Interannual variation in nitrous oxide emissions from perennial ryegrass/white clover grassland used for dairy production

Nitrous oxide (N₂O) emissions are subject to intra‐ and interannual variation due to changes in weather and management. This creates significant uncertainties when quantifying estimates of annual N₂O emissions from grazed grasslands. Despite these uncertainties, the majority of studies are short‐term in nature (<1 year) and as a consequence, there is a lack of data on interannual variation in N₂O emissions. The objectives of this study were to (i) quantify annual N₂O emissions and (ii) assess the causes of interannual variation in emissions from grazed perennial ryegrass/white clover grassland. Nitrous oxide emissions were measured from fertilized and grazed perennial ryegrass/white clover grassland (WC) and from perennial ryegrass plots that were not grazed and did not receive N input (GB), over 4 years from 2008 to 2012 in Ireland (52°51′N, 08°21′W). The annual N₂O‐N emissions (kg ha^?1; mean ± SE) ranged from 4.4 ± 0.2 to 34.4 ± 5.5 from WC and from 1.7 ± 0.8 to 6.3 ± 1.2 from GB. Interannual variation in N₂O emissions was attributed to differences in annual rainfall, monthly (December) soil temperatures and variation in N input. Such substantial interannual variation in N₂O emissions highlights the need for long‐term studies of emissions from managed pastoral systems.     

New data and collaborations at the Saccharomyces Genome Database: updated reference genome,alleles, and the Alliance of Genome Resources

Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.     

Demography of the western harvest mouse,Reithrodontomys megalotis,in eastern Kansas

Summary Reithrodontomys megalotis was live-trapped on three open field grids in eastern Kansas from August 1979 to August 1982. One grid was a control on which normal demography was monitored, and two were experimental grids where periodic removal of residents allowed the investigation of the demographic and fitness consequences of emigration. Popullations on the control grid showed an annual cycle in numbers, reaching peaks in density during the winter of each year, falling to low densities during the summer. Low summer densities were attributed, at least partially, to low trappability of R. megalotis during periods of high resource abundance. Reproduction was initiated in the spring of each year at approximately the same time as the emergence of new vegetative growth, and ceased in late fall of each year. The trappable population was composed almost entirely of adults, and the sex ratio was skewed significantly toward females. A statistically significant negative association between the number of M. ochrogaster residents and the reproductive activity of female R. megalotis residents was found. A canonical correlation analysis revealed a common seasonal component to the demography of the two species, and possible interspecific affects. Emigrating R. megalotis were a nonrandom sample of the population, with emigrants more likely to be subadult and juvenile males when compared to residents. No association was detected between the numbers of M. ochrogaster colonizing the removal grid and the numbers of R. megalotis colonizing the same removal grid, or between the number of M. ochrogaster residents on the control grid and the numbers of R. megalotis colonizing the removal grids. However, the number of R. megalotis residents on the control grid is positively correlated with the number of R. megalotis on the removal grids.     

Substrate independent ATPase activity may complicate high throughput screening

Inorganic phosphate release, [Pi], is often measured in an enzymatic reaction in a high throughput setting. Based on the published mechanism, we designed a protocol for our screening for inhibitors of SAICAR synthetase (PurC), and we found a gradual increase in [Pi] in positive control samples over the course of the day. Further investigation indicated that hydrolysis of ATP catalyzed by PurC, rather than substrate-related phosphate release, was responsible for a partial contribution to the signals in the control samples. Thus substrate-independent ATPase activity may complicate high throughput screening.     

The Mlvi-1 locus involved in the induction of rat T-cell lymphomas and the pvt-1/Mis-1 locus are identical.

Mlvi-1 defines a locus of proviral integration in rat thymomas induced by Moloney murine leukemia virus. pvt-1/Mis-1 represents an independently identified locus which becomes rearranged either by chromosomal translocation in murine plasmacytomas or by provirus insertion in retrovirus-induced murine and rat thymic lymphomas. Although it had been claimed that pvt-1/Mis-1 and Mlvi-1 represent two different loci, we present here evidence showing that they are identical. This finding demonstrates the need for rigorous characterization of any newly identified common regions of integration in retrovirus-induced neoplasms.     

On the Direction of Reading of Bacteriophage T4 Gene 43 (Deoxyribonucleic Acid Polymerase)

Amber (am) mutants of the two closely linked sites, B22 and C125, in bacteriophage T4 gene 43 [deoxyribonucleic acid (DNA) polymerase] synthesize in the nonpermissive (su(-)) Escherichia coli host gene 43 products which are devoid of DNA polymerase activity, but which retain a 3'-exonuclease activity. Diethylaminoethyl-cellulose chromatographic analysis of DNA polymerase and deoxyribonuclease activities from extracts of su(-) cells infected with single- and double-am mutants of T4 gene 43 showed that the exonuclease activity which is observed with amB22 is not seen with double mutants carrying, in addition to amB22, am mutations which map to the clockwise side of the B22 site on the circular genetic map of T4. Similarly, am mutations which map to the clockwise side of the C125 site abolish the exonuclease activity which is observed with an am mutant (amE4335) of this site. It was concluded that in these double mutants termination signals to the clockwise side of amB22 and amE4335 are encountered before the amB22 and amE4335 signals during translation of the messenger ribonucleic acid from T4 gene 43. Thus, it seems that the T4 DNA polymerase is synthesized in vivo in a direction which corresponds to a counterclockwise reading of gene 43.     

Improved calculations of compactness and a reevaluation of continuous compact units

A new method for calculating compactness (Z) that uses look-up table-based algorithms for area and volume computations is introduced. These algorithms can be used in any iterative area orvolume calculation, are more than 1000 times faster than the originalalgorithms, and have equal or better precision. With the faster algorithms it is now possible to calculate the compactness of all continuous units in a protein, and to precisely locate the optimal compact units without the screening functions and limited resolution used previously. These methods have been incorporated into a fully automatic domain finding algorithm, and this method has been applied to the 21 proteins originally analyzed as well as 12 additional proteins. This method is robust, and yields similar units even when applied to coordinates of protein crystals grown under different experimental conditions. © 1993 Wiley-Liss, Inc.     

Exocellular phosphatidylethanolamine production and multiple-metal tolerance in Pseudomonas fluorescens

Abstract Pseudomonas fluorescens appeared to circumvent the challenge imposed by millimolar amounts of metals (5 mM Al³⁺, 5 mM Fe³⁺, 2 mM Ca²⁺, 1 mM Ga³⁺ and 3 mM Zn²⁺) by the formation of phosphatidylethanolamine. This lipid moiety constituted an important organic component of an insoluble gelatinous residue in which most of the test metals were immobilized at stationary phase of growth. Ultracentrifugation and dialysis experiments showed that the metals were associated with phosphatidylethanolamine from early stages of growth. Transmission electron microscopy revealed metal rich bodies in the cytoplasm prior to their secretion in the spent fluid. These results demonstrate a role of phosphatidylethanolamine in multiple-metal homeostasis.