174 research outputs found
Managed aquifer recharge with reverse-osmosis desalinated seawater: modeling the spreading in groundwater using stable water isotopes
The spreading of reverse-osmosis desalinated seawater (DSW) in the Israeli
coastal aquifer was studied using groundwater modeling and stable water
isotopes as tracers. The DSW produced at the Hadera seawater reverse-osmosis
(SWRO) desalination plant is recharged into the aquifer through an infiltration pond at the managed
aquifer recharge (MAR) site of Menashe, Israel. The distinct difference in isotope composition between DSW
(δ18O  =  1.41 ‰;
δ2H  =  11.34 ‰) and the natural groundwater
(δ18O  =  −4.48 ‰ to −5.43 ‰;
δ2H  =  −18.41 ‰ to −22.68 ‰) makes
the water isotopes preferable for use as a tracer compared to widely used
chemical tracers, such as chloride. Moreover, this distinct difference can be
used to simplify the system to a binary mixture of two end-members:
desalinated seawater and groundwater. This approach is validated through a
sensitivity analysis, and it is especially robust when spatial data of stable
water isotopes in the aquifer are scarce. A calibrated groundwater flow and
transport model was used to predict the DSW plume distribution in the aquifer
after 50 years of MAR with DSW. The results suggest that after 50 years,
94 % of the recharged DSW was recovered by the production wells at the
Menashe MAR site. The presented methodology is useful for predicting the
distribution of reverse-osmosis desalinated seawater in various downstream
groundwater systems.</p
Supernova PTF12glz: a possible shock breakout driven through an aspherical wind
We present visible-light and ultraviolet (UV) observations of the supernova
PTF12glz. The SN was discovered and monitored in near-UV and R bands as part of
a joint GALEX and Palomar Transient Factory campaign. It is among the most
energetic Type IIn supernovae observed to date (~10^51erg). If the radiated
energy mainly came from the thermalization of the shock kinetic energy, we show
that PTF12glz was surrounded by ~1 solar mass of circumstellar material (CSM)
prior to its explosive death. PTF12glz shows a puzzling peculiarity: at early
times, while the freely expanding ejecta are presumably masked by the optically
thick CSM, the radius of the blackbody that best fits the observations grows at
~8000km/s. Such a velocity is characteristic of fast moving ejecta rather than
optically thick CSM. This phase of radial expansion takes place before any
spectroscopic signature of expanding ejecta appears in the spectrum and while
both the spectroscopic data and the bolometric luminosity seem to indicate that
the CSM is optically thick. We propose a geometrical solution to this puzzle,
involving an aspherical structure of the CSM around PTF12glz. By modeling
radiative diffusion through a slab of CSM, we show that an aspherical geometry
of the CSM can result in a growing effective radius. This simple model also
allows us to recover the decreasing blackbody temperature of PTF12glz.
SLAB-Diffusion, the code we wrote to model the radiative diffusion of photons
through a slab of CSM and evaluate the observed radius and temperature, is made
available on-line.Comment: Sumbitted to ApJ. Comments are welcom
Observational and Physical Classification of Supernovae
This chapter describes the current classification scheme of supernovae (SNe).
This scheme has evolved over many decades and now includes numerous SN Types
and sub-types. Many of these are universally recognized, while there are
controversies regarding the definitions, membership and even the names of some
sub-classes; we will try to review here the commonly-used nomenclature, noting
the main variants when possible. SN Types are defined according to
observational properties; mostly visible-light spectra near maximum light, as
well as according to their photometric properties. However, a long-term goal of
SN classification is to associate observationally-defined classes with specific
physical explosive phenomena. We show here that this aspiration is now finally
coming to fruition, and we establish the SN classification scheme upon direct
observational evidence connecting SN groups with specific progenitor stars.
Observationally, the broad class of Type II SNe contains objects showing strong
spectroscopic signatures of hydrogen, while objects lacking such signatures are
of Type I, which is further divided to numerous subclasses. Recently a class of
super-luminous SNe (SLSNe, typically 10 times more luminous than standard
events) has been identified, and it is discussed. We end this chapter by
briefly describing a proposed alternative classification scheme that is
inspired by the stellar classification system. This system presents our
emerging physical understanding of SN explosions, while clearly separating
robust observational properties from physical inferences that can be debated.
This new system is quantitative, and naturally deals with events distributed
along a continuum, rather than being strictly divided into discrete classes.
Thus, it may be more suitable to the coming era where SN numbers will quickly
expand from a few thousands to millions of events.Comment: Extended final draft of a chapter in the "SN Handbook". Comments most
welcom
Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine
Over 100 chemical types of RNA modifications have been identified in thousands of sites in all three domains of life. Recent data suggest that modifications function synergistically to mediate biological function, and that cells may coordinately modulate modification levels for regulatory purposes. However, this area of RNA biology remains largely unexplored due to the lack of robust, high-throughput methods to quantify the extent of modification at specific sites. Recently, we developed a facile enzymatic ligation-based method for detection and quantitation of methylated 2′-hydroxyl groups within RNA. Here we exploit the principles of molecular recognition and nucleic acid chemistry to establish the experimental parameters for ligation-based detection and quantitation of pseudouridine (Ψ) and N6-methyladenosine (m6A), two abundant modifications in eukaryotic rRNA/tRNA and mRNA, respectively. Detection of pseudouridylation at several sites in the large subunit rRNA derived from yeast demonstrates the feasibility of the approach for analysis of pseudouridylation in biological RNA samples
The detection rate of early UV emission from supernovae: A dedicated GALEX/PTF survey and calibrated theoretical estimates
The radius and surface composition of an exploding massive star,as well as
the explosion energy per unit mass, can be measured using early UV observations
of core collapse supernovae (SNe). We present the first results from a
simultaneous GALEX/PTF search for early UV emission from SNe. Six Type II SNe
and one Type II superluminous SN (SLSN-II) are clearly detected in the GALEX
NUV data. We compare our detection rate with theoretical estimates based on
early, shock-cooling UV light curves calculated from models that fit existing
Swift and GALEX observations well, combined with volumetric SN rates. We find
that our observations are in good agreement with calculated rates assuming that
red supergiants (RSGs) explode with fiducial radii of 500 solar, explosion
energies of 10^51 erg, and ejecta masses of 10 solar masses. Exploding blue
supergiants and Wolf-Rayet stars are poorly constrained. We describe how such
observations can be used to derive the progenitor radius, surface composition
and explosion energy per unit mass of such SN events, and we demonstrate why UV
observations are critical for such measurements. We use the fiducial RSG
parameters to estimate the detection rate of SNe during the shock-cooling phase
(<1d after explosion) for several ground-based surveys (PTF, ZTF, and LSST). We
show that the proposed wide-field UV explorer ULTRASAT mission, is expected to
find >100 SNe per year (~0.5 SN per deg^2), independent of host galaxy
extinction, down to an NUV detection limit of 21.5 mag AB. Our pilot GALEX/PTF
project thus convincingly demonstrates that a dedicated, systematic SN survey
at the NUV band is a compelling method to study how massive stars end their
life.Comment: See additional information including animations on
http://www.weizmann.ac.il/astrophysics/ultrasa
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SN 2018fif: The explosion of a large red supergiant discovered in its infancy by the Zwicky transient facility
High-cadence transient surveys are able to capture supernovae closer to their first light than ever before. Applying analytical models to such early emission, we can constrain the progenitor stars’ properties. In this paper, we present observations of SN 2018fif (ZTF 18abokyfk). The supernova was discovered close to first light and monitored by the Zwicky Transient Facility (ZTF) and the Neil Gehrels Swift Observatory. Early spectroscopic observations suggest that the progenitor of SN 2018fif was surrounded by relatively small amounts of circumstellar material compared to all previous cases. This particularity, coupled with the high-cadence multiple-band coverage, makes it a good candidate to investigate using shock-cooling models. We employ the SOPRANOS code, an implementation of the model by Sapir & Waxman and its extension to early times by Morag et al. Compared with previous implementations, SOPRANOS has the advantage of including a careful account of the limited temporal validity domain of the shock-cooling model as well as allowing usage of the entirety of the early UV data. We find that the progenitor of SN 2018fif was a large red supergiant with a radius of R = 744.0-+128.0183.0 R☉ and an ejected mass of Mej = 9.3-+5.80.4 M☉. Our model also gives information on the explosion epoch, the progenitor’s inner structure, the shock velocity, and the extinction. The distribution of radii is double-peaked, with smaller radii corresponding to lower values of the extinction, earlier recombination times, and a better match to the early UV data. If these correlations persist in future objects, denser spectroscopic monitoring constraining the time of recombination, as well as accurate UV observations (e.g., with ULTRASAT), will help break the extinction/radius degeneracy and independently determine both
SNOntology: Myriads of novel snornas or just a mirage?
<p>Abstract</p> <p>Background</p> <p>Small nucleolar RNAs (snoRNAs) are a large group of non-coding RNAs (ncRNAs) that mainly guide 2'-O-methylation (C/D RNAs) and pseudouridylation (H/ACA RNAs) of ribosomal RNAs. The pattern of rRNA modifications and the set of snoRNAs that guide these modifications are conserved in vertebrates. Nearly all snoRNA genes in vertebrates are localized in introns of other genes and are processed from pre-mRNAs. Thus, the same promoter is used for the transcription of snoRNAs and host genes.</p> <p>Results</p> <p>The series of studies by Dahai Zhu and coworkers on snoRNAs and their genes were critically considered. We present evidence that dozens of species-specific snoRNAs that they described in vertebrates are experimental artifacts resulting from the improper use of Northern hybridization. The snoRNA genes with putative intrinsic promoters that were supposed to be transcribed independently proved to contain numerous substitutions and are, most likely, pseudogenes. In some cases, they are localized within introns of overlooked host genes. Finally, an increased number of snoRNA genes in mammalian genomes described by Zhu and coworkers is also an artifact resulting from two mistakes. First, numerous mammalian snoRNA pseudogenes were considered as genes, whereas most of them are localized outside of host genes and contain substitutions that question their functionality. Second, Zhu and coworkers failed to identify many snoRNA genes in non-mammalian species. As an illustration, we present 1352 C/D snoRNA genes that we have identified and annotated in vertebrates.</p> <p>Conclusions</p> <p>Our results demonstrate that conclusions based only on databases with automatically annotated ncRNAs can be erroneous. Special investigations aimed to distinguish true RNA genes from their pseudogenes should be done. Zhu and coworkers, as well as most other groups studying vertebrate snoRNAs, give new names to newly described homologs of human snoRNAs, which significantly complicates comparison between different species. It seems necessary to develop a uniform nomenclature for homologs of human snoRNAs in other vertebrates, e.g., human gene names prefixed with several-letter code denoting the vertebrate species.</p
Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate
Expression and Processing of a Small Nucleolar RNA from the Epstein-Barr Virus Genome
Small nucleolar RNAs (snoRNAs) are localized within the nucleolus, a sub-nuclear compartment, in which they guide ribosomal or spliceosomal RNA modifications, respectively. Up until now, snoRNAs have only been identified in eukaryal and archaeal genomes, but are notably absent in bacteria. By screening B lymphocytes for expression of non-coding RNAs (ncRNAs) induced by the Epstein-Barr virus (EBV), we here report, for the first time, the identification of a snoRNA gene within a viral genome, designated as v-snoRNA1. This genetic element displays all hallmark sequence motifs of a canonical C/D box snoRNA, namely C/C′- as well as D/D′-boxes. The nucleolar localization of v-snoRNA1 was verified by in situ hybridisation of EBV-infected cells. We also confirmed binding of the three canonical snoRNA proteins, fibrillarin, Nop56 and Nop58, to v-snoRNA1. The C-box motif of v-snoRNA1 was shown to be crucial for the stability of the viral snoRNA; its selective deletion in the viral genome led to a complete down-regulation of v-snoRNA1 expression levels within EBV-infected B cells. We further provide evidence that v-snoRNA1 might serve as a miRNA-like precursor, which is processed into 24 nt sized RNA species, designated as v-snoRNA124pp. A potential target site of v-snoRNA124pp was identified within the 3′-UTR of BALF5 mRNA which encodes the viral DNA polymerase. V-snoRNA1 was found to be expressed in all investigated EBV-positive cell lines, including lymphoblastoid cell lines (LCL). Interestingly, induction of the lytic cycle markedly up-regulated expression levels of v-snoRNA1 up to 30-fold. By a computational approach, we identified a v-snoRNA1 homolog in the rhesus lymphocryptovirus genome. This evolutionary conservation suggests an important role of v-snoRNA1 during γ-herpesvirus infection
Cl gene cluster encoding several small nucleolar RNAs: a comparison amongst trypanosomatids
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