ALFA: First Operational Experience of the MPE/MPIA Laser Guide Star System for Adaptive Optics

The sodium laser guide star adaptive optics system ALFA has been constructed at the Calar Alto 3.5-m telescope. Following the first detection of the laser beacon on the wavefront sensor in 1997 the system is now being optimized for best performance. In this contribution we discuss the current status of the launch beam and the planned improvements and upgrades. We report on the performance level achieved when it is used with the adaptive optics system, and relate various aspects of our experience during operation of the system. We have begun to produce scientific results and mention two of these.Comment: 9 pages, 6 figures, LaTeX (spie.sty). SPIE conf proc 3353, Adaptive Optical System Technologies, March 199

Optimization of cw sodium laser guide star efficiency

Context: Sodium laser guide stars (LGS) are about to enter a new range of laser powers. Previous theoretical and numerical methods are inadequate for accurate computations of the return flux and hence for the design of the next-generation LGS systems. Aims: We numerically optimize the cw (continuous wave) laser format, in particular the light polarization and spectrum. Methods: Using Bloch equations, we simulate the mesospheric sodium atoms, including Doppler broadening, saturation, collisional relaxation, Larmor precession, and recoil, taking into account all 24 sodium hyperfine states and on the order of 100 velocity groups. Results: LGS return flux is limited by "three evils": Larmor precession due to the geomagnetic field, atomic recoil due to radiation pressure, and transition saturation. We study their impacts and show that the return flux can be boosted by repumping (simultaneous excitation of the sodium D2a and D2b lines with 10-20% of the laser power in the latter). Conclusions: We strongly recommend the use of circularly polarized lasers and repumping. As a rule of thumb, the bandwidth of laser radiation in MHz (at each line) should approximately equal the launched laser power in Watts divided by six, assuming a diffraction-limited spot size.Comment: 15 pages, 12 figures, to be published in Astronomy & Astrophysics, AA/2009/1310

Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis – a rich resource to identify new transcripts, proteins and to study gene regulation

Background: Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters. Results: A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 % of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file. Conclusions: The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes

Different Transport Pathways of Individual Precursor Proteins in Mitochondria

Transport of mitochondrial precursor proteins into mitochondria of Neurospora crassa was studied in a cellfree reconstituted system. Precursors were synthesized in a reticulocyte lysate programmed with Neurospora mRNA and transported into isolated mitochondria in the absence of protein synthesis. Uptake of the following precursors was investigated: apocytochrome c, ADP/ATP carrier and subunit 9 of the oligomycin-sensitive ATPase. Addition of high concentrations of unlabelled chemically prepared apocytochrome c (1–10 μM) inhibited the appearance in the mitochondrial of labelled cytochrome c synthesized in vitro because the unlabelled protein dilutes the labelled one and because the translocation system has a limited capacity [apparent V is 1–3 pmol × min−1× (mg mitochondrial protein)−1]. Concentrations of added apocytochrome c exceeding the concentrations of precursor proteins synthesized in vitro by a factor of about 104 did not inhibit the transfer of ADP/ATP carrier or ATPase subunit 9 into mitochondria. Carbonylcyanide m-chlorophenylhydrazone, an uncoupler of oxidative phosphorylation, inhibited transfer in vitro of ADP/ATP carrier and of ATPase subunit 9, but not of cytochrome c. These findings suggest that cytochrome c and the other two proteins have different import pathways into mitochondria. It can be inferred from the data presented that different 'receptors' on the mitochondrial surface mediate the specific recognition of precursor proteins by mitochondria as a first step in the transport process