Protein Information Resource: a community resource for expert annotation of protein data

The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database. To provide timely and high quality annotation and promote database interoperability, the PIR-International employs rule-based and classification-driven procedures based on controlled vocabulary and standard nomenclature and includes status tags to distinguish experimentally determined from predicted protein features. The database contains about 200 000 non-redundant protein sequences, which are classified into families and superfamilies and their domains and motifs identified. Entries are extensively cross-referenced to other sequence, classification, genome, structure and activity databases. The PIR web site features search engines that use sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. The PIR-Inter­national databases and search tools are accessible on the PIR web site at http://pir.georgetown.edu/ and at the MIPS web site at http://www.mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP.

An unusual pathway of excitation energy deactivation in carotenoids: Singlet-to-triplet conversion on an ultrafast timescale in a photosynthetic antenna

Carotenoids are important biomolecules that are ubiquitous in nature and find widespread application in medicine. In photosynthesis, they have a large role in light harvesting (LH) and photoprotection. They exert their LH function by donating their excited singlet state to nearby (bacterio)chlorophyll molecules. In photosynthetic bacteria, the efficiency of this energy transfer process can be as low as 30%. Here, we present evidence that an unusual pathway of excited state relaxation in carotenoids underlies this poor LH function, by which carotenoid triplet states are generated directly from carotenoid singlet states. This pathway, operative on a femtosecond and picosecond timescale, involves an intermediate state, which we identify as a new, hitherto uncharacterized carotenoid singlet excited state. In LH complex-bound carotenoids, this state is the precursor on the reaction pathway to the triplet state, whereas in extracted carotenoids in solution, this state returns to the singlet ground state without forming any triplets. We discuss the possible identity of this excited state and argue that fission of the singlet state into a pair of triplet states on individual carotenoid molecules constitutes the mechanism by which the triplets are generated. This is, to our knowledge, the first ever direct observation of a singlet-to-triplet conversion process on an ultrafast timescale in a photosynthetic antenna.

Molecular Characterization of an Arabidopsis Gene Encoding Hydroperoxide Lyase, a Cytochrome P-450 That Is Wound Inducible1

Hydroperoxide lyase (HPL) cleaves lipid hydroperoxides to produce volatile flavor molecules and also potential signal molecules. We have characterized a gene from Arabidopsis that is homologous to a recently cloned HPL from green pepper (Capsicum annuum). The deduced protein sequence indicates that this gene encodes a cytochrome P-450 with a structure similar to that of allene oxide synthase. The gene was cloned into an expression vector and expressed in Escherichia coli to demonstrate HPL activity. Significant HPL activity was evident when 13S-hydroperoxy-9(Z),11(E),15(Z)-octadecatrienoic acid was used as the substrate, whereas activity with 13S-hydroperoxy-9(Z),11(E)-octadecadienoic acid was approximately 10-fold lower. Analysis of headspace volatiles by gas chromatography-mass spectrometry, after addition of the substrate to E. coli extracts expressing the protein, confirmed enzyme-activity data, since cis-3-hexenal was produced by the enzymatic activity of the encoded protein, whereas hexanal production was limited. Molecular characterization of this gene indicates that it is expressed at high levels in floral tissue and is wound inducible but, unlike allene oxide synthase, it is not induced by treatment with methyl jasmonate.

The type I BMP receptor BmprIB is essential for female reproductive function

Maintenance of female reproductive competence depends on the actions of several hormones and signaling factors. Recent reports suggest roles for bone morphogenetic proteins (BMPs) in early stages of folliculogenesis. A role for the type I BMP receptor BmprIB as a regulator of ovulation rates in sheep has been described recently, but little is known about the roles of BMP signaling pathways in other aspects of reproductive function. We report here that BMPRIB is essential for multiple aspects of female fertility. Mice deficient in BmprIB exhibit irregular estrous cycles and an impaired pseudopregnancy response. BmprIB mutants produce oocytes that can be fertilized in vitro, but defects in cumulus expansion prevent fertilization in vivo. This defect is associated with decreased levels of aromatase production in granulosa cells. Unexpectedly, levels of mRNA for cyclooxygenase 2, an enzyme required for cumulus expansion, are increased. BmprIB mutants also exhibit a failure in endometrial gland formation. The expression of BmprIB in uterine linings suggests that these defects are a direct consequence of loss of BMP signaling in this tissue. In summary, these studies demonstrate the importance of BMP signaling pathways for estrus cyclicity, estradiol biosynthesis, and cumulus cell expansion in vivo and reveal sites of action for BMP signaling pathways in reproductive tissues.

Exception or extension? : reorienting the Peacock Room among James McNeill Whistler's interior designs

"Although famous for his paintings and etchings today, James McNeill Whistler (1834-1903) was also an important interior designer in the nineteenth-century British Aesthetic movement. Whistler‘s most famous and only extant interior design is Harmony in Blue and Gold: The Peacock Room (1876-77). It is also his most puzzling interior. Long considered an exception to the rule of Whistler‘s other interiors, the Peacock Room has often been overlooked in the few studies of the artist‘s interior designs"

Dinocyst datum events of several holes in the Norwegian-Greenland Sea

The presence of abundant age-diagnostic dinoflagellate cysts in Ocean Drilling Program (ODP) Hole 913B (Leg 151), Deep Sea Drilling Project Hole 338 (Leg 38) and ODP Hole 643A (Leg 104) has enabled the development of a new biostratigraphy for the Eocene-Oligocene interval in the Norwegian-Greenland Sea. This development is important because the calcareous microfossils usually used for biostratigraphy in this age interval are generally absent in high latitude sediments as a result of dissolution. In parallel with this biostratigraphic analysis, we developed a magnetic reversal stratigraphy for these Norwegian-Greenland Sea sequences. This has allowed independent age determination and has enabled the dinocyst biostratigraphy to be firmly tied into the global geomagnetic polarity timescale (GPTS). The relatively high resolution of this study has enabled identification of dinoflagellate cyst assemblages that have affinities with those from the North Sea and the North Atlantic, which allows regional correlation. Correlation of each site with the GPTS has also allowed comparison of the stratigraphic record preserved in each drill-hole. Hole 913B is the most complete and is the best-preserved record of the Eocene and Oligocene in the Northern Hemisphere high latitudes, and can serve as a reference section for palaeoenvironmental reconstructions of this age interval.

Strontium isotope ratios of planktonic foraminifera from ODP Site 119-744 on the Kerguelen Plateau, Indian Ocean (Table 1)

87Sr/86Sr ratios of well-preserved early Miocene-Oligocene planktonic foraminifers from Site 744 in the southern Indian Ocean provide the highest southern latitude Sr isotope record of this age. The isotopic data have been calibrated with the site magnetostratigraphy. 87Sr/86Sr ages were also determined using the Sr isotope-age equations of Miller et al. (1988, doi:10.1029/PA003i002p00223) and Hess et al. (1989, doi:10.1029/PA004i006p00655). There is good agreement between the calculated ages from 87Sr/86Sr measurements using these equations and those derived from magnetobiostratigraphy. In addition, these equations were useful for inference of sediment ages in intervals where the paleomagnetic record is not well resolved and the biostratigraphy is inconclusive. The Site 744 87Sr/86Sr record can be used for correlation of Antarctic and low-latitude sequences and biostratigraphical zonation of foraminifers, radiolarians, diatoms, and calcareous nannofossils. This record will assist in the development of the high southern latitude biochronology.

On the Southern Ocean CO2 uptake and the role of the biological carbon pump in the 21st century, links to supplementary material

We use a suite of eight ocean biogeochemical/ecological general circulation models from the MAREMIP and CMIP5 archives to explore the relative roles of changes in winds (positive trend of Southern Annular Mode, SAM) and in warming- and freshening-driven trends of upper ocean stratification in altering export production and CO2 uptake in the Southern Ocean at the end of the 21st century. The investigated models simulate a broad range of responses to climate change, with no agreement ona dominance of either the SAM or the warming signal south of 44° S. In the southernmost zone, i.e., south of 58° S, they concur on an increase of biological export production, while between 44 and 58° S the models lack consensus on the sign of change in export. Yet, in both regions, the models show an enhanced CO2 uptake during spring and summer. This is due to a larger CO 2 (aq) drawdown by the same amount of summer export production at a higher Revelle factor at the end of the 21st century. This strongly increases the importance of the biological carbon pump in the entire Southern Ocean. In the temperate zone, between 30 and 44° S all models show a predominance of the warming signal and a nutrient-driven reduction of export production. As a consequence, the share of the regions south of 44° S to the total uptake of the Southern Ocean south of 30° S is projected to increase at the end of the 21st century from 47 to 66% with a commensurable decrease to the north. Despite this major reorganization of the meridional distribution of the major regions of uptake, the total uptake increases largely in line with the rising atmospheric CO2. Simulations with the MITgcm-REcoM2 model show that this is mostly driven by the strong increase of atmospheric CO2, with the climate-driven changes of natural CO2 exchange offsetting that trend only to a limited degree (~10%) and with negligible impact of climate effects on anthropogenic CO2 uptake when integrated over a full annual cycle south of 30° S.

Estudios literarios.

Francisco Acuña de Figueroa.--Diógenes y sus ideas.--Los poetas de la revolución.--La religion y la ciencia. (Juicio critico sobre el libro de Draper)--César Diaz.--Juna Cárlos Gomez.--Cuadros de costumbres: El gaucho. Un gobierno de otros tiempos. Las trillas.

In memoriam. Josiah Clark, LL.D., principal of Williston Seminary 1849-1863. : Obiit [sic] May 30, 1878. /

"Published by the Trustees of Williston Seminary, for gratuitous distribution among the Alumni, and other friends of Williston Seminary"--T.p. verso.

Potters, their arts and crafts.

Mode of access: Internet.

An atlas of anatomy,

Mode of access: Internet.

A handbook for dissectors.

Beginning with 6th ed. (1967) published under title: Grant's dissector.