49 research outputs found
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Repurposing the GNAT Fold in the Initiation of Polyketide Biosynthesis.
Natural product biosynthetic pathways are replete with enzymes repurposed for new catalytic functions. In some modular polyketide synthase (PKS) pathways, a GCN5-related N-acetyltransferase (GNAT)-like enzyme with an additional decarboxylation function initiates biosynthesis. Here, we probe two PKS GNAT-like domains for the dual activities of S-acyl transfer from coenzyme A (CoA) to an acyl carrier protein (ACP) and decarboxylation. The GphF and CurA GNAT-like domains selectively decarboxylate substrates that yield the anticipated pathway starter units. The GphF enzyme lacks detectable acyl transfer activity, and a crystal structure with an isobutyryl-CoA product analog reveals a partially occluded acyltransfer acceptor site. Further analysis indicates that the CurA GNAT-like domain also catalyzes only decarboxylation, and the initial acyl transfer is catalyzed by an unidentified enzyme. Thus, PKS GNAT-like domains are re-classified as GNAT-like decarboxylases. Two other decarboxylases, malonyl-CoA decarboxylase and EryM, reside on distant nodes of the superfamily, illustrating the adaptability of the GNAT fold
QUBIC: The QU Bolometric Interferometer for Cosmology
One of the major challenges of modern cosmology is the detection of B-mode
polarization anisotropies in the CMB. These originate from tensor fluctuations
of the metric produced during the inflationary phase. Their detection would
therefore constitute a major step towards understanding the primordial
Universe. The expected level of these anisotropies is however so small that it
requires a new generation of instruments with high sensitivity and extremely
good control of systematic effects. We propose the QUBIC instrument based on
the novel concept of bolometric interferometry, bringing together the
sensitivity advantages of bolometric detectors with the systematics effects
advantages of interferometry. Methods: The instrument will directly observe the
sky through an array of entry horns whose signals will be combined together
using an optical combiner. The whole set-up is located inside a cryostat.
Polarization modulation will be achieved using a rotating half-wave plate and
interference fringes will be imaged on two focal planes (separated by a
polarizing grid) tiled with bolometers. We show that QUBIC can be considered as
a synthetic imager, exactly similar to a usual imager but with a synthesized
beam formed by the array of entry horns. Scanning the sky provides an
additional modulation of the signal and improve the sky coverage shape. The
usual techniques of map-making and power spectrum estimation can then be
applied. We show that the sensitivity of such an instrument is comparable with
that of an imager with the same number of horns. We anticipate a low level of
beam-related systematics thanks to the fact that the synthesized beam is
determined by the location of the primary horns. Other systematics should be
under good control thanks to an autocalibration technique, specific to our
concept, that will permit the accurate determination of most of the systematics
parameters.Comment: 12 pages, 10 figures, submitted to Astronomy and Astrophysic
Supermassive Black Holes in Galactic Nuclei: Past, Present and Future Research
This review discusses the current status of supermassive black hole research,
as seen from a purely observational standpoint. Since the early '90s, rapid
technological advances, most notably the launch of the Hubble Space Telescope,
the commissioning of the VLBA and improvements in near-infrared speckle imaging
techniques, have not only given us incontrovertible proof of the existence of
supermassive black holes, but have unveiled fundamental connections between the
mass of the central singularity and the global properties of the host galaxy.
It is thanks to these observations that we are now, for the first time, in a
position to understand the origin, evolution and cosmic relevance of these
fascinating objects.Comment: Invited Review, 114 pages. Because of space requirements, this
version contains low resolution figures. The full resolution version can be
downloaded from http://www.physics.rutgers.edu/~lff/publications.htm
Exploiting bacterial DNA gyrase as a drug target: current state and perspectives
DNA gyrase is a type II topoisomerase that can introduce negative supercoils into DNA at the expense of ATP hydrolysis. It is essential in all bacteria but absent from higher eukaryotes, making it an attractive target for antibacterials. The fluoroquinolones are examples of very successful gyrase-targeted drugs, but the rise in bacterial resistance to these agents means that we not only need to seek new compounds, but also new modes of inhibition of this enzyme. We review known gyrase-specific drugs and toxins and assess the prospects for developing new antibacterials targeted to this enzyme
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States
Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multimodel ensemble forecast that combined predictions from dozens of groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naïve baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-wk horizon three to five times larger than when predicting at a 1-wk horizon. This project underscores the role that collaboration and active coordination between governmental public-health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks
The United States COVID-19 Forecast Hub dataset
Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages
Rickettsia typhi central nervous system infection
A 39 year-old male was residing along the south coast of Texas, the USA, presented with fever, myalgias, headaches, and weight loss for ten days. Symptoms and manifestations progressed to include nuchal rigidity, photophobia, hyponatremia, thrombocytopenia, and transaminitis despite the intravenous administration of ceftriaxone and azithromycin. A lumbar puncture performed in the Emergency Department yielded pleocytosis and glucose cerebrospinal fluid/serum ratio of 0.35, suggestive of meningoencephalitis. Conglomerate data raised the suspicion of meningitis secondary to a zoonotic acquired infection, which was later confirmed to be Rickettsia typhi. Doxycycline is the drug of choice for the suspected Rickettsia disease. After doxycycline administration, the patient improved and was discharged home asymptomatic
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A Mononuclear Iron-Dependent Methyltransferase Catalyzes Initial Steps in Assembly of the Apratoxin A Polyketide Starter Unit
Natural
product biosynthetic pathways contain a plethora of enzymatic
tools to carry out difficult biosynthetic transformations. Here, we
discover an unusual mononuclear iron-dependent methyltransferase that
acts in the initiation steps of apratoxin A biosynthesis (AprA MT1).
Fe<sup>3+</sup>-replete AprA MT1 catalyzes one or two methyl transfer
reactions on the substrate malonyl-ACP (acyl carrier protein), whereas
Co<sup>2+</sup>, Fe<sup>2+</sup>, Mn<sup>2+</sup>, and Ni<sup>2+</sup> support only a single methyl transfer. MT1 homologues exist within
the “GNAT” (GCN5-related <i>N</i>-acetyltransferase)
loading modules of several modular biosynthetic pathways with propionyl,
isobutyryl, or pivaloyl starter units. GNAT domains are thought to
catalyze decarboxylation of malonyl-CoA and acetyl transfer to a carrier
protein. In AprA, the GNAT domain lacks both decarboxylation and acyl
transfer activity. A crystal structure of the AprA MT1-GNAT di-domain
with bound Mn<sup>2+</sup>, malonate, and the methyl donor <i>S</i>-adenosylmethionine (SAM) reveals that the malonyl substrate
is a bidentate metal ligand, indicating that the metal acts as a Lewis
acid to promote methylation of the malonyl α-carbon. The GNAT
domain is truncated relative to functional homologues. These results
afford an expanded understanding of MT1-GNAT structure and activity
and permit the functional annotation of homologous GNAT loading modules
both with and without methyltransferases, additionally revealing their
rapid evolutionary adaptation in different biosynthetic contexts
Understanding the behavior of miniaturized metamaterial-based dipole antennas in leaky wave regime
Schwann cell-derived periostin promotes autoimmune peripheral polyneuropathy via macrophage recruitment
Chronic inflammatory demyelinating polyneuropathy (CIDP) and Guillain-Barre syndrome (GBS) are inflammatory neuropathies that affect humans and are characterized by peripheral nerve myelin destruction and macrophage-containing immune infiltrates. In contrast to the traditional view that the peripheral nerve is simply the target of autoimmunity, we report here that peripheral nerve Schwann cells exacerbate the autoimmune process through extracellular matrix (ECM) protein induction. In a spontaneous autoimmune peripheral polyneuropathy (SAPP) mouse model of inflammatory neuropathy and CIDP nerve biopsies, the ECM protein periostin (POSTN) was upregulated in affected sciatic nerves and was primarily expressed by Schwann cells. Postn deficiency delayed the onset and reduced the extent of neuropathy, as well as decreased the number of macrophages infiltrating the sciatic nerve. In an in vitro assay, POSTN promoted macrophage chemotaxis in an integrin-AM (ITGAM) and ITGAV-dependent manner. The PNS-infiltrating macrophages in SAPP-affected nerves were pathogenic, since depletion of macrophages protected against the development of neuropathy. Our findings show that Schwann cells promote macrophage infiltration by upregulating Postn and suggest that POSTN is a novel target for the treatment of macrophage-associated inflammatory neuropathies