bluuebunny/crossref_metadata_2025 huggingface dataset:
Low specific contact resistance Ti∕Au contacts on ZnO
Authors: Chen J.-J. , Jang Soohwan , Anderson T. J. , Ren F. , Li Yuanjie , Kim Hyun-Sik , Gila B. P. , Norton D. P. , Pearton S. J.
Published: March 2006

Ti ∕ Au Ohmic contacts on heavily Al-doped (n∼1019cm−3) n-ZnO produce low specific contact resistivity of 2.4×10−7Ωcm2 in the as-deposited condition and extremely low minimum values of 6×10−8Ωcm2 after annealing at 300°C.The contact resistance is independent of measurement temperature after low temperature anneals, suggesting that tunneling is the dominant transport mechanism in the contacts. The contact morphology roughens after annealing at 150°C and Auger electron spectroscopy depth profiling shows Zn outdiffusion through the metal and intermixing of Au and Ti. However, the morphology does not significantly worsen after anneals at 450°C. This metallization scheme looks very attractive for the n-electrode of ZnO-based light-emitting diode structures.
Dielectric barrier plasma dynamics for active control of separated flows
Authors: Roy Subrata , Singh K. P. , Gaitonde Datta V.
Published: March 2006

The dynamics of separation mitigation with asymmetric dielectric barrier discharges is explored by considering the gas flow past a flat plate at an angle of attack. A self-consistent model utilizing motion of electrons, ions, and neutrals is employed to couple the electric force field to the momentum of the fluid. The charge separation and concomitant electric field yield a time-averaged body force which is oriented predominantly downstream, with a smaller transverse component towards the wall. This induces a wall-jet-like feature that effectively eliminates the separation bubble. The impact of several geometric and electrical operating parameters is elucidated.
A previously undescribed pathway for pyrimidine catabolism
Authors: Loh Kevin D. , Gyaneshwar Prasad , Markenscoff Papadimitriou Eirene , Fong Rebecca , Kim Kwang-Seo , Parales Rebecca , Zhou Zhongrui , Inwood William , Kustu Sydney
Published: March 2006

The b1012 operon of
Escherichia coli
K-12, which is composed of seven unidentified ORFs, is one of the most highly expressed operons under control of nitrogen regulatory protein C. Examination of strains with lesions in this operon on Biolog Phenotype MicroArray (PM3) plates and subsequent growth tests indicated that they failed to use uridine or uracil as the sole nitrogen source and that the parental strain could use them at room temperature but not at 37°C. A strain carrying an
ntrB
(Con) mutation, which elevates transcription of genes under nitrogen regulatory protein C control, could also grow on thymidine as the sole nitrogen source, whereas strains with lesions in the b1012 operon could not. Growth-yield experiments indicated that both nitrogens of uridine and thymidine were available. Studies with [
14
C]uridine indicated that a three-carbon waste product from the pyrimidine ring was excreted. After trimethylsilylation and gas chromatography, the waste product was identified by mass spectrometry as 3-hydroxypropionic acid. In agreement with this finding, 2-methyl-3-hydroxypropionic acid was released from thymidine. Both the number of available nitrogens and the waste products distinguished the pathway encoded by the b1012 operon from pyrimidine catabolic pathways described previously. We propose that the genes of this operon be named
rutA–G
for py
r
imidine
ut
ilization. The product of the divergently transcribed gene, b1013, is a tetracycline repressor family regulator that controls transcription of the b1012 operon negatively.
Vasopressin in catecholamine‐resistant septic and cardiogenic shock in very‐low‐birthweight infants
Authors: Meyer Sascha , Löffler Günther , Polcher Thorsten , Gottschling Sven , Gortner Ludwig
Published: March 2006

Aim: To evaluate vasopressin as a rescue therapy in catecholamine‐refractory septic and cardiogenic shock in very‐low‐birthweight (VLBW) infants. Methods: Prospective assessment of vasopressin therapy in three VLBW infants with catecholamine‐refractory septic shock (24+.6 wk, 600 g) and cardiogenic shock (26+.1 wk, 890 g; 26+.1 wk, 880 g) at a university hospital. Results: Adequate systemic arterial blood pressure could only be restored after vasopressin administration as a continuous infusion over a 36‐h period in the preterm suffering from septic shock; in the two neonates with cardiogenic shock, only a transient stabilization in mean arterial pressure was observed, which did not impact on the poor prognosis.

Conclusion: Although vasopressin appears to be a suitable rescue therapy in catecholamine‐resistant septic shock in VLBW infants, further evaluation in controlled clinical trials is warranted.
Morphine‐related apnoea in CPAP‐treated preterm neonates
Authors: Enders Jan , Gebauer Corinna , Pulzer Ferdinand , Robel‐Tillig Eva , Knüpfer Matthias
Published: March 2006

Background: Morphine can be used to treat pain in preterm neonates with CPAP because of its analgetic potency; however, it is known to induce apnoea. Aim: To evaluate this risk of apnoea. Methods: We retrospectively analysed 91 preterm neonates with CPAP who received morphine intravenously. The incidence of apnoea 4 h before and after morphine administration was compared. The data were analysed for three dosage groups (<0.01, 0.01–0.03 and 0.03 mg/kg) and according to the incidence of apnoea before morphine application. Results: In the whole group (gestational age 29.1±2.9 wk, morphine dosage 0.017±0.01 mg/kg) we did not find differences in apnoea before and after morphine (0.9±1.8 vs 1.1±1.8 apnoea). The only significant increase in apnoea was seen in the subgroup of patients receiving > 0.03 mg/kg (0.3±0.67 vs 1.5±2.5 apnoea). Interestingly, we found a significantly delayed increase in apnoea in the fourth hour.

Conclusion: Morphine in preterm infants with CPAP is not widely accepted practice until further randomized studies evaluate efficacy and safety. Morphine in a low dosage (≤0.03 mg/kg) did not significantly increase the apnoea rate in CPAP‐treated preterm infants. For clinical work, it is very important to note that morphine‐related apnoea may appear with a delay of approximately 4 h.
The frequency of vitamin D insufficiency in healthy female adolescents
Authors: Olmez Duygu , Bober Ece , Buyukgebiz Atilla , Cimrin Dilek
Published: March 2006

Aim: To establish the frequency and causes of vitamin D insufficiency in healthy female adolescents in Izmir, Turkey. Methods: 64 adolescents from a low‐ (Ikinci Inönü) and a high‐ (Ilica) socio‐economic settlement were included. Parents’ monthly income was classified as low, middle and high. The blood samples were drawn at the end of the summer and winter periods. Results: Vitamin D insufficiency percentages for the end‐of‐winter period were 59.4% in Ikinci Inönü and 15.6% in Ilica, and for the end of summer 25% and 15.6%, respectively. Calcidiol levels of cases from Ikinci Inönü were found to be lower compared with the levels of cases from Ilica (34±15 vs 59±24 nmol/l for end of winter, p= 0.000; 51±22 vs 65±28 nmol/l for end of summer, p= 0.03). Calcidiol levels of cases whose parental monthly income was low and whose mothers were illiterate were significantly lower than the others (48±18 vs 65±29 nmol/l for end of summer, p= 0.01; 33±16 vs 56±23 nmol/l for end of winter, p= 0.000; 45±13 vs 64±29 nmol/l for end of summer, p= 0.007; 36±17 vs 51±25 nmol/l for end of winter, p= 0.02; respectively).

Conclusion: Vitamin D insufficiency was frequent, especially in the end‐of‐winter period. Basic risk factors were low socio‐economic status, illiteracy of mothers and low calcium intake.
The G protein ?3 subunit 825C allele is associated with sudden infant death due to infection
Authors: Opdal Siri Hauge , Melien Øyvind , Rootwelt Helge , Vege Åshild , Arnestad Marianne , Rognum Torleiv Ole
Published: March 2006

Aim: To investigate the Gβ3 subunit C825T polymorphism with regard to sudden unexpected infant death. The reported association between the Gβ3s protein and increased immune cell function in humans makes this polymorphism highly interesting both with regard to sudden infant death syndrome (SIDS) and deleterious infectious disease. Methods: The cases investigated in the present study consist of 250 SIDS cases, 38 cases of sudden unexpected infant death due to infection and 99 living infant controls. Typing of the C825T polymorphism was performed by real‐time PCR with allele‐specific probes and melting curve analyses. Results: The cases of infectious death have a higher percentage of both the C allele (p=0.037 compared to the SIDS cases, p=0.022 compared to the controls) and the CC genotype (p=0.05 compared to the SIDS cases, p=0.016 compared to the controls). There were no differences between SIDS cases and controls.

Conclusion: The observed association between the 825C allele and infectious death may indicate that the presence of the 825T allele exerts a protective effect towards serious infection, possibly through enhanced G protein signalling. The C allele, on the other hand, appears to represent a disadvantage in this regard.
Shorter hospital stay for moderately preterm infants
Authors: Altman Maria , Vanpée Mireille , Bendito Ana , Norman Mikael
Published: March 2006

Aim: To determine length of hospital stay (LOS) for moderately preterm infants during the last 20 years, and to identify factors affecting the number of bed‐days. Methods: Review of LOS for all infants delivered between 30 to 34 gestational weeks during 1983, 1988, 1993, 1998 and 2002. Exclusion criteria: life‐threatening abnormalities, chromosomal anomalies and death during hospitalization. Results: 564 included infants accounted for 20% of admissions and 48% of bed‐days in the neonatal unit. Between 1983 and 2002, maternal age and use of nasal continuous positive airway pressure increased, use of antibiotics and mechanical ventilation decreased, whereas distributions for gestational age, birthweight, gender, smallness for gestational age, low Apgar score or incidence of respiratory distress syndrome did not change. For healthy inborn singletons discharged home, LOS decreased from 1983 (28±11 d, mean±SD values) to 2002 (14±7 d, p<0.05). Infants born more immature had longer LOS, but postconceptional age at discharge did not differ between age groups.

Conclusion: LOS for moderately preterm infants has decreased as a result of individualized neonatal care and organization of homecare support. Shorter LOS is of benefit to the family, prevents overcrowding in the NICU and has important economic implications.
CNF1-induced Ubiquitylation and Proteasome Destruction of Activated RhoA Is Impaired in Smurf1−/−Cells
Authors: Boyer Laurent , Turchi Laurent , Desnues Benoit , Doye Anne , Ponzio Gilles , Mege Jean-Louis , Yamashita Motozo , Zhang Ying E. , Bertoglio Jacques , Flatau Gilles , Boquet Patrice , Lemichez Emmanuel
Published: March 2006

Ubiquitylation of RhoA has emerged as an important aspect of both the virulence of Escherichia coli producing cytotoxic necrotizing factor (CNF) 1 toxin and the establishment of the polarity of eukaryotic cells. Owing to the molecular activity of CNF1, we have investigated the relationship between permanent activation of RhoA catalyzed by CNF1 and subsequent ubiquitylation of RhoA by Smurf1. Using Smurf1-deficient cells and by RNA interference (RNAi)-mediated Smurf1 knockdown, we demonstrate that Smurf1 is a rate-limiting and specific factor of the ubiquitin-mediated proteasomal degradation of activated RhoA. We further show that the cancer cell lines HEp-2, human embryonic kidney 293 and Vero are specifically deficient in ubiquitylation of either activated Rac, Cdc42, or Rho, respectively. In contrast, CNF1 produced the cellular depletion of all three isoforms of Rho proteins in the primary human cell types we have tested. We demonstrate that ectopic expression of Smurf1 in Vero cells, deficient for RhoA ubiquitylation, restores ubiquitylation of the activated forms of RhoA. We conclude here that Smurf1 ubiquitylates activated RhoA and that, in contrast to human primary cell types, some cancer cell lines have a lower ubiquitylation capacity of specific Rho proteins. Thus, both CNF1 and transforming growth factor-β trigger activated RhoA ubiquitylation through Smurf1 ubiquitin-ligase.
Nuclear RanGAP Is Required for the Heterochromatin Assembly and Is Reciprocally Regulated by Histone H3 and Clr4 Histone Methyltransferase inSchizosaccharomyces pombe
Authors: Nishijima Hitoshi , Nakayama Jun-ichi , Yoshioka Tomoko , Kusano Ayumi , Nishitani Hideo , Shibahara Kei-ichi , Nishimoto Takeharu
Published: March 2006

Although the Ran GTPase-activating protein RanGAP mainly functions in the cytoplasm, several lines of evidence indicate a nuclear function of RanGAP. We found that Schizosaccharomyces pombe RanGAP, SpRna1, bound the core of histone H3 (H3) and enhanced Clr4-mediated H3-lysine 9 (K9) methylation. This enhancement was not observed for methylation of the H3-tail containing K9 and was independent of SpRna1–RanGAP activity, suggesting that SpRna1 itself enhances Clr4-mediated H3-K9 methylation via H3. Although most SpRna1 is in the cytoplasm, some cofractionated with H3. Sprna1tsmutations caused decreases in Swi6 localization and H3-K9 methylation at all three heterochromatic regions of S. pombe. Thus, nuclear SpRna1 seems to be involved in heterochromatin assembly. All core histones bound SpRna1 and inhibited SpRna1–RanGAP activity. In contrast, Clr4 abolished the inhibitory effect of H3 on the RanGAP activity of SpRna1 but partially affected the other histones. SpRna1 formed a trimeric complex with H3 and Clr4, suggesting that nuclear SpRna1 is reciprocally regulated by histones, especially H3, and Clr4 on the chromatin to function for higher order chromatin assembly. We also found that SpRna1 formed a stable complex with Xpo1/Crm1 plus Ran-GTP, in the presence of H3.
Specific and Nonspecific Membrane-binding Determinants Cooperate in Targeting Phosphatidylinositol Transfer Protein β-Isoform to the MammalianTrans-Golgi Network
Authors: Phillips Scott E. , Ile Kristina E. , Boukhelifa Malika , Huijbregts Richard P.H. , Bankaitis Vytas A.
Published: March 2006

Phosphatidylinositol transfer proteins (PITPs) regulate the interface between lipid metabolism and specific steps in membrane trafficking through the secretory pathway in eukaryotes. Herein, we describe the cis-acting information that controls PITPβ localization in mammalian cells. We demonstrate PITPβ localizes predominantly to the trans-Golgi network (TGN) and that this localization is independent of the phospholipid-bound state of PITPβ. Domain mapping analyses show the targeting information within PITPβ consists of three short C-terminal specificity elements and a nonspecific membrane-binding element defined by a small motif consisting of adjacent tryptophan residues (the W202W203motif). Combination of the specificity elements with the W202W203motif is necessary and sufficient to generate an efficient TGN-targeting module. Finally, we demonstrate that PITPβ association with the TGN is tolerant to a range of missense mutations at residue serine 262, we describe the TGN localization of a novel PITPβ isoform with a naturally occurring S262Q polymorphism, and we find no other genetic or pharmacological evidence to support the concept that PITPβ localization to the TGN is obligately regulated by conventional protein kinase C (PKC) or the Golgi-localized PKC isoforms δ or ε. These latter findings are at odds with a previous report that conventional PKC-mediated phosphorylation of residue Ser262is required for PITPβ targeting to Golgi membranes.
Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion
Authors: Makarova Kira S. , Koonin Eugene V. , Haselkorn Robert , Galperin Michael Y.
Published: March 2006

The cyanobacterium Anabaena (Nostoc) PCC 7120 responds to starvation for nitrogen compounds by differentiating approximately every 10th cell in the filament into nitrogen-fixing cells called heterocysts. Heterocyst formation is subject to complex regulation, which involves an unusual response regulator PatA that contains a CheY-like phosphoacceptor (receiver, REC) domain at its C-terminus. PatA-like response regulators are widespread in cyanobacteria; one of them regulates phototaxis in Synechocystis PCC 6803. Sequence analysis of PatA revealed, in addition to the REC domain, a previously undetected, conserved domain, which we named PATAN (after PatA N-terminus), and a potential helix–turn–helix (HTH) domain. PATAN domains are encoded in a variety of environmental bacteria and archaea, often in several copies per genome, and are typically associated with REC, Roadblock and other signal transduction domains, or with DNA-binding HTH domains. Many PATAN domains contain insertions of a small additional domain, termed α-clip, which is predicted to form a four-helix bundle. PATAN domains appear to participate in protein–protein interactions that regulate gliding motility and processes of cell development and differentiation in cyanobacteria and some proteobacteria, such as Myxococcus xanthus and Geobacter sulfurreducens.

Contact: galperin@ncbi.nlm.nih.gov

Supplementary information:
Do You Want Fries with That? An Exploration of Serving Size, Social Welfare, and Our Waistlines
Authors: Jeitschko Thomas D. , Pecchenino Rowena A.
Published: March 2006

Given increasing obesity rates, fingers are often pointed at “big food” and their marketing practices. Restaurant meals are indeed larger than home‐cooked meals, and portion sizes have increased. We consider constrained “socially optimal”—rather than decentralized profit‐maximizing—portions to see whether welfare maximizing strategies may also be waistline‐increasing. We demonstrate that socially optimal restaurant meals are larger than average home‐cooked meals, yet the choice to “super‐size” alleviates the size discrepancy. Moreover, portion sizes at home and in restaurants increase with relative reductions in the marginal costs and/or relative increases in the fixed costs of meal preparation. (JEL I10, D11)
Bottlenecked but long-lived: high genetic diversity retained in white-tailed eagles upon recovery from population decline
Authors: Hailer Frank , Helander Björn , Folkestad Alv O , Ganusevich Sergei A , Garstad Steinar , Hauff Peter , Koren Christian , Nygård Torgeir , Volke Veljo , Vilà Carles , Ellegren Hans
Published: March 2006

Most of the white-tailed eagle (
Haliaeetus albicilla
) populations in Europe experienced dramatic declines during the twentieth century. However, owing to intense conservation actions and the ban of DDT and other persistent pollutants, populations are currently recovering. We show that despite passing through demographic bottlenecks, white-tailed eagle populations have retained significant levels of genetic diversity. Both genetic and ringing data indicate that migration between populations has not been a major factor for the maintenance of genetic variability. We argue that the long generation time of eagles has acted as an intrinsic buffer against loss of genetic diversity, leading to a shorter effective time of the experienced bottleneck. Notably, conservation actions taken in several small sub-populations have ensured the preservation of a larger proportion of the total genetic diversity than if conservation had focused on the population stronghold in Norway. For conservation programmes targeting other endangered, long-lived species, our results highlight the possibility for local retention of high genetic diversity in isolated remnant populations.
Direct uptake of soil nitrogen by mosses
Authors: Ayres Edward , van der Wal René , Sommerkorn Martin , Bardgett Richard D
Published: March 2006

Mosses are one of the most diverse and widespread groups of plants and often form the dominant vegetation in montane, boreal and arctic ecosystems. However, unlike higher plants, mosses lack developed root and vascular systems, which is thought to limit their access to soil nutrients. Here, we test the ability of two physiologically and taxonomically distinct moss species to take up soil- and wet deposition-derived nitrogen (N) in natural intact turfs using stable isotopic techniques (
15
N). Both species exhibited increased concentrations of shoot
15
N when exposed to either soil- or wet deposition-derived
15
N, demonstrating conclusively and for the first time, that mosses derive N from the soil. Given the broad physiological and taxonomic differences between these moss species, we suggest soil N uptake may be common among mosses, although further studies are required to test this prediction. Soil N uptake by moss species may allow them to compete for soil N in a wide range of ecosystems. Moreover, since many terrestrial ecosystems are N limited, soil N uptake by mosses may have implications for plant community structure and nutrient cycling. Finally, soil N uptake may place some moss species at greater risk from N pollution than previously appreciated.
Bovine tuberculosis in cattle: reduced risk on wildlife-friendly farms
Authors: Mathews F , Lovett L , Rushton S , Macdonald D.W
Published: March 2006

The associations between habitat and other factors that lead to the risk of bovine tuberculosis (bTB) in diary cattle were examined in an unmatched case–control study. Data from 60 herds with recent history of bTB and 60 controls were analysed using logistic regression. The predictors included farmland habitat, topography, indices of badger density and herd size. Information-theoretic approaches were used to identify those predictor variables explaining the greatest variation in cattle herd bTB breakdowns. Reduced risk of bTB was associated with the management of farmland in ways favourable to wildlife conservation, as encouraged by recent (2005) European Common Agricultural Policy reforms.
One day is enough: rapid and specific host–parasite interactions in a stickleback-trematode system
Authors: Rauch Gisep , Kalbe Martin , Reusch Thorsten B.H
Published: March 2006

Red Queen models of host–parasite coevolution are based on genotype by genotype host–parasite interactions. Such interactions require a genotype specific host defence and, simultaneously, a genotype specific parasite infectivity. Specificity is defined here as defence or infection ability successful against only a subset of genotypes of the same species. A specific defence depends on detectable genotypic variation on the parasite side and on a host defence mechanism that differentiates between parasite genotypes. In vertebrates, the MHC-based adaptive immune system can provide such a defence mechanism, but it needs at least several days to get fully mounted. In contrast, the innate immune system is immediately ready. The trematode parasite species used here reaches the immunologically protected eye lens of its three-spined stickleback (
Gasterosteus aculeatus
) host within 24 h. Thus, it disappears too fast for the fully mounted MHC-based adaptive immune system. In a complete cross-infection experiment using five fish-families and five parasite-clones, we found for the first time fish-family by parasite-clone interactions in vertebrates, although the parasite was only exposed to the immune system for maximally one day. Such interactions require a fast genotype specific defence, suggesting the importance of other defence mechanisms than the too slow, fully mounted adaptive immune system in vertebrates.
Egg colour reflects the amount of yolk maternal antibodies and fledging success in a songbird
Authors: Morales Judith , Sanz Juan J , Moreno Juan
Published: March 2006

Blue–green colours in avian eggs have been proposed as post-mating signals of female phenotypic quality to their mates. Egg colour may not only indicate female value, but also the quality of the eggs themselves and of resulting offspring. To date, there has been no demonstration of an association between egg colour and egg or offspring immune quality. We here show that the intensity of blue–green colour of pied flycatcherFicedula hypoleucaeggs reflects the amount of maternal antibodies in the yolk, a form of passive immunity crucial for offspring performance. Moreover, egg colour predicts fledging success. Also, incubating females in better condition lay more colourful eggs. The immunoglobulin level in incubating females is positively associated with that in the eggs. These results support the signalling hypothesis of eggshell coloration, underlining its role as an indicator of trans-generational transmission of immune defences in birds.
Transition length in turbine/compressor blade flows
Authors: Ryzhov Oleg S
Published: March 2006

High Reynolds number mathematical models for convected vortex impinging against a local hump and sound scattering into Tollmien–Schlichting eigenmodes are introduced to simulate basic mechanisms of the disturbance excitation typical of turbomachinery environments. The streamwise dimension of the transitional flow on the suction side of a blade is evaluated on the assumption that the transition length is of equal order with the extent of viscous/inviscid interaction controlling the boundary-layer response. The triple-deck theory gives a simple power law correlation to express a value of the Reynolds number based on the transition length in terms of the Reynolds number calculated with the blade cord. Precisely the same correlation stems from processing experimental data for both smooth and rough surfaces. The computation shows the explosive development of highly modulated wave packets and their rapid breakdown brought about by erratic short-scaled wiggles riding on the primary long-scaled oscillation cycles. The filling-up of distant parts of the wavenumber spectrum is at the heart of the signal distortion. This process heralds the start of deep transition terminating in fully developed turbulent flow well before reaching the upper stability branch. With the time-harmonic excitation broadly used in experiments, transition requires a much longer distance to complete. An agreement between theoretical predictions based on the assumption of indefinitely large Reynolds numbers and experimental findings from wind-tunnel observations at finite Reynolds numbers is encouraging.
Dislocation lines in the hyperbolic umbilic diffraction catastrophe
Authors: Nye J.F
Published: March 2006

The three-dimensional pattern of the hyperbolic umbilic diffraction catastrophe is computed from an integral representation. A detailed description is given of the geometrical arrangement of the wave dislocation lines (optical vortices) on which the diffraction pattern is based. From a crossed grid of nodal lines in the focal plane, two bundles of dislocation lines spring out symmetrically into the regions of 4-wave interference. Each dislocation line then follows a chain of curved segments which approximate successive steps along lattice vectors in the space group
Fmmm
. The result is a bundle of helices of non-circular cross-section that gradually straighten out until, far from the focal plane, they become the dislocations of the Pearcey diffraction pattern for the cusp catastrophe. A new phenomenon is the multiple puncturing of the caustic surface by a series of helical dislocations.
M4C3precipitation in Fe–C–Mo–V steels and relationship to hydrogen trapping
Authors: Yamasaki S , Bhadeshia H.K.D.H
Published: March 2006

Strong steels suffer from embrittlement due to dissolved hydrogen, a phenomenon which can be mitigated by trapping the hydrogen at carbide particles, where it is rendered benign. The precipitation and coarsening of plate-like M4C3carbides, during the tempering of quaternary Fe–C–Mo–V martensitic steels, has been characterized both experimentally and by developing appropriate kinetic theory. The trapping capacity is found to peak when the carbides are about 10 nm in length, indicating a role of coherency strains in trapping hydrogen atoms via elastic interactions. This suggests a method for developing alloys which are better able to resist the detrimental effects of hydrogen.
Barn swallows before barns: population histories and intercontinental colonization
Authors: Zink Robert M , Pavlova Alexandra , Rohwer Sievert , Drovetski Sergei V
Published: March 2006

The barn swallow (Hirundo rustica) is one of most widely distributed swallows, owing in part to its recent switch from natural nest sites to human structures. We conducted phylogenetic analysis of mitochondrial (mt) and nuclear DNA to explore the recent evolutionary history of this species. Strongly supported mtDNA clades corresponded to Europe, Asia and North America plus the Baikal region of Asia. Analysis of sequence data from a sex-linked nuclear gene was unable to recover the phylogenetic splits in the mtDNA tree, confirming that the main clades evolved recently. The phylogenetic pattern suggests that the ancestral area of the barn swallow was the holarctic; most divergence events are consistent with vicariance. Most unexpectedly, analyses show that barn swallows from North America colonized the Baikal region in the recent past (one fixed substitution). This dispersal direction is opposite of that for most nearctic–palearctic taxon exchanges. Although this invasion was envisioned to coincide with the appearance of new types of human dwelling in the Baikal region, calibration of molecular divergence suggests an older dispersal event. A recent history of gene flow within the main palearctic clades is consistent with range and population expansion owing to new nesting opportunities provided by human settlements. Contrary to expectation, populations in North America appear historically larger and more stable than those in the palearctic. The Baikal population apparently has not increased greatly since colonization.
Living males of the ‘ancient asexual’ Darwinulidae (Ostracoda: Crustacea)
Authors: Smith Robin J , Kamiya Takahiro , Horne David J
Published: March 2006

Three living male darwinulid ostracods of a new species of the genus
Vestalenula
have been found in Yakushima, Japan. This is the first report of living darwinulid males for over 100 years and their morphology casts doubt on the two previous records from the late 1800s. The presence of male darwinulids also calls into question the hypothesis that the family Darwinulidae is an exclusively ancient asexual group, reproducing without sex for over 200 million years (Myr). Male carapaces are of similar size and shape to A-1 juvenile females of the same species, suggesting that males may have been dismissed as A-1 juveniles in other living and fossil species. The antennae and fifth limbs are sexually dimorphic: the male antennae have six segments compared with five in the female and a series of putative chemical receptors originating at the extra segment boundary, while the male fifth limbs have well-developed grasping hooks, as in males of many ostracod groups. The lack of Zenker's Organ and of complex internal structures within the hemipenis contradicts previous hypotheses of the phylogenetic position of darwinulids.
Weak genetic structure indicates strong dispersal limits: a tale of two coral reef fish
Authors: Purcell John F.H , Cowen Robert K , Hughes Colin R , Williams Dean A
Published: March 2006

The extent of dispersal by pelagic larvae in marine environments, including coral reefs, is central for understanding local population dynamics and designing sustainable marine reserves. We present here the first example of a clear stepping-stone genetic structure throughout the Caribbean basin for a common coral reef species, the French grunt (Haemulon flavolineatum). Analysis of microsatellite DNA markers indicated that French grunt population structure may be characterized by overlapping populations throughout the Caribbean, influenced by independent population dynamics but with no fixed geographical boundaries. In addition, different spatial genetic patterns were found in different oceanographic regions. A second species, the bluehead wrasse (Thalassoma bifasciatum), has a much longer pelagic larval duration than French grunts and showed no explicit spatial pattern of genetic variation. This finding is concordant with the hypothesis of a positive relationship between larval dispersal and duration in the plankton. While the magnitude of the genetic signal of population structure in French grunts was very low (FST≈0.003), the pattern of isolation-by-distance throughout the Caribbean indicated considerable population structure with important ecological and conservation significance.
Environmental influence on the genetic basis of mosquito resistance to malaria parasites
Authors: Lambrechts Louis , Chavatte Jean-Marc , Snounou Georges , Koella Jacob C
Published: March 2006

The genetic basis of a host's resistance to parasites has important epidemiological and evolutionary consequences. Understanding this genetic basis can be complicated by non-genetic factors, such as environmental quality, which may influence the expression of genetic resistance and profoundly alter patterns of disease and the host's response to selection. In particular, understanding the environmental influence on the genetic resistance of mosquitoes to malaria gives valuable knowledge concerning the use of malaria-resistant transgenic mosquitoes as a measure of malaria control. We made a step towards this understanding by challenging eight isofemale lines of the malaria vector
Anopheles stephensi
with the rodent malaria parasite
Plasmodium yoelii yoelii
and by feeding the mosquitoes with different concentrations of glucose. The isofemale lines differed in infection loads (the numbers of oocysts), corroborating earlier studies showing a genetic basis of resistance. In contrast, the proportion of infected mosquitoes did not differ among lines, suggesting that the genetic component underlying infection load differs from the genetic component underlying infection rate. In addition, the mean infection load and, in particular, its heritable variation in mosquitoes depended on the concentration of glucose, which suggests that the environment affects the expression and the evolution of the mosquitoes' resistance in nature. We found no evidence of genotype-by-environment interactions, i.e. the lines responded similarly to environmental variation. Overall, these results indicate that environmental variation can significantly reduce the importance of genes in determining the resistance of mosquitoes to malaria infection.
Polygyny and its fitness consequences for primary and secondary female pied flycatchers
Authors: Huk Thomas , Winkel Wolfgang
Published: March 2006

In polygynous species with biparental care, the amount of paternal support often varies considerably. In the pied flycatcher (
Ficedula hypoleuca
), females mated with monogamous males receive more male assistance during the nestling phase than females mated with bigynous males, as the latter have to share their mates with another female. Bigynous males, however, give more support to their primary broods than to their secondary broods. Using a long-term dataset (31 years), the present study revealed that direct reproductive success, i.e. number of fledglings, was lower in females that mated with bigynous males, especially in secondary broods without male assistance, than in females that mated with monogamous males. Secondary broods with male assistance were more affected than primary broods. Female survival was independent of mating status. In primary broods, a delayed compensation for inferior direct reproductive success was found in terms of the number of grandoffspring, a phenomenon that did not occur in secondary broods. Delayed compensation in primary broods refers to indirect effects, i.e. good genes. According to the sexy son hypothesis, genetically superior (i.e. sexy) males may have sons with a higher number of broods belonging to a polygynous breeding status than do sons from broods with a monogamous father. This was indeed the case for sons descending from primary broods, but not for sons descending from secondary broods.
Tuataras and salamanders show that walking and running mechanics are ancient features of tetrapod locomotion
Authors: Reilly Stephen M , McElroy Eric J , Andrew Odum R , Hornyak Valerie A
Published: March 2006

The lumbering locomotor behaviours of tuataras and salamanders are the best examples of quadrupedal locomotion of early terrestrial vertebrates. We show they use the same walking (out-of-phase) and running (in-phase) patterns of external mechanical energy fluctuations of the centre-of-mass known in fast moving (cursorial) animals. Thus, walking and running centre-of-mass mechanics have been a feature of tetrapods since quadrupedal locomotion emerged over 400 million years ago. When walking, these sprawling animals save external mechanical energy with the same pendular effectiveness observed in cursorial animals. However, unlike cursorial animals (that change footfall patterns and mechanics with speed), tuataras and salamanders use only diagonal couplet gaits and indifferently change from walking to running mechanics with no significant change in total mechanical energy. Thus, the change from walking to running is not related to speed and the advantage of walking versus running is unclear. Furthermore, lumbering mechanics in primitive tetrapods is reflected in having total mechanical energy driven by potential energy (rather than kinetic energy as in cursorial animals) and relative centre-of-mass displacements an order of magnitude greater than cursorial animals. Thus, large vertical displacements associated with lumbering locomotion in primitive tetrapods may preclude their ability to increase speed.
Coherent sea-level fluctuations along the global continental slope
Authors: Hughes Chris W , Meredith Michael P
Published: March 2006

Signals in sea-level or, more properly, sub-surface pressure (SSP; sea-level corrected for the inverse barometer effect) are expected to propagate rapidly along the continental slope due to the effect of sloping topography on wave modes, resulting in strongly correlated SSP over long-distances. Observations of such correlations around the Arctic and Antarctic are briefly reviewed, and then extended using satellite altimetry to the rest of the global continental slope. It is shown that such long-distance correlations are common, especially in extra-tropical regions. Simple correlations from altimetry cannot, however, establish the wave speed, or whether waves are responsible for the correlations as opposed to large-scale coherence in the forcing. A case study around South America is used to highlight some of the complications, and is found to strengthen the case for the importance of wave modes in such long-distance SSP coherence, although more detailed
in situ
data are required to resolve the cause of the correlations.
Using continuous GPS and absolute gravity to separate vertical land movements and changes in sea-level at tide-gauges in the UK
Authors: Teferle F.N , Bingley R.M , Williams S.D.P , Baker T.F , Dodson A.H
Published: March 2006

Researchers investigating climate change have used historical tide-gauge measurements from all over the world to investigate the changes in sea-level that have occurred over the last century or so. However, such estimates are a combination of any true sea-level variations and any vertical movements of the land at the specific tide-gauge. For a tide- gauge record to be used to determine the climate related component of changes in sea-level, it is therefore necessary to correct for the vertical land movement component of the observed change in sea-level.

In 1990, the Institute of Engineering Surveying and Space Geodesy and Proudman Oceanographic Laboratory started developing techniques based on the Global Positioning System (GPS) for measuring vertical land movements (VLM) at tide-gauges in the UK. This paper provides brief details of these early developments and shows how they led to the establishment of continuous GPS (CGPS) stations at a number of tide-gauges. The paper then goes on to discuss the use of absolute gravity (AG), as an independent technique for measuring VLM at tide-gauges. The most recent results, from CGPS time-series dating back to 1997 and AG time-series dating back to 1995/1996, are then used to demonstrate the complementarity of these two techniques and their potential for providing site-specific estimates of VLM at tide-gauges in the UK.
Exploiting protein structure data to explore the evolution of protein function and biological complexity
Authors: Marsden Russell L , Ranea Juan A.G , Sillero Antonio , Redfern Oliver , Yeats Corin , Maibaum Michael , Lee David , Addou Sarah , Reeves Gabrielle A , Dallman Timothy J , Orengo Christine A
Published: March 2006

New directions in biology are being driven by the complete sequencing of genomes, which has given us the protein repertoires of diverse organisms from all kingdoms of life. In tandem with this accumulation of sequence data, worldwide structural genomics initiatives, advanced by the development of improved technologies in X-ray crystallography and NMR, are expanding our knowledge of structural families and increasing our fold libraries. Methods for detecting remote sequence similarities have also been made more sensitive and this means that we can map domains from these structural families onto genome sequences to understand how these families are distributed throughout the genomes and reveal how they might influence the functional repertoires and biological complexities of the organisms.

We have used robust protocols to assign sequences from completed genomes to domain structures in the CATH database, allowing up to 60% of domain sequences in these genomes, depending on the organism, to be assigned to a domain family of known structure. Analysis of the distribution of these families throughout bacterial genomes identified more than 300 universal families, some of which had expanded significantly in proportion to genome size. These highly expanded families are primarily involved in metabolism and regulation and appear to make major contributions to the functional repertoire and complexity of bacterial organisms.

When comparisons are made across all kingdoms of life, we find a smaller set of universal domain families (approx. 140), of which families involved in protein biosynthesis are the largest conserved component. Analysis of the behaviour of other families reveals that some (e.g. those involved in metabolism, regulation) have remained highly innovative during evolution, making it harder to trace their evolutionary ancestry. Structural analyses of metabolic families provide some insights into the mechanisms of functional innovation, which include changes in domain partnerships and significant structural embellishments leading to modulation of active sites and protein interactions.
Transcriptional noise and cellular heterogeneity in mammalian macrophages
Authors: Ramsey S , Ozinsky A , Clark A , Smith K.D , de Atauri P , Thorsson V , Orrell D , Bolouri H
Published: March 2006

Transcriptional noise is known to play a crucial role in heterogeneity in bacteria and yeast. Mammalian macrophages are known to exhibit cell-to-cell variation in their responses to pathogens, but the source of this heterogeneity is not known. We have developed a detailed stochastic model of gene expression that takes into account scaling effects due to cell size and genome complexity. We report the results of applying this model to simulating gene expression variability in mammalian macrophages, demonstrating a possible molecular basis for heterogeneity in macrophage signalling responses. We note that the nature of predicted transcriptional noise in macrophages is different from that in yeast and bacteria. Some molecular interactions in yeast and bacteria are thought to have evolved to minimize the effects of the high-frequency noise observed in these species. Transcriptional noise in macrophages results in slow changes to gene expression levels and would not require the type of spike-filtering circuits observed in yeast and bacteria.
Rigorous performance evaluation in protein structure modelling and implications for computational biology
Authors: Moult John
Published: March 2006

In principle, given the amino acid sequence of a protein, it is possible to compute the corresponding three-dimensional structure. Methods for modelling structure based on this premise have been under development for more than 40 years. For the past decade, a series of community wide experiments (termed Critical Assessment of Structure Prediction (CASP)) have assessed the state of the art, providing a detailed picture of what has been achieved in the field, where we are making progress, and what major problems remain. The rigorous evaluation procedures of CASP have been accompanied by substantial progress. Lessons from this area of computational biology suggest a set of principles for increasing rigor in the field as a whole.
Novel arylpyrazole compounds selectively modulate glucocorticoid receptor regulatory activity
Authors: Wang Jen-Chywan , Shah Nilesh , Pantoja Carlos , Meijsing Sebastiaan H. , Ho Joseph D. , Scanlan Thomas S. , Yamamoto Keith R.
Published: March 2006

The activities of intracellular receptors are regulated by their cognate ligands. Here we show that a series of related arylpyrazole compounds, which specifically bind the glucocorticoid receptor (GR), selectively modulated GR-regulated biological functions in preadipocyte, preosteoblast, and lung epithelial cell lines. Indeed, when we monitored 17 endogenous GR target genes in one of these cell types, we found that distinct arylpyrazole compounds induced different expression patterns. We showed by chromatin immunoprecipitation that the arylpyrazole compounds regulated, in a gene-specific manner, either GR occupancy of the genomic glucocorticoid response element (GRE) or events after GR association, such as histone modification. Overall, our results establish that subtle differences in ligand chemistry can profoundly influence the transcriptional regulatory activity of GR, and that endogenous genes bearing natural GREs are especially sensitive detectors of these differences.
PER-dependent rhythms in CLK phosphorylation and E-box binding regulate circadian transcription
Authors: Yu Wangjie , Zheng Hao , Houl Jerry H. , Dauwalder Brigitte , Hardin Paul E.
Published: March 2006

Transcriptional activation by CLOCK-CYCLE (CLK-CYC) heterodimers and repression by PERIOD-TIMELESS (PER-TIM) heterodimers are essential for circadian oscillator function in Drosophila. PER-TIM was previously found to interact with CLK-CYC to repress transcription, and here we show that this interaction inhibits binding of CLK-CYC to E-box regulatory elements in vivo. Coincident with the interaction between PER-TIM and CLK-CYC is the hyperphosphorylation of CLK. This hyperphosphorylation occurs in parallel with the PER-dependent entry of DOUBLE-TIME (DBT) kinase into a complex with CLK-CYC, where DBT destabilizes both CLK and PER. Once PER and CLK are degraded, a novel hypophosphorylated form of CLK accumulates in parallel with E-box binding and transcriptional activation. These studies suggest that PER-dependent rhythms in CLK phosphorylation control rhythms in E-box-dependent transcription and CLK stability, thus linking PER and CLK function during the circadian cycle and distinguishing the transcriptional feedback mechanism in flies from that in mammals.