Structure and organization of the bovine beta-globin genes

Genomic clones spanning the entire cow beta-globin gene locus have been isolated and characterized. These clones demonstrate that the linkage of embryonic-like (epsilon) genes and pseudogenes (psi) to the previously described fetal (gamma) and adult (beta) genes is as follows: 5'-epsilon 3-epsilon 4-psi 3-beta-epsilon 1-epsilon 2-psi 1- psi 2-gamma-3'. Present data indicate that, like that of the goat, the fetal and adult genes arose via block duplication of an ancestral four- gene set: epsilon-epsilon-psi-beta. This duplication event preceded the divergence of cows and goats, which occurred greater than or equal to 18-20 Myr ago. However, cows do not have the additional four-gene block containing a preadult/stress globin gene (beta C). Furthermore, the cow fetal cluster contains an extra beta-like pseudogene, which apparently arose by a small-scale duplication. The fixation of this duplication may indicate a possible evolutionary role for pseudogenes.      

Solution structure of YKR049C, a putative redox protein from Saccharomyces cerevisiae

YKR049C is a mitochondrial protein in Saccharomyces cerevisiae that is conserved among yeast species, including Candida albicans. However, no biological function for YKR049C has been ascribed based on its primary sequence information. In the present study, NMR spectroscopy was used to determine the putative biological function of YKR049C based on its solution structure. YKR049C shows a well-defined thioredoxin fold with a unique insertion of helices between two beta-strands. The central beta-sheet divides the protein into two parts; a unique face and a conserved face. The 'unique face' is located between beta2 and beta3. Interestingly, the sequences most conserved among YKR049C families are found on this 'unique face', which incorporates L109 to E114. The side chains of these conserved residues interact with residues on the helical region with a stretch of hydrophobic surface. A putative active site composed by two short helices and a single Cys97 was also well observed. Our findings suggest that YKR049C is a redox protein with a thioredoxin fold containing a single active cysteine.     

ABACUS, a direct method for protein NMR structure computation via assembly of fragments

The ABACUS algorithm obtains the protein NMR structure from unassigned NOESY distance restraints. ABACUS works as an integrated approach that uses the complete set of available NMR experimental information in parallel and yields spin system typing, NOE spin pair identities, sequence specific resonance assignments, and protein structure, all at once. The protocol starts from unassigned molecular fragments (including single amino acid spin systems) derived from triple-resonance (1)H/(13)C/(15)N NMR experiments. Identifications of connected spin systems and NOEs precede the full sequence specific resonance assignments. The latter are obtained iteratively via Monte Carlo-Metropolis and/or probabilistic sequence selections, molecular dynamics structure computation and BACUS filtering (A. Grishaev and M. Llinás, J Biomol NMR 2004;28:1-10). ABACUS starts from scratch, without the requirement of an initial approximate structure, and improves iteratively the NOE identities in a self-consistent fashion. The procedure was run as a blind test on data recorded on mth1743, a 70-amino acid genomic protein from M. thermoautotrophicum. It converges to a structure in ca. 15 cycles of computation on a 3-GHz processor PC. The calculated structures are very similar to the ones obtained via conventional methods (1.22 A backbone RMSD). The success of ABACUS on mth1743 further validates BACUS as a NOESY identification protocol.     

Carbon and water fluxes in a calcareous grassland under elevated CO2

1. As part of a long-term study of the effects of elevated CO₂ on biodiversity and ecosystem function in a calcareous grassland, we measured ecosystem carbon dioxide and water-vapour fluxes over 24-h periods during the 1994 and 1995 growing seasons. Data were used to derive CO₂ and H₂O gas-exchange response functions to quantum flux density (QFD).
2. The relative increase in net ecosystem CO₂ flux (NEC) owing to CO₂ enrichment increased as QFD rose. Daytime NEC at high QFD under elevated CO₂ increased by 25% to 60%, with the greatest increases in the spring and after mowing in June when above-ground biomass was lowest. There was much less stimulation of NEC in early June and again in October when the canopy was fully developed. Night-time NEC was not significantly altered under elevated CO₂.
3. Short-term reversal of CO₂ concentrations between treatments after two seasons of CO₂ exposure provided evidence for a 50% downward adjustment of NEC expressed per unit above-ground plant dry weight. However, when expressed on a land area basis, this difference disappeared because of a c. 20% increase in above-ground biomass under elevated CO₂.
4. Ecosystem evapotranspiration (ET) was not significantly altered by elevated CO₂ when averaged over all measurement dates and positions. However, ET was reduced 3–18% at high QFD in plots at the top of the slope at our study site. In summary, CO₂ enrichment resulted in a large stimulation of ecosystem CO₂ capture, especially during periods of a large demand of carbon in relationship to its supply, and resulted in a relatively small and variable effect on ecosystem water consumption.     

Allocation of Photosynthate to Individual Tubers of Solanum tuberosum L.: II. RELATIONSHIP BETWEEN GROWTH RATE, CARBOHYDRATE CONCENTRATION AND 14C-PARTITIONING WITHIN TUBERS

Potato plants (Solanum tuberosum L.) were grown in water culturein a controlled environment. The growth rates of individualtubers were closely reflected by their ¹⁴C-content 20 h after¹⁴CO₂ had been applied to the aerial parts of the shoot for4 h. The ¹⁴C-content of the tuber (sink strength) was significantlycorrelated to the ¹⁴C-concentration of the tuber tissue (¹⁴Cg^–1 fr. wt.=sink activity). The sink activity, which differedbetween individual tubers by up to a factor of 10, was alsoclosely related to the conversion rates of ¹⁴C into the starchand the remainder as well as to the ¹⁴C-content in the ethanolsoluble fraction. This indicates the simultaneous use of photosynthatefor growth and storage in the growing tubers. No preferenceof photosynthate utilization for either of these processes couldbe detected in relation to the sink activity of the tubers.Tubers with high sink activity imported ¹⁴C-labelled photosynthateat higher rates although their tissue contained higher concentrationsof reducing sugars and sucrose than the tissue of tubers withlow sink activity. Despite the close relationship between sinkactivity and the rate of starch synthesis (¹⁴C-conversion intostarch), no significant correlation was found between sink activityand the actual starch concentration of the tissue. The applicationof zeatin riboside directly onto individual tubers increasedtheir growth rates in comparison to non-treated tubers of thesame plant. The results indicate the importance of both growthand storage processes for the regulation of sink activity inyoung potato tubers. Key words: Potato tuber, ¹⁴C-photosynthate partitioning, zeatin riboside application     

Model system using coliphage phi X174 for testing virus removal by air filters.

Short-term (15-min-duration) and long-term (5- to 6-day-duration) test procedures have been developed for determining the efficiency of the removal of bacteriophage phi X174 by air-sterilizing filters. These procedures were sensitive enough to measure a 10(8)-fold reduction in the number of bacteriophage. A filter commonly used in industrial air sterilizations (Domnick-Hunter Bio-X borosilicate glass) effected a 10(8)-fold removal of viable phage in both short-term and long-term tests. A prototype low-flux, hollow-fiber membrane gave similar results; however, a prototype high-flux, hollow-fiber membrane removed only about 99.999% of the bacteriophage in short-term tests.     

Use of wild type and nickel resistantNeurospora crassa for removal of Ni2+ from aqueous medium

Summary A novel nickel resistant, hyperaccumulatingN.crassa nir-2 mutant, isolated by us, sequestered 90% of Ni²⁺ from medium with 120 mg/l Ni²⁺. The parent wild strain showed comparable efficiency only at much lower concentrations (<10mg/l). The initial rapid rate and efficiency of Ni²⁺ removal could be maintained beyond 2 h by fresh addition of mycelial biomass. The results have been discussed from the stand point of the utility of metal resistant fungi in the control of environmental pollution.