around the world. Seaweeds currently contribute to an estimated 51% of the global mariculture production, with a long-term growth rate of 6% per year, and an estimated market value of more than US$11.3 billion. Viral infections could have a substantial impact on the ecology and aquaculture of seaweeds, but surprisingly little is known about virus diversity in macroalgal hosts. Using metagenomic sequencing, we characterized viral communities associated with healthy and bleached specimens of the commercially important green seaweed Ulva. We identified 20 putative new and divergent viruses, of which the majority belonged to the Circular Rep-Encoding Single-Stranded (CRESS) DNA viruses [single-stranded (ss)DNA genomes], Durnavirales [double-stranded (ds)RNA], and Picornavirales (ssRNA). Other newly identified RNA viruses were related to the Ghabrivirales, the Mitoviridae, and the Tombusviridae. Bleached Ulva samples contained particularly high viral read numbers. While reads matching assembled CRESS DNA viruses and picorna-like viruses were nearly absent from the healthy Ulva samples (confirmed by qPCR), they were very abundant in the bleached specimens. Therefore, bleaching in Ulva could be caused by one or a combination of the identified viruses but may also be the result of another causative agent or abiotic stress, with the viruses simply proliferating in already unhealthy seaweed tissue. This study highlights how little we know about the diversity and ecology of seaweed viruses, especially in relation to the health and diseases of the algal host, and emphasizes the need to better characterize the algal virosphere. IMPORTANCE Green seaweeds of the genus Ulva are considered a model system to study microbial interactions with the algal host. Remarkably little is known, however, about viral communities associated with green seaweeds, especially in relation to the health of the host. In this study, we characterized the viral communities associated with healthy and bleached Ulva. Our findings revealed the presence of 20 putative novel viruses associated with Ulva, encompassing both DNA and RNA viruses. The majority of these viruses were found to be especially abundant in bleached Ulva specimens. This is the first step toward understanding the role of viruses in the ecology and aquaculture of this green seaweed.</p

International round-robin experiment for angle-resolved light scattering measurement

International audienc

Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic

The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples prior to the autumn peak. 1918 IAV genomic diversity is consistent with a combination of local transmission and long-distance dispersal events. Comparison of genomes before and during the pandemic peak shows variation at two sites in the nucleoprotein gene associated with resistance to host antiviral response, pointing at a possible adaptation of 1918 IAV to humans. Finally, local molecular clock modeling suggests a pure pandemic descent of seasonal H1N1 IAV as an alternative to the hypothesis of origination through an intrasubtype reassortment.Peer Reviewe

Endogenous viral elements in shrew genomes provide insights into Pestivirus ancient history

As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large dataset of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general