Molecular outflow launched beyond the disk edge

One of the long-standing problems of star formation is the excess of angular momentum of the parent molecular cloud. In the classical picture, a fraction of angular momentum of the circumstellar material is removed by the magneto-centrifugally driven disk wind that is launched from a wide region throughout the disk. In this work, we investigate the kinematics in the envelope-disk transition zone of the Class I object BHB07-11, in the B59 core. For this purpose, we used the Atacama Large Millimeter/submillimeter Array in extended configuration to observe the thermal dust continuum emission ($\lambda_0 \sim$ 1.3 mm) and molecular lines (CO, C$^{18}$O and H$_2$CO), which are suitable tracers of disk, envelope, and outflow dynamics at a spatial resolution of $\sim 30$ AU. We report a bipolar outflow that was launched at symmetric positions with respect to the disk ($\sim$80~AU in radius), but was concentrated at a distance of 90--130~AU from the disk center. The two outflow lobes had a conical shape and the gas inside was accelerating. The large offset of the launching position coincided with the landing site of the infall material from the extended spiral structure (seen in dust) onto the disk. This indicates that bipolar outflows are efficiently launched within a narrow region outside the disk edge. We also identify a sharp transition in the gas kinematics across the tip of the spiral structure, which pinpoints the location of the so-called centrifugal barrier.Comment: 5 pages, 5 figures, Accepted for publication in A&A Letter

Magnetic field in a young circumbinary disk

We use polarization observations of a circumbinary disk to investigate how the polarization properties change at distinct frequency bands. Our goal is to discern the main mechanism responsible for the polarization through comparison between our observations and model predictions. We used ALMA to perform full polarization observations at 97.5 GHz, 233 GHz and 343.5 GHz. The target is the Class I object BHB07-11, which is the youngest object in the Barnard 59 protocluster. Complementary VLA observations at 34.5 GHz revealed a binary system within the disk. We detect an extended and structured polarization pattern remarkably consistent among all three bands. The distribution of polarized intensity resembles a horseshoe shape with polarization angles following this morphology. From the spectral index between bands 3 and 7, we derive a dust opacity index $\beta \sim 1$ consistent with maximum grain sizes larger than expected to produce self-scattering polarization in each band. The polarization morphology do not match predictions from self-scattering. On the other hand, marginal correspondence is seen between our maps and predictions from radiation field assuming the brightest binary component as main radiation source. Molecular line data from BHB07-11 indicates disk rotation. We produced synthetic polarization maps from a rotating magnetized disk model assuming combined poloidal and toroidal magnetic field components. The magnetic field vectors (i. e., the polarization vectors rotated by 90\degr) are better represented by a model with poloidal magnetic field strength about 3 times the toroidal one. The similarity of our polarization patterns among the three bands provides a strong evidence against self-scattering and radiation fields. On the other hand, our data are reasonably well reproduced by a model of disk with toroidal magnetic field components slightly smaller than poloidal ones.Comment: 8 pages, 8 figures, accepted for publication in Astronomy & Astrophysic

Improvement of DNA minicircle production by optimization of the secondary structure of the 5′-UTR of ParA resolvase

The use of minicircles in gene therapy applications is dependent on the availability of high-producer cell systems. In order to improve the performance of minicircle production in Escherichia coli by ParA resolvase-mediated in vivo recombination, we focus on the 5′ untranslated region (5′-UTR) of parA messenger RNA (mRNA). The arabinose-inducible P[subscript BAD]/araC promoter controls ParA expression and strains with improved arabinose uptake are used. The 27-nucleotide-long 5′-UTR of parA mRNA was optimized using a predictive thermodynamic model. An analysis of original and optimized mRNA subsequences predicted a decrease of 8.6–14.9 kcal/mol in the change in Gibbs free energy upon assembly of the 30S ribosome complex with the mRNA subsequences, indicating a more stable mRNA-rRNA complex and enabling a higher (48–817-fold) translation initiation rate. No effect of the 5′-UTR was detected when ParA was expressed from a low-copy number plasmid (∼14 copies/cell), with full recombination obtained within 2 h. However, when the parA gene was inserted in the bacterial chromosome, a faster and more effective recombination was obtained with the optimized 5′-UTR. Interestingly, the amount of this transcript was 2.6–3-fold higher when compared with the transcript generated from the original sequence, highlighting that 5′-UTR affects the level of the transcript. A Western blot analysis confirmed that E. coli synthesized higher amounts of ParA with the new 5′-UTR (∼1.8 ± 0.7-fold). Overall, these results show that the improvements made in the 5′-UTR can lead to a more efficient translation and hence to faster and more efficient minicircle generation.MIT-Portugal ProgramFundação para a Ciência e a Tecnologia (PhD grant SFRH/BD/33786/2009

Error threshold in finite populations

A simple analytical framework to study the molecular quasispecies evolution of finite populations is proposed, in which the population is assumed to be a random combination of the constiyuent molecules in each generation,i.e., linkage disequilibrium at the population level is neglected. In particular, for the single-sharp-peak replication landscape we investigate the dependence of the error threshold on the population size and find that the replication accuracy at threshold increases linearly with the reciprocal of the population size for sufficiently large populations. Furthermore, in the deterministic limit our formulation yields the exact steady-state of the quasispecies model, indicating then the population composition is a random combination of the molecules.Comment: 14 pages and 4 figure

Formation of dense structures induced by filament collisions. Correlation of density, kinematics and magnetic field in the Pipe nebula

Context. The Pipe nebula is a molecular cloud that lacks star formation feedback and has a relatively simple morphology and velocity structure. This makes it an ideal target to test cloud evolution through collisions. Aims. We aim at drawing a comprehensive picture of this relatively simple cloud to better understand the formation and evolution of molecular clouds on large scales. Methods. We use archival data to compare the optical polarization properties, the visual extinction, and the 13CO velocities and linewidths of the entire cloud in order to identify trends among the observables. Results. The Pipe nebula can be roughly divided in two filaments with different orientations and gas velocity ranges: E-W at 2-4 km s-1 and N-S at 6-7 km s-1. The two filaments overlap at the bowl, where the gas shows a velocity gradient spanning from 2 to 7 km s-1. Compared to the rest of the Pipe nebula, the bowl gas appears to be denser and exhibits larger linewidths. In addition, the polarization data at the bowl shows lower angular dispersion and higher polarization degree. Cores in the bowl tend to cluster in space and tend to follow the 13CO velocity gradient. In the stem, cores tend to cluster in regions with properties similar to those of the bowl. Conclusions. The velocity pattern points to a collision between the filaments in the bowl region. The magnetic field seems to be compressed and strengthened in the shocked region. The proportional increase of density and magnetic field strength by a factor similar to the Alfv\'enic Mach number suggests a continuous shock at low Alfv\'enic Mach number under flux-freezing. Shocked regions seem to enhance the formation and clustering of dense cores.Comment: 5 pages, 2 figures. Accepted for publication in A&