The Crystal Structure and Small-Angle X-Ray Analysis of CsdL/TcdA Reveal a New tRNA Binding Motif in the MoeB/E1 Superfamily

Cyclic N⁶-threonylcarbamoyladenosine (‘cyclic t⁶A’, ct⁶A) is a non-thiolated hypermodification found in transfer RNAs (tRNAs) in bacteria, protists, fungi and plants. In bacteria and yeast cells ct⁶A has been shown to enhance translation fidelity and efficiency of ANN codons by improving the faithful discrimination of aminoacylated tRNAs by the ribosome. To further the understanding of ct⁶A biology we have determined the high-resolution crystal structures of CsdL/TcdA in complex with AMP and ATP, an E1-like activating enzyme from Escherichia coli, which catalyzes the ATP-dependent dehydration of t⁶A to form ct⁶A. CsdL/TcdA is a dimer whose structural integrity and dimer interface depend critically on strongly bound K⁺ and Na⁺ cations. By using biochemical assays and small-angle X-ray scattering we show that CsdL/TcdA can associate with tRNA with a 1:1 stoichiometry and with the proper position and orientation for the cyclization of t⁶A. Furthermore, we show by nuclear magnetic resonance that CsdL/TcdA engages in transient interactions with CsdA and CsdE, which, in the latter case, involve catalytically important residues. These short-lived interactions may underpin the precise channeling of sulfur atoms from cysteine to CsdL/TcdA as previously characterized. In summary, the combination of structural, biophysical and biochemical methods applied to CsdL/TcdA has afforded a more thorough understanding of how the structure of this E1-like enzyme has been fine tuned to accomplish ct⁶A synthesis on tRNAs while providing support for the notion that CsdA and CsdE are able to functionally interact with CsdL/TcdA.     

Interactions Crucial for Three-Dimensional Domain Swapping in the HP-RNase Variant PM8

The structural determinants that are responsible for the formation of higher order associations of folded proteins remain unknown. We have investigated the role on the dimerization process of different residues of a domain-swapped dimer human pancreatic ribonuclease variant. This variant is a good model to study the dimerization and swapping processes because dimer and monomer forms interconvert, are easily isolated, and only one dimeric species is produced. Thus, simple models for the swapping process can be proposed. The dimerization (dissociation constant) and swapping propensity have been studied using different variants with changes in residues that belong to different putative molecular determinants of dimerization. Using NMR spectroscopy, we show that these mutations do not substantially alter the overall conformation and flexibility, but affect the residue level stability. Overall, the most critical residues for the swapping process are those of one subunit that interact with the hinge loop of another one-subunit residue, stabilizing it in a conformation that favors the interchange. Tyr²⁵, Gln¹⁰¹, and Pro¹⁹, with Asn¹⁷, Ser²¹, and Ser²³, are found to be the most significant; notably, Glu¹⁰³ and Arg¹⁰⁴, which were postulated to form salt bridges that would stabilize the dimer, are not critical for dimerization.     

Phytoplankton composition in the Weddell-Scotia Confluence area during austral spring in relation to hydrography

During the EPOS leg 2 cruise of the RV Polarstern, carried out in late austral spring of 1988–1989, the composition of phytoplankton in relation to the distribution of hydrographic parameters was studied in four successive transects carried out along 49°W and 47°W, across the Weddell-Scotia Confluence (WSC) and the marginal ice zone (which overlapped in part). In all transects, a maximum of phytoplankton biomass was found in the WSC, in surface waters stabilized by ice melting. Different phytoplankton assemblages could be distinguished. North of the Scotia Front (the northern limit of the WSC) diatoms with Chaetoceros neglectus, Nitzschia spp. and (Thalassiosira gravida) dominated the phytoplankton community. This assemblage appeared to have seeded a biomass maximum which occupied, during the first transect, an area of the WSC, south of the Scotia Front. The southernmost stations of the first transect and all the stations to the south of the Scotia Front in the other transects were populated by a flagellate assemblage (with a cryptomonad, Pyramimonas spp. and Phaeocystis sp.) and an assemblage of diatoms (Corethron criophilum and Tropidoneis vanheurkii among others) associated to the presence of ice. During the last three transects, the flagellate assemblage formed a bloom in the low salinity surface layers of the WSC zone. The bulk of the biomass maximum was formed by the cryptomonad which reached concentrations up to 4×10⁶ cells l^–1 towards the end of the cruise. Multivariate analysis is used to summarize phytoplankton composition variation. The relationships between the distribution of the different assemblages and the hydrographic conditions indicate that the change of dominance from diatoms to flagellates in the WSC zone was related to the presence of water masses from different origin.Data presented here were collected during the European Polarstern Study (EPOS) sponsored by the European Science Foundation     

Entire hemithorax irradiation for Masaoka stage IVa thymomas

Thymomas are rare neoplasms that have an indolent growth with a preferentially intra-thoracic dissemination pattern. Surgery is currently the standard treatment of thymomas; however radiotherapy is often used in an adjuvant setting due to a high sensitivity of these tumors to such treatment. Postoperative entire hemithoracic irradiation has been used in selected Masaoka stage IVa cases after complete surgical excision of metastatic lesions.In the present article, the authors report three cases of Masaoka stage IVa thymoma that underwent entire hemithorax irradiation after surgical excision of metastatic lesions. The first two patients presented as stage IVa thymomas. The third case consisted of a pleural recurrence of a thymoma.Hemithoracic irradiation with low doses has been used by different authors; the available data shows that it is a well-tolerated treatment that could potentially lead to better loco-regional control and increased overall survival.     

Assessment of prey overlap between a native (Polistes humilis) and an introduced (Vespula germanica) social wasp using morphology and phylogenetic analyses of 16S rDNA

Abstract In newly invaded communities, interspecific competition is thought to play an important role in determining the success of the invader and its impact on the native community. In southern Australia, the native Polistes humilis was the predominant social wasp prior to the arrival of the exotic Vespula germanica (Hymenoptera: Vespidae). Both species forage for similar resources (water, pulp, carbohydrate and protein prey), and concerns have arisen about potential competition between them. The aim of this study was to identify the protein foods that these wasps feed on. As many prey items are masticated by these wasps to the degree that they cannot be identified using conventional means, morphological identification was complemented by sequencing fragments of the mitochondrial 16S rRNA gene. GenBank searches using blast and phylogenetic analyses were used to identify prey items to at least order level. The results were used to construct complete prey inventories for the two species. These indicate that while P. humilis is restricted to feeding on lepidopteran larvae, V. germanica collects a variety of prey of invertebrate and vertebrate origin. Calculated values of prey overlap between the two species are used to discuss the implications of V. germanica impacting on P. humilis. Results obtained are compared to those gained by solely 'conventional' methods, and the advantages of using DNA-based taxonomy in ecological studies are emphasized.