218 research outputs found
Detection of peptidases in Trypanosoma cruzi epimastigotes using chromogenic and fluorogenic substrates
Detergent extracts of Trypanosoma cruzi epimastigotes catalysed the hydrolysis of a range of amino-acyl and peptidyl p-nitro-anilides and aminomethylcoumarins. At least three enzymes were detected that cleave Z-Phe-Arg-MCA. Two of these were optimally active at alkaline pH, the other at pH 4·0. Of the two enzymes with alkaline pH optima, one was a cysteine peptidase and was unable to cleave Bz-Arg-MCA readily, whilst the other cleaved Bz-Arg-MCA and was inhibited by diisopropyl fluorophosphate. The acidic enzyme was similar to cathespin L of other eukayrotes with respect to its pH profile, substrate-specificity and inhibitor-sensitivity. Evidence was presented that epimastigotes contain a cysteine-type dipeptidyl aminopeptidase, one or more aminopeptidases, and a serine peptidase that cleaves Boc-Ala-Ala-pNA. Digitonin solubilization of the activities from cells supports the hypothesis that the cathespin L-like enzyme and the dipeptidyl aminopeptidase are lysosomal, whilst the Bz-Arg-MCA hydrolase, the aminopeptidases and the Boc-Ala-Ala-pNA serine peptidase are cytosoli
Modelling of SN 2013dx associated with the low-redshift GRB130702A points to diversity in GRB/SN properties
The properties of the broad-lined Type Ic supernova (SN) 2013dx, associated with the long gamma-ray burst GRB 130702A at a redshift z = 0.145, are derived via spectral modelling. SN 2013dx was similar in luminosity to other GRB/SNe, with a derived value of the mass of 56Ni ejected in the explosion of ≈0.4 M⊙. However, its spectral properties suggest a smaller explosion kinetic energy. Radiation transport models were used to derive a plausible mass and density distribution of the SN ejecta in a one-dimensional approximation. While the mass ejected in the explosion that is obtained from the modelling (Mej ≈ 9 M⊙) is similar to that of all other well-studied GRB/SNe, the kinetic energy is significantly smaller (EK ∼ 1052 erg). This leads to a smaller EK/Mej ratio, ≈1051 erg/M⊙, which is reflected in the narrower appearance of the spectral lines. While the low EK does not represent a problem for the scenario in which magnetar energy aids powering the explosion and the nucleosynthesis, it is nevertheless highly unusual. SNe Ic with similar EK have never been seen in coincidence with a GRB, and no well-observed GRB/SN has shown similarly low EK and EK/Mej
SN 2016coi/ASASSN-16fp: An example of residual helium in a type Ic supernova?
The optical observations of Ic-4 supernova (SN) 2016coi/ASASSN-16fp, from
to days after explosion, are presented along with analysis
of its physical properties. The SN shows the broad lines associated with SNe
Ic-3/4 but with a key difference. The early spectra display a strong absorption
feature at \AA\ which is not seen in other SNe~Ic-3/4 at this
epoch. This feature has been attributed to He I in the literature. Spectral
modelling of the SN in the early photospheric phase suggests the presence of
residual He in a C/O dominated shell. However, the behaviour of the He I lines
are unusual when compared with He-rich SNe, showing relatively low velocities
and weakening rather than strengthening over time. The SN is found to rise to
peak d after core-collapse reaching a bolometric luminosity of Lp
\ergs. Spectral models, including the nebular epoch, show
that the SN ejected \msun\ of material, with \msun\ below
5000 \kms, and with a kinetic energy of erg. The
explosion synthesised \msun\ of 56Ni. There are significant
uncertainties in E(B-V)host and the distance however, which will affect Lp and
MNi. SN 2016coi exploded in a host similar to the Large Magellanic Cloud (LMC)
and away from star-forming regions. The properties of the SN and the
host-galaxy suggest that the progenitor had of \msun\
and was stripped almost entirely down to its C/O core at explosion.Comment: Accepted for publication in MNRAS. Updated to reflect the published
version, minor typographical changes onl
A dynamical model reveals gene co-localizations in nucleus
Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the observed co-localization of genes within a defined subnuclear region. A simple standard Brownian motion model in two and three dimensions shows that preferential co-localization is possible for co-regulated genes without any direct interaction, and suggests the occurrence may be due to a limitation in the number of available transcription factors. Experimental data of chromatin movements demonstrates that fractional rather than standard Brownian motion is more appropriate to model gene mobilizations, and we tested our dynamical model against recent static experimental data, using a sub-diffusion process by which the genes tend to colocalize more easily. Moreover, in order to compare our model with recently obtained experimental data, we studied the association level between genes and factors, and presented data supporting the validation of this dynamic model. As further applications of our model, we applied it to test against more biological observations. We found that increasing transcription factor number, rather than factory number and nucleus size, might be the reason for decreasing gene co-localization. In the scenario of frequency-or amplitude-modulation of transcription factors, our model predicted that frequency-modulation may increase the co-localization between its targeted genes
Carnegie Supernova Project-II: The Near-infrared Spectroscopy Program
Shifting the focus of Type Ia supernova (SN Ia) cosmology to the
near-infrared (NIR) is a promising way to significantly reduce the systematic
errors, as the strategy minimizes our reliance on the empirical
width-luminosity relation and uncertain dust laws. Observations in the NIR are
also crucial for our understanding of the origins and evolution of these
events, further improving their cosmological utility. Any future experiments in
the rest-frame NIR will require knowledge of the SN Ia NIR spectroscopic
diversity, which is currently based on a small sample of observed spectra.
Along with the accompanying paper, Phillips et al. (2018), we introduce the
Carnegie Supernova Project-II (CSP-II), to follow up nearby SNe Ia in both the
optical and the NIR. In particular, this paper focuses on the CSP-II NIR
spectroscopy program, describing the survey strategy, instrumental setups, data
reduction, sample characteristics, and future analyses on the data set. In
collaboration with the Harvard-Smithsonian Center for Astrophysics (CfA)
Supernova Group, we obtained 661 NIR spectra of 157 SNe Ia. Within this sample,
451 NIR spectra of 90 SNe Ia have corresponding CSP-II follow-up light curves.
Such a sample will allow detailed studies of the NIR spectroscopic properties
of SNe Ia, providing a different perspective on the properties of the unburned
material, radioactive and stable nickel produced, progenitor magnetic fields,
and searches for possible signatures of companion stars.Comment: 20 pages, 7 figures, accepted for publication in PAS
Carnegie Supernova Project-II: Extending the Near-Infrared Hubble Diagram for Type Ia Supernovae to
The Carnegie Supernova Project-II (CSP-II) was an NSF-funded, four-year
program to obtain optical and near-infrared observations of a "Cosmology"
sample of Type Ia supernovae located in the smooth Hubble flow (). Light curves were also obtained of a "Physics"
sample composed of 90 nearby Type Ia supernovae at selected for
near-infrared spectroscopic time-series observations. The primary emphasis of
the CSP-II is to use the combination of optical and near-infrared photometry to
achieve a distance precision of better than 5%. In this paper, details of the
supernova sample, the observational strategy, and the characteristics of the
photometric data are provided. In a companion paper, the near-infrared
spectroscopy component of the project is presented.Comment: 43 pages, 10 figures, accepted for publication in PAS
Robustness of circadian clocks to daylight fluctuations: hints from the picoeucaryote Ostreococcus tauri
The development of systemic approaches in biology has put emphasis on
identifying genetic modules whose behavior can be modeled accurately so as to
gain insight into their structure and function. However most gene circuits in a
cell are under control of external signals and thus quantitative agreement
between experimental data and a mathematical model is difficult. Circadian
biology has been one notable exception: quantitative models of the internal
clock that orchestrates biological processes over the 24-hour diurnal cycle
have been constructed for a few organisms, from cyanobacteria to plants and
mammals. In most cases, a complex architecture with interlocked feedback loops
has been evidenced. Here we present first modeling results for the circadian
clock of the green unicellular alga Ostreococcus tauri. Two plant-like clock
genes have been shown to play a central role in Ostreococcus clock. We find
that their expression time profiles can be accurately reproduced by a minimal
model of a two-gene transcriptional feedback loop. Remarkably, best adjustment
of data recorded under light/dark alternation is obtained when assuming that
the oscillator is not coupled to the diurnal cycle. This suggests that coupling
to light is confined to specific time intervals and has no dynamical effect
when the oscillator is entrained by the diurnal cycle. This intringuing
property may reflect a strategy to minimize the impact of fluctuations in
daylight intensity on the core circadian oscillator, a type of perturbation
that has been rarely considered when assessing the robustness of circadian
clocks
SN 2016coi/ASASSN-16fp: an example of residual helium in a type Ic supernova?
The optical observations of Ic-4 supernova (SN) 2016coi/ASASSN-16fp, from ∼2 to ∼450 d after explosion, are presented along with analysis of its physical properties. The SN shows the broad lines associated with SNe Ic-3/4 but with a key difference. The early spectra display a strong absorption feature at ∼5400 Å which is not seen in other SNe Ic-3/4 at this epoch. This feature has been attributed to He I in the literature. Spectral modelling of the SN in the early photospheric phase suggests the presence of residual He in a C/O dominated shell. However, the behaviour of the He I lines is unusual when compared with He-rich SNe, showing relatively low velocities and weakening rather than strengthening over time. The SN is found to rise to peak ∼16 d after core-collapse reaching a bolometric luminosity of Lp∼3 × 1042 erg s−1. Spectral models, including the nebular epoch, show that the SN ejected 2.5–4 M⊙ of material, with ∼1.5 M⊙ below 5000 km s−1, and with a kinetic energy of (4.5–7) × 1051 erg. The explosion synthesized ∼0.14 M⊙ of 56Ni. There are significant uncertainties in E(B − V)host and the distance, however, which will affect Lp and MNi. SN 2016coi exploded in a host similar to the Large Magellanic Cloud (LMC) and away from star-forming regions. The properties of the SN and the host-galaxy suggest that the progenitor had MZAMS of 23–28 M⊙ and was stripped almost entirely down to its C/O core at explosion
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