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 $\sim 2$ to $\sim450$ 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 $\sim 5400$ \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 $\sim 16$ d after core-collapse reaching a bolometric luminosity of Lp $\sim 3\times10^{42}$ \ergs. Spectral models, including the nebular epoch, show that the SN ejected $2.5-4$ \msun\ of material, with $\sim 1.5$ \msun\ below 5000 \kms, and with a kinetic energy of $(4.5-7)\times10^{51}$ erg. The explosion synthesised $\sim 0.14$ \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 $M_\mathrm{ZAMS}$ of $23-28$ \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 z∼0.1z\sim0.1

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 $\sim100$ Type Ia supernovae located in the smooth Hubble flow ($0.03 \lesssim z \lesssim 0.10$). Light curves were also obtained of a "Physics" sample composed of 90 nearby Type Ia supernovae at $z \leq 0.04$ 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