Significance of bound water to local chain conformations in protein crystals.

We examine how the polypeptide chain in protein crystal structures exploits the multivalent hydrogen-bonding potential of bound water molecules. This shows that multiple interactions with a single water molecule tend to occur locally along the chain. A distinctive internal-coordinate representation of the local water-binding segments reveals several consensus conformations. The fractional water occupancy of each was found by comparison of the total number of conformations in the database regardless of the presence or absence of bound water. The water molecule appears particularly frequently in type II beta-turn geometries and an N-terminal helix feature. This work constitutes a first step into assessing not only the generality but also the significance of specific water binding in globular proteins.

Submillisecond folding of monomeric lambda repressor.

The folding kinetics of a truncated form of the N-terminal domain of phage lambda repressor [lambda 6-85] has been investigated by using the technique of dynamic NMR. lambda 6-85 has been shown previously to fold in a purely two-state fashion. This allows the determination of folding and unfolding rates from simulation of the exchange-broadened aromatic resonances of Tyr-22. The folding kinetics were determined over a range of 1.35 to 3.14 M urea. The urea dependence of both folding and unfolding rate constants is exponential, suggesting that the rate-determining step is invariant at the urea concentrations studied. The folding and unfolding rates extrapolated to 0 M urea at 37 degrees C are 3600 +/- 400 s-1 and 27 +/- 6 s-1, respectively. The observed lambda 6-85 folding rate constant exceeds that of other fast-folding globular proteins by a factor of 14-54. The urea dependence of the folding and unfolding rate constants suggests that the transition state of the rate-determining step is considerably more exposed to solvent than previously studied protein-folding transition states. The surprising rapidity of lambda 6-85 folding and unfolding may be the consequence of its all-helical secondary structure. These kinetic results clearly demonstrate that all of the fundamental events of protein folding can occur on the submillisecond time scale.

Pex1, a pollen-specific gene with an extensin-like domain.

We report here the identification of a pollen-specific gene from Zea mays that contains multiple Ser-(Pro)n repeats, the motif found in the cell wall-associated extensins. Sequence analysis reveals that the encoded protein has a putative globular domain at the N terminus and an extensin-like domain at the C terminus. The Pex1 (pollen extensin-like) gene is expressed exclusively in pollen, not in vegetative or female tissues, and is not induced in leaves upon wounding. We propose that the encoded protein may have a role in reproduction, either as a structural element deposited in the pollen tube wall during its rapid growth or as a sexual recognition molecule that interacts with partner molecules in the pistil.

Avaliação do processamento por atrito linear em chapas da liga de titânio Ti-6Al-4V.

Esta tese tem por objetivo a aplicação do processamento por atrito linear na liga de titânio Ti-6Al-4V. Derivado da solda por atrito linear, é um processo recente desenvolvido na década de 90 para união de alumínio. Sua aplicação em outros tipos de materiais como aços e ligas de alto desempenho, em especial o titânio, tem interessado a industria. A metodologia utilizada nesta tese para avaliar o processamento por atrito linear, consistiu na execução de ensaios mecânicos de tração em condições mistas em chapas da liga de titânio Ti-6Al-4V. A máquina utilizada para o processamento das chapas foi um centro de usinagem CNC convencional, adaptado com dispositivos especiais. Além dos ensaios de tração em condições mistas, foram executadas medições de microdurezas nas regiões atingidas pelo processo, avaliação das microestruturas resultantes e medições de tensão residual para uma caracterização mais ampla do processo. As microestruturas na região processada são caracterizadas por uma estrutura totalmente transformada. As temperaturas de pico na região processada excederam a temperatura -transus durante o processamento e a transformação da fase + ocorreu durante a fase de resfriamento. A transformação da fase para resultou na formação de agulhas de fase nos contornos e pelo interior dos grãos da fase . Pequenas regiões com estrutura equiaxial de grãos ( globular) foram observados na zona de processamento. A abordagem dos resultados quantitativos foi feita de forma estatística, visando identificar os parâmetros de maior interação com os resultados observados. Foi identificado nesta tese que a rotação da ferramenta apresentou a maior influência nos resultados de tensão residual, microdureza e tensão de escoamento. Uma importante contribuição à modelagem da tensão de escoamento para materiais anisotrópicos é proposta, baseado em um critério de escoamento ortotrópico. Equações complementares baseadas nos testes mistos de tração e cisalhamento são propostas para modificar o modelo ortotrópico. O intuito deste modelo é indicar em que condições o material tem seu regime de escoamento atingido, podendo servir de base para simulações práticas de peças em condições similares.

New galactic star clusters discovered in the VVV survey. Candidates projected on the inner disk and bulge

Context. VISTA Variables in the Vía Láctea (VVV) is one of six ESO Public Surveys using the 4 meter Visible and Infrared Survey Telescope for Astronomy (VISTA). The VVV survey covers the Milky Way bulge and an adjacent section of the disk, and one of the principal objectives is to search for new star clusters within previously unreachable obscured parts of the Galaxy. Aims. The primary motivation behind this work is to discover and analyze obscured star clusters in the direction of the inner Galactic disk and bulge. Methods. Regions of the inner disk and bulge covered by the VVV survey were visually inspected using composite JHKS color images to select new cluster candidates on the basis of apparent overdensities. DR1, DR2, CASU, and point spread function photometry of 10 × 10 arcmin fields centered on each candidate cluster were used to construct color–magnitude and color–color diagrams. Follow-up spectroscopy of the brightest members of several cluster candidates was obtained in order to clarify their nature. Results. We report the discovery of 58 new infrared cluster candidates. Fundamental parameters such as age, distance, and metallicity were determined for 20 of the most populous clusters.

The Gaia-ESO Survey: The analysis of high-resolution UVES spectra of FGK-type stars

Context. The ongoing Gaia-ESO Public Spectroscopic Survey is using FLAMES at the VLT to obtain high-quality medium-resolution Giraffe spectra for about 105 stars and high-resolution UVES spectra for about 5000 stars. With UVES, the Survey has already observed 1447 FGK-type stars. Aims. These UVES spectra are analyzed in parallel by several state-of-the-art methodologies. Our aim is to present how these analyses were implemented, to discuss their results, and to describe how a final recommended parameter scale is defined. We also discuss the precision (method-to-method dispersion) and accuracy (biases with respect to the reference values) of the final parameters. These results are part of the Gaia-ESO second internal release and will be part of its first public release of advanced data products. Methods. The final parameter scale is tied to the scale defined by the Gaia benchmark stars, a set of stars with fundamental atmospheric parameters. In addition, a set of open and globular clusters is used to evaluate the physical soundness of the results. Each of the implemented methodologies is judged against the benchmark stars to define weights in three different regions of the parameter space. The final recommended results are the weighted medians of those from the individual methods. Results. The recommended results successfully reproduce the atmospheric parameters of the benchmark stars and the expected Teff-log  g relation of the calibrating clusters. Atmospheric parameters and abundances have been determined for 1301 FGK-type stars observed with UVES. The median of the method-to-method dispersion of the atmospheric parameters is 55 K for Teff, 0.13 dex for log  g and 0.07 dex for [Fe/H]. Systematic biases are estimated to be between 50−100 K for Teff, 0.10−0.25 dex for log  g and 0.05−0.10 dex for [Fe/H]. Abundances for 24 elements were derived: C, N, O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Zr, Mo, Ba, Nd, and Eu. The typical method-to-method dispersion of the abundances varies between 0.10 and 0.20 dex. Conclusions. The Gaia-ESO sample of high-resolution spectra of FGK-type stars will be among the largest of its kind analyzed in a homogeneous way. The extensive list of elemental abundances derived in these stars will enable significant advances in the areas of stellar evolution and Milky Way formation and evolution.

Three-Dimensional Structure and Disposition of the Air Conducting and Gas Exchange Conduits of the Avian Lung: The Domestic Duck (Cairina moschata)

The anatomy of the domestic duck lung was studied macroscopically, by casting and by light, transmission, and scanning electron microscopy. The lung had four categories of secondary bronchi (SB), namely, the medioventral (MV, 4-5), laterodorsal (LD, 6-10), lateroventral (LV, 2-4), and posterior secondary bronchi (PO, 36-44). The neopulmonic parabronchi formed an intricate feltwork on the ventral third of the lung and inosculated those from the other SB. The lung parenchyma was organized into cylindrical parabronchi separated by thin septa containing blood vessels. Atria were shallow and well-fortified by epithelial ridges reinforced by smooth muscle bundles and gave rise to 2-6 elongate infundibulae. Air capillaries arose either directly from the atria or from infundibulae and were tubular or globular in shape with thin interconnecting branches. The newly described spatial disposition of the conducting air conduits closely resembles that of the chicken. This remarkable similarity between the categories, numbers, and 3D arrangement of the SB in the duck and chicken points to a convergence in function-oriented design. To illuminate airflow dynamics in the avian lung, precise directions of airflow in the various categories of SB and parabronchi need to be characterized.

(Table 1) Crystal sizes of measured samples

Due to experimental difficulties grain size distributions of gas hydrate crystallites are largely unknown in natural samples. For the first time, we were able to determine grain size distributions of six natural gas hydrates for samples retrieved from the Gulf of Mexico and from Hydrate Ridge offshore Oregon from varying depths. High-energy synchrotron radiation provides high photon fluxes as well as high penetration depth and thus allows for investigation of bulk sediment samples. The gas hydrate crystallites appear to be (log-) normally distributed in the natural samples and to be of roughly globular shape. The mean grain sizes are in the range from 300-600 µm with a tendency for bigger grains to occur in greater depth, possibly indicating a difference in the formation age. Laboratory produced methane hydrate, starting from ice and aged for 3 weeks, shows half a log-normal curve with a mean value of ~40 µm. This one order-of-magnitude smaller grain sizes suggests that care must be taken when transposing grain-size sensitive (petro-)physical data from laboratory-made gas hydrates to natural settings.

Organic carbon and amino acid concentration of Karelian shungite rocks from the lake Onego area, Russia

The study of amino acids in the Precambrian shungite rocks of Karelia showed that their contents vary within 25-89 µg/g depending on proportions between shungite and mineral components. It was established that the amino acids exhibit an excess of L-enantiomers. In the shungite rocks, they form organomineral complexes with silica and aluminosilicates, being built in the globular structure of shungite matter. There are several sources of amino acids in shungites: secondary synthesis, microbial pollution, and original amino acids of organic matter in shungite rocks.

(Table 1) Distribution of Lower Cretaceous calcareous nannofossils at DSDP Hole 93-603B

Upper Berriasian to lower Aptian calcareous nannofossil assemblages have been studied from a siliciclastic deep-sea fan complex and a subjacent limestone sequence drilled beneath the lower continental rise in the western North American Basin, 270 miles (435 km) off Cape Hatteras, North Carolina (USA). Sharp lithologic facies changes and reworking by turbidites complicate the biostratigraphic interpretation, but provide an excellent opportunity to better distinguish "nearshore" from open-ocean nannofossil species, and to investigate the introduction of neritic taxa into the deep-see environment, a phenomenon that appears to have been widespread within the circum-North Atlantic during Neocomian times. Well-preserved assemblages in dark, carbonaceous claystones were probably displaced from the oxygen minimum zone along the upper slope or outer shelf. Neritic, continental margin species prevalent in this facies include the holococcolith Zebrashapka vanhintei n. gen., n. sp., Lithraphidites alatus magnus n. spp., Pickelhaube furtiva n. gen., and a host of nannoconids and micrantholiths. A qualitative evaluation of widely used guide fossils suggests that the triad of proposed markers for the base of Roth's Zone NC3 make their first appearances in the following (ascending) order: Diadorhombus rectus, TUbodiscus verenae, Calcicalathina oblongata. Of these, we chose the nominative species for the zone, T. verenae, to mark its base and to approximate the Berriasian/Valangian boundary. Cyclagelosphaera deflandrei is strongly affected by diagenesis and is therefore not a reliable index species for the base of Zone NC4 near the Valanginian/Hauterivian boundary (the last occurrence of T. verenae is also not suitable there). In addition, Lithraphidites bollii, a form apparently confined to the low latitudes of the Tethyan region, was absent at the more temperate Site 603 and not available as a subzonal marker for the upper Hautervian-lower Barremian (mid-NC4 and mid-NC5, respectively). Cruciellipsis cuvillieri, however, provides a reliable datum just below the Hauterivian/Barremian boundary (base of NC5), despite the potential for reworking in this section. Nannoconids tend to be reworked in this section, and do not provide trustworthy forms to mark the Barremian/Aptian boundary (base of NC6). Hayesites irregularis n. comb, probably does provide a useful first appearance datum within the lower Aptian, if it is not confused with a more birefringent and globular form, Rucinolithus terebrodentarius n. sp. Rhagodiscus angustus is mimicked by a similar form (Zeughrabdotusl pseudoangustus n. sp.), which apparently ranges down to the Hauterivian, thus Lithastrinus floralis provides a more useful first appearance datum for the base of the middle-upper Aptian Rhagodiscus angustus Zone (NC7). Aside from the new taxa mentioned above, the following are also described: Cretarhabdusl delicatus n. sp. and Cyclagelosphaera jiangii n. sp.

(Table 1) Crystal sizes of measured samples from the Bush Hill region in the Gulf of Mexico and from ODP Leg 204 at the Hydrate Ridge offshore Oregon

The grain sizes of gas hydrate crystallites are largely unknown in natural samples. Single grains are hardly detectable with electron or optical microscopy. For the first time, we have used high-energy synchrotron diffraction to determine grain sizes of six natural gas hydrates retrieved from the Bush Hill region in the Gulf of Mexico and from ODP Leg 204 at the Hydrate Ridge offshore Oregon from varying depth between 1 and 101 metres below seafloor. High-energy synchrotron radiation provides high photon fluxes as well as high penetration depth and thus allows for investigation of bulk sediment samples. Gas hydrate grain sizes were measured at the Beam Line BW 5 at the HASYLAB/Hamburg. A 'moving area detector method', originally developed for material science applications, was used to obtain both spatial and orientation information about gas hydrate grains within the sample. The gas hydrate crystal sizes appeared to be (log-)normally distributed in the natural samples. All mean grain sizes lay in the range from 300 to 600 µm with a tendency for bigger grains to occur in greater depth. Laboratory-produced methane hydrate, aged for 3 weeks, showed half a log-normal curve with a mean grain size value of c. 40 µm. The grains appeared to be globular shaped.

Early Cretaceous planktonic foraminifera from the Tethys

Early Cretaceous planktonic foraminiferal assemblages include rare planispiral and pseudoplanispiral morphotypes with elongate chambers that BouDagher-Fadel et al. assigned to Schackoina or accommodated in the new genus Claviblowiella. New findings of well-preserved planktonic foraminiferal faunas from the Lesches en Diois (SE France) section, the Cismon core (NE Italy), the Calabianca (NW Sicily) section and the Upper Aptian of Deep Sea Drilling Project (DSDP) Site 545 drilled off Morocco, have allowed a better understanding of the morphological features of these rare, unevenly distributed taxa. Our data demonstrate that each small planispiral species with globular chambers has a corresponding "clavate" morphotype which (as the "normal" forms) exhibits a smooth, finely perforate wall. Consequently, the latter have been assigned here to the genus Globigerinelloides and treated as subspecies of the "non-clavate" taxa. The (clavate) subspecies belonging to the genus Globigerinelloides here retained are G. duboisi sigali Longoria, G. maridalensis elongatus subsp. nov., G. blowi lobatus subsp. nov. and G. paragottisi clavatus subsp. nov., while Globigerinelloides minai Obregòn de la Parra is not retained. In addition, a new genus, Pseudoschackoina, type species Planomalina saundersi Bolli (senior synonym of Hastigerinoides cepedai Obregòn de la Parra, has been formalised for individuals possessing elongate, pointed, laterally compressed chambers, bearing tubulospines arranged on a pseudoplanispiral (dysaxial) coiling mode. Stratigraphically, in the sections studied the first taxon to appear is Pseudoschackoina saundersi, in the uppermost part of the Selli Level (=OAE1a), immediately followed, just above the OAE1a, by all the "clavate" globigerinelloidids. Regarding the last occurrences, Pseudoschackoina saundersi and G. maridalensis elongatus disappear in the lower part of the Globigerinelloides algerianus Zone, Globigerinelloides paragottisi clavatus at the top of the same zone, while Globigerinelloides blowi lobatus and G. duboisi sigali range up to the lower part of the Ticinella bejaouaensis Zone.

Cladoceran functional assemblages and functional diversity indices from Mallusjärvi and Tiiläänjärvi (southern Finland) sediment cores

will be submitted by the author