56 research outputs found
Why Orange Guaymas Basin Beggiatoa spp. Are Orange: Single-Filament-Genome-Enabled Identification of an Abundant Octaheme Cytochrome with Hydroxylamine Oxidase, Hydrazine Oxidase, and Nitrite Reductase Activities
ABSTRACT Orange, white, and yellow vacuolated Beggiatoaceae filaments are visually dominant members of microbial mats found near sea floor hydrothermal vents and cold seeps, with orange filaments typically concentrated toward the mat centers. No marine vacuolate Beggiatoaceae are yet in pure culture, but evidence to date suggests they are nitrate-reducing, sulfide-oxidizing bacteria. The nearly complete genome sequence of a single orange Beggiatoa (ā Candidatus Maribeggiatoaā) filament from a microbial mat sample collected in 2008 at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) was recently obtained. From this sequence, the gene encoding an abundant soluble orange-pigmented protein in Guaymas Basin mat samples (collected in 2009) was identified by microcapillary reverse-phase high-performance liquid chromatography (HPLC) nano-electrospray tandem mass spectrometry (Ī¼LCāMS-MS) of a pigmented band excised from a denaturing polyacrylamide gel. The predicted protein sequence is related to a large group of octaheme cytochromes whose few characterized representatives are hydroxylamine or hydrazine oxidases. The protein was partially purified and shown by in vitro assays to have hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities. From what is known of Beggiatoaceae physiology, nitrite reduction is the most likely in vivo role of the octaheme protein, but future experiments are required to confirm this tentative conclusion. Thus, while present-day genomic and proteomic techniques have allowed precise identification of an abundant mat protein, and its potential activities could be assayed, proof of its physiological role remains elusive in the absence of a pure culture that can be genetically manipulated
A Wireless Brain-Machine Interface for Real-Time Speech Synthesis
This is the published version, also available here: http://dx.doi.org/10.1371/journal.pone.0008218.Background
Brain-machine interfaces (BMIs) involving electrodes implanted into the human cerebral cortex have recently been developed in an attempt to restore function to profoundly paralyzed individuals. Current BMIs for restoring communication can provide important capabilities via a typing process, but unfortunately they are only capable of slow communication rates. In the current study we use a novel approach to speech restoration in which we decode continuous auditory parameters for a real-time speech synthesizer from neuronal activity in motor cortex during attempted speech.
Methodology/Principal Findings
Neural signals recorded by a Neurotrophic Electrode implanted in a speech-related region of the left precentral gyrus of a human volunteer suffering from locked-in syndrome, characterized by near-total paralysis with spared cognition, were transmitted wirelessly across the scalp and used to drive a speech synthesizer. A Kalman filter-based decoder translated the neural signals generated during attempted speech into continuous parameters for controlling a synthesizer that provided immediate (within 50 ms) auditory feedback of the decoded sound. Accuracy of the volunteer's vowel productions with the synthesizer improved quickly with practice, with a 25% improvement in average hit rate (from 45% to 70%) and 46% decrease in average endpoint error from the first to the last block of a three-vowel task.
Conclusions/Significance
Our results support the feasibility of neural prostheses that may have the potential to provide near-conversational synthetic speech output for individuals with severely impaired speech motor control. They also provide an initial glimpse into the functional properties of neurons in speech motor cortical areas
A Wireless Brain-Machine Interface for Real-Time Speech Synthesis
Background: Brain-machine interfaces (BMIs) involving electrodes implanted into the human cerebral cortex have recently been developed in an attempt to restore function to profoundly paralyzed individuals. Current BMIs for restoring communication can provide important capabilities via a typing process, but unfortunately they are only capable of slow communication rates. In the current study we use a novel approach to speech restoration in which we decode continuous auditory parameters for a real-time speech synthesizer from neuronal activity in motor cortex during attempted speech.
Methodology/Principal Findings: Neural signals recorded by a Neurotrophic Electrode implanted in a speech-related region of the left precentral gyrus of a human volunteer suffering from locked-in syndrome, characterized by near-total paralysis with spared cognition, were transmitted wirelessly across the scalp and used to drive a speech synthesizer. A Kalman filter-based decoder translated the neural signals generated during attempted speech into continuous parameters for controlling a synthesizer that provided immediate (within 50 ms) auditory feedback of the decoded sound. Accuracy of the volunteer's vowel productions with the synthesizer improved quickly with practice, with a 25% improvement in average hit rate (from 45% to 70%) and 46% decrease in average endpoint error from the first to the last block of a three-vowel task.
Conclusions/Significance: Our results support the feasibility of neural prostheses that may have the potential to provide near-conversational synthetic speech output for individuals with severely impaired speech motor control. They also provide an initial glimpse into the functional properties of neurons in speech motor cortical areas.National Institute on Deafness and Other Communication Disorders (U.S.) (Grant R44-DC007050)National Institute on Deafness and Other Communication Disorders (U.S.) (Grant R01-DC007683)National Institute on Deafness and Other Communication Disorders (U.S.) (Grant R01-DC002852)Center of Excellence for Learning in Education, Science, and Technology (SBE-0354378
Discovery and Follow-up of ASASSN-19dj: An X-ray and UV Luminous TDE in an Extreme Post-Starburst Galaxy
We present observations of ASASSN-19dj, a nearby tidal disruption event (TDE)
discovered in the post-starburst galaxy KUG 0810+227 by the All-Sky Automated
Survey for Supernovae (ASAS-SN) at a distance of d 98 Mpc. We observed
ASASSN-19dj from 21 to 392 days relative to peak UV/optical emission using
high-cadence, multi-wavelength spectroscopy and photometry. From the ASAS-SN
-band data, we determine that the TDE began to brighten on 2019 February 6.8
and for the first 25 days the rise was consistent with a flux
power-law. ASASSN-19dj peaked in the UV/optical on 2019 March 6.5 (MJD =
58548.5) at a bolometric luminosity of . Initially remaining roughly constant in X-rays and slowly fading
in the UV/optical, the X-ray flux increased by over an order of magnitude
225 days after peak, resulting from the expansion of the X-ray emitting
surface. The late-time X-ray emission is well-fit by a blackbody with an
effective radius of and a temperature of
. Analysis of Catalina Real-Time Transient
Survey images reveals a nuclear outburst roughly 14.5 years earlier with a
smooth decline and a luminosity of erg
s, although the nature of the flare is unknown. ASASSN-19dj occurred in
the most extreme post-starburst galaxy yet to host a TDE, with Lick
H = \AA.Comment: 25 pages, 14 figures. Will be submitted to MNRAS. For a short video
description please see https://youtu.be/WjTZwO7vcF
Phocine distemper Virus: Current knowledge and future directions
Phocine distemper virus (PDV) was first recognized in 1988 following a massive epidemic in harbor and grey seals in north-western Europe. Since then, the epidemiology of infection in North Atlantic and Arctic pinnipeds has been investigated. In the western North Atlantic endemic infection in harp and grey seals predates the European epidemic, with relatively small, localized mortality events occurring primarily in harbor seals. By contrast, PDV seems not to have become established in European harbor seals following the 1988 epidemic and a second event of similar magnitude and extent occurred in 2002. PDV is a distinct species within the Morbillivirus genus with minor sequence variation between outbreaks over time. There is now mounting evidence of PDV-like viruses in the North Pacific/Western Arctic with serological and molecular evidence of infection in pinnipeds and sea otters. However, despite the absence of associated mortality in the region, there is concern that the virus may infect the large Pacific harbor seal and northern elephant seal populations or the endangered Hawaiian monk seals. Here, we review the current state of knowledge on PDV with particular focus on developments in diagnostics, pathogenesis, immune response, vaccine development, phylogenetics and modeling over the past 20 years
Pipeline for Large-Scale Microdroplet Bisulfite PCR-Based Sequencing Allows the Tracking of Hepitype Evolution in Tumors
Cytosine methylation provides an epigenetic level of cellular plasticity that is important for development, differentiation and cancerogenesis. We adopted microdroplet PCR to bisulfite treated target DNA in combination with second generation sequencing to simultaneously assess DNA sequence and methylation. We show measurement of methylation status in a wide range of target sequences (total 34 kb) with an average coverage of 95% (median 100%) and good correlation to the opposite strand (rhoā=ā0.96) and to pyrosequencing (rhoā=ā0.87). Data from lymphoma and colorectal cancer samples for SNRPN (imprinted gene), FGF6 (demethylated in the cancer samples) and HS3ST2 (methylated in the cancer samples) serve as a proof of principle showing the integration of SNP data and phased DNA-methylation information into āhepitypesā and thus the analysis of DNA methylation phylogeny in the somatic evolution of cancer
Strong Carbon Features and a Red Early Color in the Underluminous Type Ia SN 2022xkq
We present optical, infrared, ultraviolet, and radio observations of SN
2022xkq, an underluminous fast-declining type Ia supernova (SN Ia) in NGC 1784
( Mpc), from to 180 days after explosion. The
high-cadence observations of SN 2022xkq, a photometrically transitional and
spectroscopically 91bg-like SN Ia, cover the first days and weeks following
explosion which are critical to distinguishing between explosion scenarios. The
early light curve of SN 2022xkq has a red early color and exhibits a flux
excess which is more prominent in redder bands; this is the first time such a
feature has been seen in a transitional/91bg-like SN Ia. We also present 92
optical and 19 near-infrared (NIR) spectra, beginning 0.4 days after explosion
in the optical and 2.6 days after explosion in the NIR. SN 2022xkq exhibits a
long-lived C I 1.0693 m feature which persists until 5 days post-maximum.
We also detect C II 6580 in the pre-maximum optical spectra. These
lines are evidence for unburnt carbon that is difficult to reconcile with the
double detonation of a sub-Chandrasekhar mass white dwarf. No existing
explosion model can fully explain the photometric and spectroscopic dataset of
SN 2022xkq, but the considerable breadth of the observations is ideal for
furthering our understanding of the processes which produce faint SNe Ia.Comment: 38 pages, 16 figures, accepted for publication in ApJ, the figure 15
input models and synthetic spectra are now available at
https://zenodo.org/record/837925
Diversity arrays technology (DArT) markers in apple for genetic linkage maps
Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52ā54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55ā76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage
Experiment for cryogenic large-aperture intensity mapping: instrument design
The experiment for cryogenic large-aperture intensity mapping (EXCLAIM) is a balloon-borne telescope designed to survey star formation in windows from the present to zāā=āā3.5. During this time, the rate of star formation dropped dramatically, while dark matter continued to cluster. EXCLAIM maps the redshifted emission of singly ionized carbon lines and carbon monoxide using intensity mapping, which permits a blind and complete survey of emitting gas through statistics of cumulative brightness fluctuations. EXCLAIM achieves high sensitivity using a cryogenic telescope coupled to six integrated spectrometers employing kinetic inductance detectors covering 420 to 540 GHz with spectral resolving power Rāā=āā512 and angular resolution ā4āāarcāmin. The spectral resolving power and cryogenic telescope allow the survey to access dark windows in the spectrum of emission from the upper atmosphere. EXCLAIM will survey 305āādeg2 in the Sloan Digital Sky Survey Stripe 82 field from a conventional balloon flight in 2023. EXCLAIM will also map several galactic fields to study carbon monoxide and neutral carbon emission as tracers of molecular gas. We summarize the design phase of the mission
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