Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri

Background The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. Results Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system. Conclusions In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.publishedVersio

Coherent control of mid-infrared frequency comb by optical injection of near-infrared light

We demonstrate the use of a low power near-infrared laser illuminating the front facet of a quantum cascade laser (QCL) as an optical actuator for the coherent control of a mid-infrared frequency comb. We show that with appropriate current control of the QCL comb and intensity modulation of the near-infrared laser, a tight phase lock of a comb line to a distributed feedback laser is possible with 2 MHz of locking bandwidth and 200 mrad of residual phase noise. A characterization of the whole scheme is provided, showing the limits of the electrical actuation, which we bypassed using the optical actuation. Both comb degrees of freedom can be locked by performing electrical injection locking of the repetition rate in parallel. However, we show that the QCL acts as a fast near-infrared light detector such that injection locking can also be achieved through modulation of the near-infrared light. These results on the coherent control of a QCL frequency comb are particularly interesting for coherent averaging in dual-comb spectroscopy and for mid-infrared frequency comb applications requiring high spectral purity.ISSN:2378-096

Synchronization of frequency combs by optical injection

Optical frequency combs based on semiconductor lasers are a promising technology for monolithic integration of dual-comb spectrometers. However, the stabilization of offset frequency fceo remains a challenging feat due the lack of octave-spanning spectra. In a dual-comb configuration, the uncorrelated jitter of the offset frequencies leads to a non-periodic signal resulting in broadened beatnotes with a limited signal-to-noise ratio (SNR). Hence, expensive data acquisition schemes and complex signal processing are currently required. Here, we show that the offset frequencies of two frequency combs can be synchronized by optical injection locking, which allows full phase-stabilization when combined with electrical injection locking of both repetition frequencies f rep. A single comb line isolated via an optical Vernier filter serves as Master oscillator for injection locking. The resulting dual-comb signal is periodic and stable over thousands of periods. This enables coherent averaging using analog electronics, which increases the SNR and reduces the data size by one and three orders of magnitude, respectively. The presented method will enable fully phase-stabilized dual-comb spectrometers by leveraging on integrated optical filters and provides access for comparing and stabilizing f ceo to narrow-linewidth optical references.ISSN:1094-408

Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri

Background The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. Results Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system. Conclusions In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen