A vertebrate case study of the quality of assemblies derived from next-generation sequences

The unparalleled efficiency of next-generation sequencing (NGS) has prompted widespread adoption, but significant problems remain in the use of NGS data for whole genome assembly. We explore the advantages and disadvantages of chicken genome assemblies generated using a variety of sequencing and assembly methodologies. NGS assemblies are equivalent in some ways to a Sanger-based assembly yet deficient in others. Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references

Design and experimental demonstration of a large pedestal thulium-doped fibre

We present a novel large-mode-area thulium-doped fibre with a large pedestal design. We discuss the advantages of this large pedestal fibre in the context of overcoming limitations imposed by cleaving and splicing tolerances. Finally we demonstrate the use of such a fibre in constructing monolithic fibre lasers operating at 1.95 µm with 170 W of output power, 0.1 nm line-width and a diffraction limited beam quality of M2X,Y = 1.02, 1.03

Mitigation of spectral broadening in high peak power holmium-doped fiber sources

Holmium fibre lasers are required for remote sensing, LIDAR and some medical applications [1]. In addition, pulsed Holmium fibre lasers also offer an attractive power scalable alternative to Ho:YAG and Ho:YLF lasers for pumping mid-infrared optical parametric oscillators (OPOs). In these applications it is necessary to operate at a high peak power (>20 kW) with minimal spectral broadening (<;2 nm bandwidth) [2]. This is challenging due to the onset of nonlinear effects such as modulation instability (MI) and stimulated Brillouin scattering (SBS). In an effort to increase the thresholds for the onset of various nonlinear mechanisms, we implement strategies such as transitioning to a core-pumped configuration, minimizing intensity fluctuations in the master oscillator, operating with a large mode-field diameter [3] and aggressive spectral filtering. The schematic of the high peak power amplifier is shown in Fig. 1(a). The master oscillator produced 5 ns pulses at 2077 nm with a FWHM of 0.5 nm and peak power of 1.5 kW at a 100 kHz repetition rate. These were spectrally filtered and injected into the active fibre via an in-house fabricated wavelength division multiplexer (WDM) device. A single mode 1950 nm thulium pump laser is also injected into this device [4]. Both the 2077 nm master oscillator signal and the 1950 nm pump radiation exit the WDM propagating in a robustly single mode 15 μm, 0.1 NA core. This fibre is then spliced to an adiabatically tapered (from 20/200 μm to 60/600 μm) active holmium-doped fibre with a dopant concentration of 0.5 wt.%. A 2 m length of active fibre is used for this amplifier. The output end of the amplifier is terminated by a CO2 laser splice 1cm x 1cm x 1cm end cap with an AR coating at 1.9 - 2.1 μm. The output is then collimated and analysed using power meters (Ophir), photodiodes (EOT extended InGaAs), optical spectrum analyser (Yokogawa) and an imaging detector (Pyrocam III)

Selection Bias in Prenatal Care Utilization: An Interdisciplinary Framework and Review of the Literature

Since there are no randomized trials of standard prenatal care, it is difficult to assess its impact on birth outcomes without controlling for selection processes that can inhibit or promote its use. In this article, we develop a typology of selection processes in prenatal care utilization, identifying four distinct types of selection and their possible biasing effects on estimates of prenatal care efficacy. Second, using an interdisciplinary frame-work, we review the published studies on birth outcomes that consider selectivity in prenatal care, all of which have been published in the economics literature. The results from these studies suggest that selectivity in the use of care does exist and that the predominant process is one of adverse selection. This implies that analyses failing to control for selection will underestimate the effects of prenatal care. Third, we discuss the public health policy implications of these findings and offer an agenda for future research.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68461/2/10.1177_107755879605300401.pd

Stylonychia lemnae DDE_TNP_is1595 contigs

Contigs in fasta format

Data from: The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes

The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (~5%) of its precursor “silent” germline micronuclear genome by a process of “unscrambling” and fragmentation. The tiny macronuclear “nanochromosomes” typically encode single, protein-coding genes (a small portion, 10%, encode 2–8 genes), have minimal noncoding regions, and are differentially amplified to an average of ~2,000 copies. We report the high-quality genome assembly of ~16,000 complete nanochromosomes (~50 Mb haploid genome size) that vary from 469 bp to 66 kb long (mean ~3.2 kb) and encode ~18,500 genes. Alternative DNA fragmentation processes ~10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ~4.0%), suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb) suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing studies of rearrangements arising during evolution and disease

Fourteen-Genome Comparison Identifies DNA Markers for Severe-Disease-Associated Strains of Clostridium difficile▿†

Clostridium difficile is a common cause of infectious diarrhea in hospitalized patients. A severe and increased incidence of C. difficile infection (CDI) is associated predominantly with the NAP1 strain; however, the existence of other severe-disease-associated (SDA) strains and the extensive genetic diversity across C. difficile complicate reliable detection and diagnosis. Comparative genome analysis of 14 sequenced genomes, including those of a subset of NAP1 isolates, allowed the assessment of genetic diversity within and between strain types to identify DNA markers that are associated with severe disease. Comparative genome analysis of 14 isolates, including five publicly available strains, revealed that C. difficile has a core genome of 3.4 Mb, comprising ∼3,000 genes. Analysis of the core genome identified candidate DNA markers that were subsequently evaluated using a multistrain panel of 177 isolates, representing more than 50 pulsovars and 8 toxinotypes. A subset of 117 isolates from the panel had associated patient data that allowed assessment of an association between the DNA markers and severe CDI. We identified 20 candidate DNA markers for species-wide detection and 10,683 single nucleotide polymorphisms (SNPs) associated with the predominant SDA strain (NAP1). A species-wide detection candidate marker, the sspA gene, was found to be the same across 177 sequenced isolates and lacked significant similarity to those of other species. Candidate SNPs in genes CD1269 and CD1265 were found to associate more closely with disease severity than currently used diagnostic markers, as they were also present in the toxin A-negative and B-positive (A-B+) strain types. The genetic markers identified illustrate the potential of comparative genomics for the discovery of diagnostic DNA-based targets that are species specific or associated with multiple SDA strains