Engineering topics

Larsen, N.

Publications and source records attributed to Larsen, N..

5 records

NASA NTRS1999

A new version of the RDP (Ribosomal Database Project)

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.

Non-NASA Center↗

NASA NTRS1994

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective

The 16S and 23S rRNA higher-order structures inferred from comparative analysis are now quite refined. The models presented here differ from their immediate predecessors only in minor detail. Thus, it is safe to assert that all of the standard secondary-structure elements in (prokaryotic) rRNAs have been identified, with approximately 90% of the individual base pairs in each molecule having independent comparative support, and that at least some of the tertiary interactions have been revealed. It is interesting to compare the rRNAs in this respect with tRNA, whose higher-order structure is known in detail from its crystal structure (36) (Table 2). It can be seen that rRNAs have as great a fraction of their sequence in established secondary-structure elements as does tRNA. However, the fact that the former show a much lower fraction of identified tertiary interactions and a greater fraction of unpaired nucleotides than the latter implies that many of the rRNA tertiary interactions remain to be located. (Alternatively, the ribosome might involve protein-rRNA rather than intramolecular rRNA interactions to stabilize three-dimensional structure.) Experimental studies on rRNA are consistent to a first approximation with the structures proposed here, confirming the basic assumption of comparative analysis, i.e., that bases whose compositions strictly covary are physically interacting. In the exhaustive study of Moazed et al. (45) on protection of the bases in the small-subunit rRNA against chemical modification, the vast majority of bases inferred to pair by covariation are found to be protected from chemical modification, both in isolated small-subunit rRNA and in the 30S subunit. The majority of the tertiary interactions are reflected in the chemical protection data as well (45). On the other hand, many of the bases not shown as paired in Fig. 1 are accessible to chemical attack (45). However, in this case a sizeable fraction of them are also protected against chemical modification (in the isolated rRNA), which suggests that considerable higher-order structure remains to be found (although all of it may not involve base-base interactions and so may not be detectable by comparative analysis). The agreement between the higher-order structure of the small-subunit rRNA and protection against chemical modification is not perfect, however; some bases shown to covary canonically are accessible to chemical modification (45).(ABSTRACT TRUNCATED AT 400 WORDS).

Review↗

NASA NTRS1993

An intron within the 16S ribosomal RNA gene of the archaeon Pyrobaculum aerophilum

The 16S rRNA genes of Pyrobaculum aerophilum and Pyrobaculum islandicum were amplified by the polymerase chain reaction, and the resulting products were sequenced directly. The two organisms are closely related by this measure (over 98% similar). However, they differ in that the (lone) 16S rRNA gene of Pyrobaculum aerophilum contains a 713-bp intron not seen in the corresponding gene of Pyrobaculum islandicum. To our knowledge, this is the only intron so far reported in the small subunit rRNA gene of a prokaryote. Upon excision the intron is circularized. A secondary structure model of the intron-containing rRNA suggests a splicing mechanism of the same type as that invoked for the tRNA introns of the Archaea and Eucarya and 23S rRNAs of the Archaea. The intron contains an open reading frame whose protein translation shows no certain homology with any known protein sequence.

NASA Discipline Exobiology↗

NASA NTRS1992

Observations of Ozone-aerosol Correlated Behaviour in the Lower Stratosphere During the EASOE Campaign

The question of possible interactions between ozone and stratospheric aerosol has been open for a long time. Measurements carried out after the Mt. Agung and El Chicon eruptions showed evidence of negative correlations between the presence of volcanic stratospheric aerosols and ozone concentration. Evidence for negative correlations in the polar winter has been also found. It is only after the discovery of the Antarctic ozone hole that catalytic effects related to low temperature heterogeneous chemistry have become the object of much investigation, now extended to the role of volcanic aerosol in the ozone reduction. These phenomena can be the object of various interpretations, not mutually exclusive, including the effect of transport, diffuse radiation as well as heterogeneous chemistry. The present paper provides preliminary results of simultaneous measurements of ozone and aerosol, carried out at Thule, Greenland, during the winter 1991-92. The European Stratospheric Ozone Experiment (EASOE) was aimed at monitoring the winter Arctic stratosphere in order to obtain a deeper insight of the ozone destruction processes taking place in the polar regions. A large amount of aerosol was injected into the lower stratosphere by the recent eruption of Volcano Pinatubo. A lidar system, already operational in Thule since November 1990, has provided detailed measurements of the stratospheric aerosol concentration during EASOE. In the same period, a large number of ozonesondes were launched. Although no PSC formation was detected over Thule, the simultaneous measurement of the stratospheric aerosol and ozone profiles give the possibility to study interactions occurring in the stratosphere between these two constituents.

Digirolamo, P.↗

NASA NTRS1992

The Ribosomal Database Project

The Ribosomal Database Project (RDP) complies ribosomal sequences and related data, and redistributes them in aligned and phylogenetically ordered form to its user community. It also offers various software packages for handling, analyzing and displaying sequences. In addition, the RDP offers (or will offer) certain analytic services. At present the project is in an intermediate stage of development.

Non-NASA Center↗