95 research outputs found
An Integrated-Photonics Optical-Frequency Synthesizer
Integrated-photonics microchips now enable a range of advanced
functionalities for high-coherence applications such as data transmission,
highly optimized physical sensors, and harnessing quantum states, but with
cost, efficiency, and portability much beyond tabletop experiments. Through
high-volume semiconductor processing built around advanced materials there
exists an opportunity for integrated devices to impact applications cutting
across disciplines of basic science and technology. Here we show how to
synthesize the absolute frequency of a lightwave signal, using integrated
photonics to implement lasers, system interconnects, and nonlinear frequency
comb generation. The laser frequency output of our synthesizer is programmed by
a microwave clock across 4 THz near 1550 nm with 1 Hz resolution and
traceability to the SI second. This is accomplished with a heterogeneously
integrated III/V-Si tunable laser, which is guided by dual
dissipative-Kerr-soliton frequency combs fabricated on silicon chips. Through
out-of-loop measurements of the phase-coherent, microwave-to-optical link, we
verify that the fractional-frequency instability of the integrated photonics
synthesizer matches the reference-clock instability for a 1
second acquisition, and constrain any synthesis error to while
stepping the synthesizer across the telecommunication C band. Any application
of an optical frequency source would be enabled by the precision optical
synthesis presented here. Building on the ubiquitous capability in the
microwave domain, our results demonstrate a first path to synthesis with
integrated photonics, leveraging low-cost, low-power, and compact features that
will be critical for its widespread use.Comment: 10 pages, 6 figure
Targeted single molecule sequencing methodology for ovarian hyperstimulation syndrome
BACKGROUND: One of the most significant issues surrounding next generation sequencing is the cost and the difficulty assembling short read lengths. Targeted capture enrichment of longer fragments using single molecule sequencing (SMS) is expected to improve both sequence assembly and base-call accuracy but, at present, there are very few examples of successful application of these technologic advances in translational research and clinical testing. We developed a targeted single molecule sequencing (T-SMS) panel for genes implicated in ovarian response to controlled ovarian hyperstimulation (COH) for infertility. RESULTS: Target enrichment was carried out using droplet-base multiplex polymerase chain reaction (PCR) technology (RainDanceÂź) designed to yield amplicons averaging 1Â kb fragment size from candidate 44 loci (99.8% unique base-pair coverage). The total targeted sequence was 3.18Â Mb per sample. SMS was carried out using single molecule, real-time DNA sequencing (SMRTÂź Pacific BiosciencesÂź), average raw read lengthâ=â1178 nucleotides, 5% of the amplicons >6000 nucleotides). After filtering with circular consensus (CCS) reads, the mean read length was 3200 nucleotides (97% CCS accuracy). Primary data analyses, alignment and filtering utilized the Pacific BiosciencesÂź SMRT portal. Secondary analysis was conducted using the Genome Analysis Toolkit for SNP discovery l and wANNOVAR for functional analysis of variants. Filtered functional variants 18 of 19 (94.7%) were further confirmed using conventional Sanger sequencing. CCS reads were able to accurately detect zygosity. Coverage within GC rich regions (i.e.VEGFR; 72% GC rich) was achieved by capturing long genomic DNA (gDNA) fragments and reading into regions that flank the capture regions. As proof of concept, a non-synonymous LHCGR variant captured in two severe OHSS cases, and verified by conventional sequencing. CONCLUSIONS: Combining emulsion PCR-generated 1Â kb amplicons and SMRT DNA sequencing permitted greater depth of coverage for T-SMS and facilitated easier sequence assembly. To the best of our knowledge, this is the first report combining emulsion PCR and T-SMS for long reads using human DNA samples, and NGS panel designed for biomarker discovery in OHSS. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1451-2) contains supplementary material, which is available to authorized users
Future Atmospheric Rivers and Impacts on Precipitation: Overview of the ARTMIP Tier 2 HighâResolution Global Warming Experiment
Atmospheric rivers (ARs) are long, narrow synoptic scale weather features important for Earthâs hydrological cycle typically transporting water vapor poleward, delivering precipitation important for local climates. Understanding ARs in a warming climate is problematic because the AR response to climate change is tied to how the feature is defined. The Atmospheric River Tracking Method Intercomparison Project (ARTMIP) provides insights into this problem by comparing 16 atmospheric river detection tools (ARDTs) to a common data set consisting of high resolution climate change simulations from a global atmospheric general circulation model. ARDTs mostly show increases in frequency and intensity, but the scale of the response is largely dependent on algorithmic criteria. Across ARDTs, bulk characteristics suggest intensity and spatial footprint are inversely correlated, and most focus regions experience increases in precipitation volume coming from extreme ARs. The spread of the AR precipitation response under climate change is large and dependent on ARDT selection
A Single Nucleotide Polymorphism within the Novel Sex-Linked Testis-Specific Retrotransposed PGAM4 Gene Influences Human Male Fertility
The development of novel fertilization treatments, including in vitro fertilization and intracytoplasmic injection, has made pregnancy possible regardless of the level of activity of the spermatozoa; however, the etiology of male-factor infertility is poorly understood. Multiple studies, primarily through the use of transgenic animals, have contributed to a list of candidate genes that may affect male infertility in humans. We examined single nucleotide polymorphisms (SNPs) as a cause of male infertility in an analysis of spermatogenesis-specific genes.We carried out the prevalence of SNPs in the coding region of phosphoglycerate mutase 4 (PGAM4) on the X chromosome by the direct sequencing of PCR-amplified DNA from male patients. Using RT-PCR and western blot analyses, we identified that PGAM4 is a functional retrogene that is expressed predominantly in the testes and is associated with male infertility. PGAM4 is expressed in post-meiotic stages, including spermatids and spermatozoa in the testes, and the principal piece of the flagellum and acrosome in ejaculated spermatozoa. A case-control study revealed that 4.5% of infertile patients carry the G75C polymorphism, which causes an amino acid substitution in the encoded protein. Furthermore, an assay for enzymatic activity demonstrated that this polymorphism decreases the enzyme's activity both in vitro and in vivo.These results suggest that PGAM4, an X-linked retrogene, is a fundamental gene in human male reproduction and may escape meiotic sex chromosome inactivation. These findings provide fresh insight into elucidating the mechanisms of male infertility
Relative sea-level rise around East Antarctica during Oligocene glaciation
During the middle and late Eocene (âŒ48-34 Myr ago), the Earth's climate cooled and an ice sheet built up on Antarctica. The stepwise expansion of ice on Antarcticainduced crustal deformation and gravitational perturbations around the continent. Close to the ice sheet, sea level rosedespite an overall reduction in the mass of the ocean caused by the transfer of water to the ice sheet. Here we identify the crustal response to ice-sheet growth by forcing a glacial-hydro isostatic adjustment model with an Antarctic ice-sheet model. We find that the shelf areas around East Antarctica first shoaled as upper mantle material upwelled and a peripheral forebulge developed. The inner shelf subsequently subsided as lithosphere flexure extended outwards from the ice-sheet margins. Consequently the coasts experienced a progressive relative sea-level rise. Our analysis of sediment cores from the vicinity of the Antarctic ice sheet are in agreement with the spatial patterns of relative sea-level change indicated by our simulations. Our results are consistent with the suggestion that near-field processes such as local sea-level change influence the equilibrium state obtained by an icesheet grounding line
The Atmospheric River Tracking Method Intercomparison Project (ARTMIP): Quantifying Uncertainties in Atmospheric River Climatology
Atmospheric rivers (ARs) are now widely known for their association with highâimpact weather events and longâterm water supply in many regions. Researchers within the scientific community have developed numerous methods to identify and track of ARsâa necessary step for analyses on gridded data sets, and objective attribution of impacts to ARs. These different methods have been developed to answer specific research questions and hence use different criteria (e.g., geometry, threshold values of key variables, and time dependence). Furthermore, these methods are often employed using different reanalysis data sets, time periods, and regions of interest. The goal of the Atmospheric River Tracking Method Intercomparison Project (ARTMIP) is to understand and quantify uncertainties in AR science that arise due to differences in these methods. This paper presents results for key ARârelated metrics based on 20+ different AR identification and tracking methods applied to ModernâEra Retrospective Analysis for Research and Applications Version 2 reanalysis data from January 1980 through June 2017. We show that AR frequency, duration, and seasonality exhibit a wide range of results, while the meridional distribution of these metrics along selected coastal (but not interior) transects are quite similar across methods. Furthermore, methods are grouped into criteriaâbased clusters, within which the range of results is reduced. AR case studies and an evaluation of individual method deviation from an allâmethod mean highlight advantages/disadvantages of certain approaches. For example, methods with less (more) restrictive criteria identify more (less) ARs and ARârelated impacts. Finally, this paper concludes with a discussion and recommendations for those conducting ARârelated research to consider.Fil: Rutz, Jonathan J.. National Ocean And Atmospheric Administration; Estados UnidosFil: Shields, Christine A.. National Center for Atmospheric Research; Estados UnidosFil: Lora, Juan M.. University of Yale; Estados UnidosFil: Payne, Ashley E.. University of Michigan; Estados UnidosFil: Guan, Bin. California Institute of Technology; Estados UnidosFil: Ullrich, Paul. University of California at Davis; Estados UnidosFil: O'Brien, Travis. Lawrence Berkeley National Laboratory; Estados UnidosFil: Leung, Ruby. Pacific Northwest National Laboratory; Estados UnidosFil: Ralph, F. Martin. Center For Western Weather And Water Extremes; Estados UnidosFil: Wehner, Michael. Lawrence Berkeley National Laboratory; Estados UnidosFil: Brands, Swen. Meteogalicia; EspañaFil: Collow, Allison. Universities Space Research Association; Estados UnidosFil: Goldenson, Naomi. University of California at Los Angeles; Estados UnidosFil: Gorodetskaya, Irina. Universidade de Aveiro; PortugalFil: Griffith, Helen. University of Reading; Reino UnidoFil: Kashinath, Karthik. Lawrence Bekeley National Laboratory; Estados UnidosFil: Kawzenuk, Brian. Center For Western Weather And Water Extremes; Reino UnidoFil: Krishnan, Harinarayan. Lawrence Berkeley National Laboratory; Estados UnidosFil: Kurlin, Vitaliy. University of Liverpool; Reino UnidoFil: Lavers, David. European Centre For Medium-range Weather Forecasts; Estados UnidosFil: Magnusdottir, Gudrun. University of California at Irvine; Estados UnidosFil: Mahoney, Kelly. Universidad de Lisboa; PortugalFil: Mc Clenny, Elizabeth. University of California at Davis; Estados UnidosFil: Muszynski, Grzegorz. University of Liverpool; Reino Unido. Lawrence Bekeley National Laboratory; Estados UnidosFil: Nguyen, Phu Dinh. University of California at Irvine; Estados UnidosFil: Prabhat, Mr.. Lawrence Bekeley National Laboratory; Estados UnidosFil: Qian, Yun. Pacific Northwest National Laboratory; Estados UnidosFil: Ramos, Alexandre M.. Universidade Nova de Lisboa; PortugalFil: Sarangi, Chandan. Pacific Northwest National Laboratory; Estados UnidosFil: Viale, Maximiliano. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Centro CientĂfico TecnolĂłgico Conicet - Mendoza. Instituto Argentino de NivologĂa, GlaciologĂa y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de NivologĂa, GlaciologĂa y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de NivologĂa, GlaciologĂa y Ciencias Ambientales; Argentin
Robust estimation of bacterial cell count from optical density
Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data
Comparative transcriptomics reveals shared gene expression changes during independent evolutionary origins of stem and hypocotyl/root tubers in <i>Brassica</i> (Brassicaceae)
<div><p>Plant succulence provides a classic example of evolutionary convergence in over 40 plant families. If evolutionary parallelism is in fact responsible for separate evolutionary origins of expanded storage tissues in stems, hypocotyls, and roots, we expect similar gene expression profiles in stem and hypocotyl / root tubers. We analyzed RNA-Seq transcript abundance patterns in stem and hypocotyl / root tubers of the <i>Brassica</i> crops kohlrabi (<i>B</i>. <i>oleracea</i>) and turnip (<i>B</i>. <i>rapa</i>) and compared their transcript expression profiles to those in the conspecific thin-stemmed and thin-rooted crops flowering kale and pak choi, respectively. Across these four cultivars, 38,192 expressed gene loci were identified. Of the 3,709 differentially-expressed genes (DEGs) in the turnip: pak choi comparison and the 6,521 DEGs in the kohlrabi: kale comparison, turnips and kohlrabies share a statistically disproportionate overlap of 841 DEG homologs in their tubers (<i>p</i> value < 1e-10). This overlapping set is statistically enriched in biochemical functions that are also associated with tuber induction in potatoes and sweet potatoes: sucrose metabolism, lipoxygenases, auxin metabolism, and meristem development. These shared expression profiles in tuberous stems and root / hypocotyls in <i>Brassica</i> suggest parallel employment of shared molecular genetic pathways during the evolution of tubers in stems, hypocotyls and roots of <i>Brassica</i> crops and more widely in other tuberous plants as well.</p></div
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