Design of a data model for developing laboratory information management and analysis systems for protein production

Data management has emerged as one of the central issues in the high-throughput processes of taking a protein target sequence through to a protein sample. To simplify this task, and following extensive consultation with the international structural genomics community, we describe here a model of the data related to protein production. The model is suitable for both large and small facilities for use in tracking samples, experiments, and results through the many procedures involved. The model is described in Unified Modeling Language (UML). In addition, we present relational database schemas derived from the UML. These relational schemas are already in use in a number of data management projects.     

Fluctuations of transfer RNAs between classical and hybrid states

Adjacent transfer RNAs (tRNAs) in the A- and P-sites of the ribosome are in dynamic equilibrium between two different conformations called classical and hybrid states before translocation. Here, we have used single-molecule fluorescence resonance energy transfer to study the effect of Mg(2+) on tRNA dynamics with and without an acetyl group on the A-site tRNA. When the A-site tRNA is not acetylated, tRNA dynamics do not depend on [Mg(2+)], indicating that the relative positions of the substrates for peptide-bond formation are not affected by Mg(2+). In sharp contrast, when the A-site tRNA is acetylated, Mg(2+) lengthens the lifetime of the classical state but does not change the lifetime of the hybrid state. Based on these findings, the classical state resembles a state with direct stabilization of tertiary structure by Mg(2+) ions whereas the hybrid state resembles a state with little Mg(2+)-assisted stabilization. The antibiotic viomycin, a translocation inhibitor, suppresses tRNA dynamics, suggesting that the enhanced fluctuations of tRNAs after peptide-bond formation drive spontaneous attempts at translocation by the ribosome.     

Functional analysis of the invariant residue G791 of Escherichia coli 16S rRNA

The nucleotide at position 791(G791) of E. coli 16S rRNA was previously identified as an invariant residue for ribosomal function. In order to characterize the functional role of G791, base substitutions were introduced at this position, and mutant ribosomes were analyzed with regard to their protein synthesis ability, via the use of a specialized ribosome system. These ribosomal RNA mutations attenuated the ability of ribosomes to conduct protein synthesis by more than 65%. A transition mutation (G to A) exerted a moderate effect on ribosomal function, whereas a transversion mutation (G to C or U) resulted in a loss of protein synthesis ability of more than 90%. The sucrose gradient profiles of ribosomes and primer extension analysis showed that the loss of protein-synthesis ability of mutant ribosomes harboring a base substitution from G to U at position 791 stems partially from its inability to form 70S ribosomes. These findings show the involvement of the nucleotide at position 791 in the association of ribosomal subunits and protein synthesis steps after 70S formation, as well as the possibility of using 16S rRNA mutated at position 791 for the selection of second-site revertants in order to identify ligands that interact with G791 in protein synthesis.     

Effect of luteinizing hormone (LH), pregnancy-specific protein B (PSPB), or arachidonic acid (AA) on secretion of progesterone and prostaglandins (PG) E (PGE; PGE(1) and PGE(2)) and F(2alpha) (PGF(2alpha)) by ovine corpora lutea of the estrous cycle or pregnancy in vitro

LH regulates luteal progesterone secretion during the estrous cycle in ewes and cows. However, PGE, not LH, stimulated ovine luteal progesterone secretion in vitro at day 90 of pregnancy and at day 200 in cows. The hypophysis is not obligatory after day 50 nor the ovaries after day 55 to maintain pregnancy in ewes. LH has been reported to regulate ovine placental PGE secretion up to day 50 of pregnancy and by pregnancy-specific protein B (PSPB) after day 50 of pregnancy. The objective of this experiment was to determine if and when a switch from LH to PGE occurred as the luteotropin regulating luteal progesterone secretion during pregnancy in ewes. Ovine luteal tissue slices of the estrous cycle (days 8, 11, 13, and 15) or pregnancy (days 8, 11, 13, 15, 20, 30, 40, 50, 60, and 90) were incubated in vitro with vehicle, LH, AA (precursor to PGE(2) and PGF(2alpha) synthesis), or PSPB in M199 for 4 h and 8 h. Concentrations of progesterone in jugular venous plasma of bred ewes increased (P< or =0.05) after day 50 and continued to increase through day 90. Secretion of progesterone by luteal tissue of non-bred ewes on days 8, 11, 13 and 15 and by bred ewes on days 8, 11, 13, 15, 20, 30, 40, and 50 was increased (P< or =0.05) by LH, but not by luteal tissue from pregnant ewes after day 50 (P> or =0.05). LH-stimulated progesterone secretion by luteal tissue from day 15 bred ewes was greater (P< or =0.05) than day 15 luteal tissue from non-bred ewes. Concentrations of progesterone in media were increased (P< or =0.05) when luteal tissue from pregnant ewes on day 50, 60, or 90 were incubated with AA or PSPB. Concentrations of PGE in media of non-bred ewes on days 8, 11, 13, or 15 and bred ewes on days 8 and 11 did not differ (P> or =0.05). Concentrations of PGE were increased (P< or =0.05) in media by luteal slices from bred ewes on days 13, 15, 20, 30, 40, 50, 60, and 90 of vehicle, LH, AA or PSPB-treated ewes. In addition, PSPB increased (P< or =0.05) PGE in media by luteal slices from pregnant ewes only on days 40, 50, 60, and 90. Concentrations of PGF(2alpha) were increased in media (P<0.05) of vehicle, AA, LH, or PSPB-treated luteal tissue from non-bred ewes and bred ewes on day 15 and by luteal tissue from bred ewes on days 20 and 30 after which concentrations of PGF(2alpha) in media declined (P< or =0.05) and did not differ (P> or =0.05) from non-bred or bred ewes on days 8, 11, or 13. It is concluded that LH regulates luteal progesterone secretion during the estrous cycle of non-bred ewes and up to day 50 of pregnancy, while only PGE regulates luteal progresterone secretion by ovine corpora lutea from days 50 to 90 of pregnancy. In addition, PSPB appears to regulate luteal secretion of progesterone from days 50 to 90 of pregnancy through stimulation of PGE secretion by ovine luteal tissue.     

Mithramycin inhibits etoposide resistance in glucose-deprived HT-29 human colon carcinoma cells

Physiological cell conditions such as glucose deprivation and hypoxia play roles in the development of drug resistance in solid tumors. These tumor-specific conditions cause decreased expression of DNA topoisomerase IIalpha, rendering cells resistant to topo II target drugs such as etoposide. Thus, targeting tumor-specific conditions such as a low glucose environment may be a novel strategy in the development of anticancer drugs. On this basis, we established a novel screening program for anticancer agents with preferential cytotoxic activity in cancer cells under glucose-deprived conditions. We recently isolated an active compound, AA-98, from Streptomyces sp. AA030098 that can prevent stress-induced etoposide resistance in vitro. Furthermore, LC-MS and various NMR spectroscopic methods identified AA-98 as mithramycin, which belongs to the aureolic acid group of antitumor compounds. We found that mithramycin prevents the etoposide resistance that is induced by glucose deprivation. The etoposide-chemosensitive action of mithramycin was just dependent on strict low glucose conditions, and resulted in the selective cell death of etoposide-resistant HT-29 human colon cancer cells.     

The Kinetochore-Microtubule Coupling Machinery Is Repurposed in Sensory Nervous System Morphogenesis

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Mobility is related to species traits in noctuid moths

1. Mobility is important for the understanding of how species survive in fragmented landscapes and cope with increasing rates of habitat and climate change. However, mobility is a difficult trait to explore and is poorly known in most taxa. Species traits have been studied in relation to range shifts, extinction risks, and responses to habitat area and isolation, and have also been suggested as good estimators of mobility. Here we explore the relation between mobility and species traits in noctuid moths. 2. We sampled noctuid moths by an automatic light‐trap on an island far out in the Baltic Sea. We compared traits of the non‐resident species on the island with traits of a species pool of assumed potential migrants from the Swedish mainland. 3. Mobility was significantly related to adult activity period, length of flight period, and the interaction between host‐plant specificity and distribution area. Widely distributed host‐plant generalists were more mobile than host‐plant specialists with more restricted distribution, and species with an adult activity period in August to September moved to the island to a higher extent than species with an adult activity period in May to July. Our results remained qualitatively robust in additional analyses, after controlling for phylogeny and including all species recorded on the island, except for the trait ‘length of flight period’. 4. Our results highlight the importance of the relation between mobility and species traits. Noctuid moths with certain traits move over longer distances than earlier known. This finding is important to include when predicting range dynamics in fragmented and changing landscapes, and when conservation measures of species are devised.     

Macaronesia: a source of hidden genetic diversity for post‐glacial recolonization of western Europe in the leafy liverwort Radula lindenbergiana

Aim Bryophytes exhibit apparently low rates of endemism in Macaronesia and differ from angiosperms in their diversity patterns by the widespread occurrence of endemics within and among archipelagos. This paper investigates the phylogeography of the leafy liverwort Radula lindenbergiana to determine: (1) whether or not morphologically cryptic diversification has occurred in Macaronesia, and (2) the relationships between Macaronesian and continental populations. Location Macaronesia, Europe, Africa. Methods Eighty‐four samples were collected across the species’ distribution range and sequenced at four chloroplast DNA (cpDNA) loci (atpB–rbcL, trnG, trnL and rps4). Phylogenetic reconstructions and Bayesian ancestral area reconstructions were used in combination with population genetics statistics (H, N_ST, F_ST) to describe the pattern of present genetic diversity in R. lindenbergiana and infer its biogeographic history. Results Patterns of genetic diversity in R. lindenbergiana exhibit a striking westwards gradient, wherein haplotype (0.90) and nucleotide (0.0038 ± 0.0019) diversity peak in Macaronesia, with a substantial endemic component. We found 20.9% of the genetic variance between biogeographic regions, and most pairwise F_ST comparisons between regions are significantly different from zero. The global N_ST (0.78) is significantly higher than the global F_ST (0.20), providing evidence for the presence of phylogeographic signal in the data. Ancestral area reconstructions suggest that the haplotypes currently found in western Europe share a Macaronesian common ancestor. Main conclusions The haplotype diversification exhibited by R. lindenbergiana in Macaronesia is comparable to that reported for many angiosperm groups at the species level. The apparent lack of radiation among Macaronesian bryophytes may thus reflect the reduced morphology of bryophytes in comparison with angiosperms. The high diversity found among Macaronesian haplotypes, especially in Madeira and the Canary Islands, and the significant N_ST/F_ST ratio between Macaronesia and all the other biogeographic regions (an indication that mutation rate exceeds dispersal rates) suggest that Macaronesian archipelagos could have served as a refugium during the Quaternary glaciations. Many haplotypes currently found in Europe share a Macaronesian common ancestor, and this further suggests that Macaronesia might have played a key role in the back‐colonization of the continent.