bluuebunny/crossref_metadata_2025 huggingface dataset:
Crustal types and Tertiary tectonic evolution of the Alborán sea, western Mediterranean
Authors: Booth‐Rea G. , Ranero C. R. , Martínez‐Martínez J. M. , Grevemeyer I.
Published: October 2007

Multichannel seismic reflection images across the transition between the east Alborán and the Algero‐Balearic basins show how crustal thickness decreases from about 5 s two‐way traveltime (TWTT, ∼15 km thick) in the west (east Alborán basin) to ∼2 s TWTT typical of oceanic crust (∼6 km thick) in the east (Algero‐Balearic basin). We have differentiated three different crustal domains in this transition, mainly on the basis of crustal thickness and seismic signature. Boundaries between the three crustal domains are transitional and lack evidence for major faults. Tilted blocks related to extension are very scarce and all sampled basement outcrops are volcanic, suggesting a strong relationship between magmatism and crustal structure. Stratigraphic correlation of lithoseismic units with sedimentary units of southeastern Betic basins indicates that sediments onlap igneous basement approximately at 12 Ma in the eastern area and at 8 Ma in the western area. Linking seismic crustal structure with magmatic geochemical evidence suggests that the three differentiated crustal domains may represent, from west to east, thin continental crust modified by arc magmatism, magmatic‐arc crust, and oceanic crust. Middle to late Miocene arc and oceanic crust formation in the east Alborán and Algero‐Balearic basins, respectively, occurred during westward migration of the Gibraltar accretionary wedge and shortening in the Betic‐Rif foreland basins. Arc magmatism and associated backarc oceanic crust formation were related to early to middle Miocene subduction and rollback of the Flysch Trough oceanic basement. Subduction of this narrow slab beneath the Alborán basin was coeval with collision of the Alborán domain with the Iberian and African passive margins and subsequent subcontinental‐lithosphere edge delamination along the Betic‐Rif margins.
Ubiquitous low‐velocity layer atop the 410‐km discontinuity in the northern Rocky Mountains
Authors: Jasbinsek John , Dueker Kenneth
Published: October 2007

Receiver functions from three 30‐station IRIS‐PASSCAL small‐aperture arrays (2–15 km station spacing) operated for 10 months each in the northern Rocky Mountains show a ubiquitous negative polarity P to S conversion just preceding the 410‐km discontinuity arrival. Data from the three arrays were sorted into NW, SE, and SW back‐azimuth quadrants and stacked to form nine quadrant stacks. Remarkably, the negative polarity arrival (NPA) is apparent in 8 of the 9 quadrant stacks, with 7 of the 8 having well‐correlated waveforms. Each quadrant stack also contains clear P to S conversions from the 410‐ and 660‐km discontinuities. Moveout analysis shows that all the major phases display the correct moveout for forward scattered P‐S phases. The waveshapes for the seven similar NPA‐410 km discontinuity arrivals are modeled with a five‐parameter “double gradient slab” model that is parameterized as follows: a top gradient thickness and shear velocity decrease; a constant velocity layer; bottom gradient thickness; and shear velocity increase. Model misfit is assessed via a grid search over the model space using a reflectivity code to calculate synthetic seismograms. Model likelihood is determined by calculating 1‐ and 2‐D marginal probability density functions (PDF) for the five parameters. The 1‐D marginals display a range of peak values, although significant overlap is observed for the top gradient thickness and its associated velocity decrement. From the peak value of the summary PDF, we find the top velocity gradient to be sharp (<6.4 km) and the shear velocity decrement to be large (8.9% Vs). Defining an effective thickness of the low‐velocity layer as the mean layer thickness plus half the mean gradient thicknesses, the 410 low‐velocity layer thickness is found to be 22 km. A review of changes in the physical state required to match our new 410‐LVL constraints suggests that the water‐filter model remains an operative hypothesis to test.
Convergent blooms of Karenia brevis along the Texas coast
Authors: Hetland Robert D. , Campbell Lisa
Published: October 2007

A numerical model of wind‐driven surface flow in the Gulf of Mexico is used to examine physical controls on harmful algal bloom formation along the Texas coast. Karenia brevis, which blooms frequently in the Gulf of Mexico, has a relatively slow growth rate (doubling times of 2–3 days). Increases in K. brevis concentration cannot be explained simply in terms of growth. We hypothesize that the primary mechanism responsible for bloom formation in the western Gulf of Mexico is convergence due to downwelling at the coast. Convergence along the Texas coast caused by seasonal downwelling winds can concentrate the plankton up to 1000 times. This is surprising because the modeled cells do not grow; the simulated increase in concentration is due to physical processes alone. The numerical model qualitatively reproduces both the timing and magnitude of bloom initiation along the coast, but does not predict the details of the migration of the bloom along the coast after it has formed, or the destruction of the bloom. The result of this simulation is significant because it implies that K. brevis blooms may be caused primarily by physical processes and that cell division is not an important factor in bloom formation.
Measurements of the viscous tangential stress in the airflow above wind waves
Authors: Veron F. , Saxena G. , Misra S. K.
Published: October 2007

The stress and drag at the surface of the ocean are crucial parameters for both short term forecasting and the modeling of long‐term global climate trends. However, the partition between viscous, turbulent, and wave stresses, and in particular the effects of airflow separation are not well understood. We present direct measurements of the velocity in the airflow above wind‐generated waves. We observe intermittent separation of the viscous sublayer past the crest of the wind waves leading to dramatic along‐wave variability in the surface viscous tangential stress. These results hold for wind speeds that would normally be considered low to moderate. These viscous stress measurements in the airflow above the wavy surface, and within the separated region are, to the best of the authors' knowledge, the first of this kind.
Maintenance of ecosystem nitrogen limitation by ephemeral forest disturbance: An assessment using MODIS, Hyperion, and Landsat ETM+
Authors: McNeil Brenden E. , de Beurs Kirsten M. , Eshleman Keith N. , Foster Jane R. , Townsend Philip A.
Published: October 2007

Ephemeral disturbances, such as non‐lethal insect defoliations and crown damage from meteorological events, can significantly affect the delivery of ecosystem services by helping maintain nitrogen (N) limitation in temperate forest ecosystems. However, the impacts of these disturbances are difficult to observe across the broad‐scales at which they affect ecosystem function. Using remotely sensed measures and field data, we find support for the hypothesis that ephemeral disturbances help maintain landscape‐wide ecosystem N limitation. Specifically, a phenology‐based defoliation index derived from daily MODIS satellite imagery predicts three ecosystem responses from oak‐dominated forested watersheds: elevated stream water N export (R2 = 0.48), decreased foliar N (R2 = 0.69, assessed with Hyperion imagery), and reduced vegetation growth vigor (R2 = 0.49, assessed with Landsat ETM+ imagery). The results indicate that ephemeral disturbances and other forest stressors may sustain N limitation by reducing the ability of trees to compete for –and retain‐ soil available N.
Utility of thermal sharpening over Texas high plains irrigated agricultural fields
Authors: Agam Nurit , Kustas William P. , Anderson Martha C. , Li Fuqin , Colaizzi Paul D.
Published: October 2007

Irrigated crop production in the Texas high plains (THP) is dependent on water extracted from the Ogallala Aquifer, an area suffering from sever water shortage. Water management in this area is therefore highly important. Thermal satellite imagery at high temporal (∼daily) and high spatial (∼100 m) resolutions could provide important surface boundary conditions for vegetation stress and water use monitoring, mainly through energy balance models such as DisALEXI. At present, however, no satellite platform collects such high spatiotemporal resolution data. The objective of this study is to examine the utility of an image sharpening technique (TsHARP) for retrieving land surface temperature at high spatial resolution (down to 60 m) from moderate spatial resolution (1 km) imagery, which is typically available at higher (∼daily) temporal frequency. A simulated sharpening experiment was applied to Landsat 7 imagery collected over the THP in September 2002 to examine its utility over both agricultural and natural vegetation cover. The Landsat thermal image was aggregated to 960 m resolution and then sharpened to its native resolution of 60 m and to various intermediate resolutions. The algorithm did not provide any measurable improvement in estimating high‐resolution temperature distributions over natural land cover. In contrast, TsHARP was shown to retrieve high‐resolution temperature information with good accuracy over much of the agricultural area within the scene. However, in recently irrigated fields, TsHARP could not reproduce the temperature patterns. Therefore we conclude that TsHARP is not an adequate substitute for 100‐m‐scale observations afforded by the current Landsat platforms. Should the thermal imager be removed from follow‐on Landsat platforms, we will lose valuable capacity to monitor water use at the field scale, particularly in many agricultural regions where the typical field size is ∼100 × 100 m. In this scenario, sharpened thermal imagery from instruments like MODIS or VIIRS would be the suboptimal alternative.
Effects of the El Niño–Southern Oscillation and the Quasi‐Biennial Oscillation on polar temperatures in the stratosphere
Authors: Garfinkel C. I. , Hartmann D. L.
Published: October 2007

Reanalysis data are used to study the effects of the Quasi‐Biennial Oscillation (QBO) and the El Niño–Southern Oscillation (ENSO) on the stratosphere. During the boreal winter in the Arctic, Warm ENSO (WENSO) months are found to be significantly warmer and Cold ENSO (CENSO) months significantly colder than climatology. The QBO is also found to have a large effect on the Arctic stratosphere during the late fall/early winter; Westerly QBO (WQBO) poles are colder, and Easterly QBO (EQBO) poles are warmer. In the first half of the 50 years of interest, WENSO and EQBO have had a tendency to be correlated in time, and thus their signals are difficult to disentangle. In order to isolate each effect from the other, composites are taken of QBO months under near‐neutral ENSO conditions, which show a clear effect in late fall/early winter. Because of the bimodality of QBO, producing a meaningful composite of ENSO months under near‐neutral QBO is difficult, as the number of available months is quite small. To distinguish ENSO from QBO and to further study the QBO, we compare composites of months with four different combinations of QBO and ENSO anomalies, which confirms that ENSO does have a significant effect on the polar vortex. These groupings are also studied after removing the 2 years following one of the three major volcanic eruptions during the 50 years of data and during the post‐1979 satellite era only as well. These composites show distinct ENSO and QBO effects of comparable magnitude.
A quick trip through openness, freedom and transparency
Authors: Foerstner Konrad
Published: October 2007

This talk aims to give scientists an introduction to the concepts of openness, freedom and transparency and their applications (not only) for science. It covers the topics of open source, open formats, Creative Commons, open access, and open science/knowledge. A video of the talk is available on the author's website.
Tripeptidyl peptidase II promotes fat formation in a conserved fashion
Authors: McKay Renée M , McKay James P , Suh Jae Myoung , Avery Leon , Graff Jonathan M
Published: October 2007

Tripeptidyl peptidase II (TPPII) is a multifunctional and evolutionarily conserved protease. In the mammalian hypothalamus, TPPII has a proposed anti‐satiety role affected by degradation of the satiety hormone cholecystokinin 8. Here, we show that TPPII also regulates the metabolic homoeostasis of Caenorhabditis elegans; TPPII RNA interference (RNAi) decreases worm fat stores. However, this occurs independently of feeding behaviour and seems to be a function within fat‐storing tissues. In mammalian cell culture, TPPII stimulates adipogenesis and TPPII RNAi blocks adipogenesis. The pro‐adipogenic action of TPPII seems to be independent of protease function, as catalytically inactive TPPII also increases adipogenesis. Mice that were homozygous for an insertion in the Tpp2 locus were embryonic lethal. However, Tpp2 heterozygous mutants were lean compared with wild‐type littermates, although food intake was normal. These findings indicate that TPPII has central and peripheral roles in regulating metabolism and that TPPII actions in fat‐storing tissues might be an ancient function carried out in a protease‐independent manner.
A reversible form of lysine acetylation in the ER and Golgi lumen controls the molecular stabilization of BACE1
Authors: Costantini Claudio , Ko Mi Hee , Jonas Mary Cabell , Puglielli Luigi
Published: October 2007

The lipid second messenger ceramide regulates the rate of β cleavage of the Alzheimer's disease APP (amyloid precursor protein) by affecting the molecular stability of the β secretase BACE1 (β-site APP cleaving enzyme 1). Such an event is stimulated in the brain by the normal process of aging, and is under the control of the general aging programme mediated by the insulin-like growth factor 1 receptor. In the present study we report that BACE1 is acetylated on seven lysine residues of the N-terminal portion of the nascent protein. This process involves lysine acetylation in the lumen of the ER (endoplasmic reticulum) and is followed by deacetylation in the lumen of the Golgi apparatus, once the protein is fully mature. We also show that specific enzymatic activities acetylate (in the ER) and deacetylate (in the Golgi apparatus) the lysine residues. This process requires carrier-mediated translocation of acetyl-CoA into the ER lumen and is stimulated by ceramide. Site-directed mutagenesis indicates that lysine acetylation is necessary for nascent BACE1 to leave the ER and move ahead in the secretory pathway, and for the molecular stabilization of the protein.
Deacetylation of the retinoblastoma tumour suppressor protein by SIRT1
Authors: Wong Sharon , Weber Jason D.
Published: October 2007

The activity of Rb (retinoblastoma protein) is regulated by phosphorylation and acetylation events. Active Rb is hypophosphorylated and acetylated on multiple residues. Inactivation of Rb involves concerted hyper-phosphorylation by cyclin–CDK (cyclin-dependent kinase) complexes combined with deacetylation of appropriate lysine residues within Rb. In the present study, using in vivo co-immunoprecipitation experiments, we identified mammalian SIRT1 (sirtuin 1) as a binding partner for Rb and its family members p107 and p130. Formation of Rb–SIRT1 complexes required the pocket domain of Rb. p300 catalysed the acetylation of Rb, and SIRT1 was a potent deacetylase for Rb. The ability of SIRT1 to catalyse the deacetylation of Rb was dependent on NAD and was inhibited by the SIRT1 inhibitor nicotinamide. Deacetylated lysine residues within Rb formed a domain similar to the SIRT1-targeted domain of the p53 tumour suppressor protein. Cultures of arrested cells, via contact inhibition or DNA damage, exhibited decreased Rb phosphorylation and increased Rb acetylation. Overexpression of SIRT1 in either confluent or etoposide-treated cells resulted in a significant reduction in Rb acetylation, which was restored with nicotinamide. Gene knockdown of SIRT1 by siRNA (short interfering RNA) produced an accumulation of acetylated Rb. This increase was augmented further when siRNA against SIRT1 was used in conjunction with nicotinamide. In conclusion, our results demonstrate that SIRT1 is an in vitro and in vivo deacetylase for the Rb tumour suppressor protein.
Human nuclear pregnane X receptor cross-talk with CREB to repress cAMP activation of the glucose-6-phosphatase gene
Authors: Kodama Susumu , Moore Rick , Yamamoto Yukio , Negishi Masahiko
Published: October 2007

The nuclear PXR (pregnane X receptor) was originally characterized as a key transcription factor that activated hepatic genes encoding drug-metabolizing enzymes. We have now demonstrated that PXR also represses glucagon-activated transcription of the G6Pase (glucose-6-phosphatase) gene by directly binding to CREB [CRE (cAMP-response element)-binding protein]. Adenoviral-mediated expression of human PXR (hPXR) and its activation by rifampicin strongly repressed cAMP-dependent induction of the endogenous G6Pase gene in Huh7 cells. Using the −259 bp G6Pase promoter construct in cell-based transcription assays, repression by hPXR of PKA (cAMP-dependent protein kinase)-mediated promoter activation was delineated to CRE sites. GST (glutathione transferase) pull-down and immunoprecipitation assays were employed to show that PXR binds directly to CREB, while gel-shift assays were used to demonstrate that this binding prevents CREB interaction with the CRE. These results are consistent with the hypothesis that PXR represses the transcription of the G6Pase gene by inhibiting the DNA-binding ability of CREB. In support of this hypothesis, treatment with the mouse PXR activator PCN (pregnenolone 16α-carbonitrile) repressed cAMP-dependent induction of the G6Pase gene in primary hepatocytes prepared from wild-type, but not from PXR-knockout, mice, and also in the liver of fasting wild-type, but not PXR-knockout, mice. Moreover, ChIP (chromatin immunoprecipitation) assays were performed to show a decreased CREB binding to the G6Pase promoter in fasting wild-type mice after PCN treatment. Thus drug activation of PXR can repress the transcriptional activity of CREB, down-regulating gluconeogenesis.
Differential modulation of Alzheimer's disease amyloid β-peptide accumulation by diverse classes of metal ligands
Authors: Caragounis Aphrodite , Du Tai , Filiz Gulay , Laughton Katrina M. , Volitakis Irene , Sharples Robyn A. , Cherny Robert A. , Masters Colin L. , Drew Simon C. , Hill Andrew F. , Li Qiao-Xin , Crouch Peter J. , Barnham Kevin J. , White Anthony R.
Published: October 2007

Biometals have an important role in AD (Alzheimer's disease) and metal ligands have been investigated as potential therapeutic agents for treatment of AD. In recent studies the 8HQ (8-hydroxyquinoline) derivative CQ (clioquinol) has shown promising results in animal models and small clinical trials; however, the actual mode of action in vivo is still being investigated. We previously reported that CQ–metal complexes up-regulated MMP (matrix metalloprotease) activity in vitro by activating PI3K (phosphoinositide 3-kinase) and JNK (c-jun N-terminal kinase), and that the increased MMP activity resulted in enhanced degradation of secreted Aβ (amyloid β) peptide. In the present study, we have further investigated the biochemical mechanisms by which metal ligands affect Aβ metabolism. To achieve this, we measured the effects of diverse metal ligands on cellular metal uptake and secreted Aβ levels in cell culture. We report that different classes of metal ligands including 8HQ and phenanthroline derivatives and the sulfur compound PDTC (pyrrolidine dithiocarbamate) elevated cellular metal levels (copper and zinc), and resulted in substantial loss of secreted Aβ. Generally, the ability to inhibit Aβ levels correlated with a higher lipid solubility of the ligands and their capacity to increase metal uptake. However, we also identified several ligands that potently inhibited Aβ levels while only inducing minimal change to cellular metal levels. Metal ligands that inhibited Aβ levels [e.g. CQ, 8HQ, NC (neocuproine), 1,10-phenanthroline and PDTC] induced metal-dependent activation of PI3K and JNK, resulting in JNK-mediated up-regulation of metalloprotease activity and subsequent loss of secreted Aβ. The findings in the present study show that diverse metal ligands with high lipid solubility can elevate cellular metal levels resulting in metalloprotease-dependent inhibition of Aβ. Given that a structurally diverse array of ligands was assessed, the results are consistent with the effects being due to metal transport rather than the chelating ligand interacting directly with a receptor.
The farnesoid X receptor induces fetuin-B gene expression in human hepatocytes
Authors: Murakami Takeshi , Walczak Robert , Caron Sandrine , Duhem Christian , Vidal Vincent , Darteil Raphaël , Staels Bart
Published: October 2007

FXR (farnesoid X receptor), a nuclear receptor activated by BAs (bile acids), is a key factor in the regulation of BA, lipid and carbohydrate metabolism. The recent development of synthetic FXR agonists and knockout mouse models has accelerated the discovery of FXR target genes. In the present study, we identify human fetuin-B as a novel FXR target gene. Treatment with FXR agonists increased fetuin-B expression in human primary hepatocytes and in the human hepatoma HepG2 cell line. In contrast, fetuin-B expression was not responsive to FXR agonist treatment in murine primary hepatocytes. Fetuin-B induction by FXR agonist was abolished upon FXR knockdown by siRNA (small interfering RNA). In addition to the previously described P1 promoter, we show that the human fetuin-B gene is also transcribed from an alternative promoter, termed P2. Transcription via the P2 promoter was induced by FXR agonist treatment, whereas P1 promoter activity was not sensitive to FXR agonist treatment. Two putative FXR-response elements [IR-1 (inverted repeat-1)] were identified in the region –1.6 kb upstream of the predicted P2 transcriptional start site. Both motifs bound FXR–RXR (retinoid X receptor) complexes in vitro and were activated by FXR in transient transfection reporter assays. Mutations in the IR-1 sites abolished FXR–RXR binding and activation. Taken together, these results identify human fetuin-B as a new FXR target gene in human hepatocytes.
The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations
Authors: Just Victoria J. , Burrell Matthew R. , Bowater Laura , McRobbie Iain , Stevenson Clare E. M. , Lawson David M. , Bornemann Stephen
Published: October 2007

Oxalate decarboxylase (EC 4.1.1.2) catalyses the conversion of oxalate into carbon dioxide and formate. It requires manganese and, uniquely, dioxygen for catalysis. It forms a homohexamer and each subunit contains two similar, but distinct, manganese sites termed sites 1 and 2. There is kinetic evidence that only site 1 is catalytically active and that site 2 is purely structural. However, the kinetics of enzymes with mutations in site 2 are often ambiguous and all mutant kinetics have been interpreted without structural information. Nine new site-directed mutants have been generated and four mutant crystal structures have now been solved. Most mutants targeted (i) the flexibility (T165P), (ii) favoured conformation (S161A, S164A, D297A or H299A) or (iii) presence (Δ162–163 or Δ162–164) of a lid associated with site 1. The kinetics of these mutants were consistent with only site 1 being catalytically active. This was particularly striking with D297A and H299A because they disrupted hydrogen bonds between the lid and a neighbouring subunit only when in the open conformation and were distant from site 2. These observations also provided the first evidence that the flexibility and stability of lid conformations are important in catalysis. The deletion of the lid to mimic the plant oxalate oxidase led to a loss of decarboxylase activity, but only a slight elevation in the oxalate oxidase side reaction, implying other changes are required to afford a reaction specificity switch. The four mutant crystal structures (R92A, E162A, Δ162–163 and S161A) strongly support the hypothesis that site 2 is purely structural.
Heterodimerization, trafficking and membrane topology of the two proteins, Ostα and Ostβ, that constitute the organic solute and steroid transporter
Authors: Li Na , Cui Zhifeng , Fang Fang , Lee Jin Young , Ballatori Nazzareno
Published: October 2007

Co-immunoprecipitation studies using mouse ileal proteins and transfected HEK-293 (human embryonic kidney-293) cells revealed that the two proteins, Ostα and Ostβ, which generate the organic-solute transporter are able to immunoprecipitate each other, indicating a heteromeric complex. Mouse ileal Ostα protein appeared on Western blots largely as bands of 40 and 80 kDa, the latter band consistent with an Ostα homodimer, and both of these bands were sensitive to digestion by the glycosidase PNGase F (peptide:N-glycosidase F). Ostβ appeared as bands of 17 and 19 kDa, and these bands were not sensitive to PNGase F. Both the 40 and 80 kDa forms of Ostα, and only the 19 kDa form of Ostβ, were detected among the immunoprecipitated proteins, indicating that the interaction between Ostα and Ostβ is associated with specific post-translational processing. Additional evidence for homodimerization of Ostα and for a direct interaction between Ostα and Ostβ was provided by BiFC (bimolecular fluorescence complementation) analysis of HEK-293 cells transfected with Ostα and Ostβ tagged with yellow-fluorescent-protein fragments. BiFC analysis and surface immunolabelling of transfected HEK-293 cells also indicated that the C-termini of both Ostα and Ostβ are facing the intracellular space. The interaction between Ostα and Ostβ was required not only for delivery of the proteins to the plasma membrane, but it increased their stability, as noted in transfected HEK-293 cells and in tissues from Ostα-deficient (Ostα−/−) mice. In Ostα−/− mice, Ostβ mRNA levels were maintained, yet Ostβ protein was not detectable, indicating that Ostβ protein is not stable in the absence of Ostα. Overall, these findings identify the membrane topology of Ostα and Ostβ, demonstrate that these proteins are present as heterodimers and/or heteromultimers, and indicate that the interaction between Ostα and Ostβ increases the stability of the proteins and is required for delivery of the heteromeric complex to the plasma membrane.
The terminal step in vitamin C biosynthesis in Trypanosoma cruzi is mediated by a FMN-dependent galactonolactone oxidase
Authors: Logan Flora J. , Taylor Martin C. , Wilkinson Shane R. , Kaur Harparkash , Kelly John M.
Published: October 2007

Humans lack the ability to synthesize vitamin C (ascorbate) due to the absence of gulonolactone oxidase, the last enzyme in the biosynthetic pathway in most other mammals. The corresponding oxidoreductase in trypanosomes therefore represents a target that may be therapeutically exploitable. This is reinforced by our observation that Trypanosoma cruzi, the causative agent of Chagas' disease, lacks the capacity to scavenge ascorbate from its environment and is therefore dependent on biosynthesis to maintain intracellular levels of this vitamin. Here, we show that T. cruzi galactonolactone oxidase (TcGAL) can utilize both L-galactono-γ-lactone and D-arabinono-γ-lactone as substrates for synthesis of vitamin C, in reactions that obey Michaelis–Menten kinetics. It is >20-fold more active than the analogous enzyme from the African trypanosome Trypanosoma brucei. FMN is an essential cofactor for enzyme activity and binds to TcGAL non-covalently. In other flavoproteins, a histidine residue located within the N-terminal flavin-binding motif has been shown to be crucial for cofactor binding. Using site-directed mutagenesis, we show that the corresponding residue in TcGAL (Lys-55) is not essential for this interaction. In contrast, we find that histidine and tryptophan residues (His-447 and Trp-448), localized within a C-terminal motif (HWXK) that is a feature of ascorbate-synthesizing enzymes, are necessary for the FMN association. The conserved lysine residue within this motif (Lys-450) is not required for cofactor binding, but its replacement by glycine renders the protein completely inactive.
Evaluation of pH during cytostomal endocytosis and vacuolar catabolism of haemoglobin in Plasmodium falciparum
Authors: Klonis Nectarios , Tan Olivia , Jackson Katherine , Goldberg Daniel , Klemba Michael , Tilley Leann
Published: October 2007

The DV (digestive vacuole) of the malaria parasite, Plasmodium falciparum, is the site of Hb (haemoglobin) digestion and haem detoxification and, as a consequence, the site of action of CQ (chloroquine) and related antimalarials. However, the precise pH of the DV and the endocytic vesicles that feed it has proved difficult to ascertain. We have developed new methods using EGFP [enhanced GFP (green fluorescent protein)] to measure the pH of intracellular compartments. We have generated a series of transfectants in CQ-sensitive and -resistant parasite strains expressing GFP chimaeras of the DV haemoglobinase, plasmepsin II. Using a quantitative flow cytometric assay, the DV pH was determined to be 5.4–5.5. No differences were detected between CQ-sensitive and -resistant strains. We have also developed a method that relies on the pH dependence of GFP photobleaching kinetics to estimate the pH of the DV compartment. This method gives a pH estimate consistent with the intensity-based measurement. Accumulation of the pH-sensitive probe, LysoSensor Blue, in the DV confirms the acidity of this compartment and shows that the cytostomal vesicles are not measurably acidic, indicating that they are unlikely to be the site of Hb digestion or the site of CQ accumulation. We show that a GFP probe located outside the DV reports a pH value close to neutral. The transfectants and methods that we have developed represent useful tools for investigating the pH of GFP-containing compartments and should be of general use in other systems.
High-fat diets: healthy or unhealthy?
Authors: Guldstrand Marie C. , Simberg Caroline L.
Published: October 2007

In the current dietary recommendations for the treatment and prevention of Type 2 diabetes and its related complications, there is flexibility in the proportion of energy derived from monounsaturated fat and carbohydrate as a replacement for saturated fat. Over the last few years, several population studies have shown that subjects eating a lot of refined grains and processed foods have a much larger increase in waist circumference than those following a diet higher in monounsaturated fat, protein and carbohydrates rich in fibre and whole grain. In the present issue of Clinical Science, Sinitskaya and co-workers have demonstrated that, in normal-weight rodents categorized into groups of high-fat and medium-carbohydrate [53%/30% of energy as fat/carbohydrate; 19.66 kJ/g (4.7 kcal/g)], high-fat and low-carbohydrate [67%/9% of energy as fat/carbohydrate; 21.76 kJ/g (5.2 kcal/g)] and high-fat and carbohydrate-free [75%/0% of energy as fat/carbohydrate; 24.69 kJ/g (5.9 kcal/g)] diets, the high-fat diets containing carbohydrates were both obesogenic and diabetogenic, whereas the very-high-fat and carbohydrate-free diet was not obesogenic but led to insulin resistance and higher risk of cardiovascular disease. This finding may indicate that high-fat diets could easily give rise to an unhealthy diet when combined with carbohydrates, highlighting the significance of macronutrient composition, rather than caloric content, in high-fat diets.
Electron transport through single conjugated organic molecules: Basis set effects in ab initio calculations
Authors: Ke San-Huang , Baranger Harold U. , Yang Weitao
Published: October 2007

We investigate electron transport through single conjugated molecules—including benzenedithiol, oligophenylene ethynylenes of different lengths, and a ferrocene-containing molecule sandwiched between two gold electrodes with different contact structures—by using a single-particle Green function method combined with density functional theory calculation. We focus on the effect of the basis set in the ab initio calculation. It is shown that the position of the Fermi energy in the transport gap is sensitive to the molecule-lead charge transfer which is affected by the size of basis set. This can dramatically change, by orders of magnitude, the conductance for long molecules, though the effect is only minor for short ones. A resonance around the Fermi energy tends to pin the position of the Fermi energy and suppress this effect. The result is discussed in comparison with experimental data.
Hyperthermal (1–100eV) nitrogen ion scattering damage to D-ribose and 2-deoxy-D-ribose films
Authors: Deng Zongwu , Bald Ilko , Illenberger Eugen , Huels Michael A.
Published: October 2007

Highly charged heavy ion traversal of a biological medium can produce energetic secondary fragment ions. These fragment ions can in turn cause collisional and reactive scattering damage to DNA. Here we report hyperthermal (1–100eV) scattering of one such fragment ion (N+) from biologically relevant sugar molecules D-ribose and 2-deoxy-D-ribose condensed on polycrystalline Pt substrate. The results indicate that N+ ion scattering at kinetic energies down to 10eV induces effective decomposition of both sugar molecules and leads to the desorption of abundant cation and anion fragments. Use of isotope-labeled molecules (5-C13 D-ribose and 1-D D-ribose) partly reveals some site specificity of the fragment origin. Several scattering reactions are also observed. Both ionic and neutral nitrogen atoms abstract carbon from the molecules to form CN− anion at energies down to ∼5eV. N+ ions also abstract hydrogen from hydroxyl groups of the molecules to form NH− and NH2− anions. A fraction of O∕O− fragments abstract hydrogen to form OH−. The formation of H3O+ ions also involves hydrogen abstraction as well as intramolecular proton transfer. These findings suggest a variety of severe damaging pathways to DNA molecules which occur on the picosecond time scale following heavy ion irradiation of a cell, and prior to the late diffusion-limited homogeneous chemical processes.
Stretching single molecular DNA by temperature gradient
Authors: Jiang Hong-Ren , Sano Masaki
Published: October 2007

The authors present a method to control the conformation of DNA by using temperature gradient. The conformations of one end tethered and two ends tethered DNA are measured in different temperature gradients up to 3K∕μm. The results show that temperature gradient can exert force on a single DNA and create internal tension within it. The magnitude of the force is of the order of 0.1pN and is enough to manipulate and stretch DNA. This way of manipulating DNA requires no beads and provides local control, while none of the other methods can satisfy these two requirements at the same time.
Molecular dynamics simulation of the forces between colloidal nanoparticles in n-decane solvent
Authors: Qin Yong , Fichthorn Kristen A.
Published: October 2007

Molecular dynamics is utilized to simulate solvation forces between two nanoparticles immersed in liquid n-decane. Three types of solvophilic nanoparticles are investigated with sizes in the 1–6nm range: small and large amorphous spheres and crystalline cubes. We find that the solvation forces are negligible for the small spheres, which have diameters comparable to the end-to-end distance of all-trans decane, and we attribute this to the inability of the small spheres to induce decane ordering in the interparticle gap. The cubic nanoparticles (and to a lesser extent, the large spheres) are able to induce the formation of solidlike, n-decane layers in their gap for certain nanoparticle separations, and the transition between layered and disordered structures leads to solvation forces that oscillate between repulsion and attraction as the nanoparticle separation is varied. We find that the Derjaguin approximation [B. V. Derjaguin, Kolloid-Z. 69, 155 (1934)] is not effective at describing the dependence of the solvation forces on nanoparticle size and shape—contrasting results from a previous study involving these nanoparticles in Lennard-Jones solvent [Y. Qin and K. A. Fichthorn, J. Chem. Phys. 119, 9745 (2003)]. In particular, we find that for decane, the magnitude of the repulsive solvation forces is sensitive to nanoparticle size and shape, a phenomenon we attribute to the size and rigid-rod structure of n-decane, which makes its ordering in the interparticle gap sensitive to the size and the surface roughness of the nanoparticles.
Protein mechanical unfolding: A model with binary variables
Authors: Imparato A. , Pelizzola A. , Zamparo M.
Published: October 2007

A simple model, recently introduced as a generalization of the Wako-Saitô model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model proteins, together with their energy landscape, are studied on the basis of the exact solution of the model. Afterwards, the kinetic response of the molecules to a force is considered, discussing both force clamp and dynamic loading protocols and showing that theoretical expectations are verified. The kinetic parameters characterizing the protein unfolding are evaluated by using computer simulations and agree nicely with experimental results, when these are available. Finally, the extended Jarzynski equality is exploited to investigate the possibility of reconstructing the free energy landscape of proteins with pulling experiments.
Coordination structures of lithium-methylamine clusters from infrared spectroscopy and ab initio calculations
Authors: Salter Tom E. , Ellis Andrew M.
Published: October 2007

Spectra of clusters formed between lithium atoms and methylamine molecules are reported for the first time. Mass-selective infrared spectra of Li(NH2CH3)n have been recorded in both the N–H and C–H stretching fundamental regions. The infrared spectra are broadly in agreement with ab initio predictions, showing redshifted N–H stretching bands relative to free methylamine and a strong enhancement of the N–H stretching fundamentals relative to the C–H stretching fundamentals. The ab initio calculations suggest that, for n=3, the methylamine molecules bunch together on one side of the lithium atom to minimize repulsive interactions with the unpaired electron density. The addition of a fourth methylamine molecule results in closure of the inner solvation shell and, thus, Li(NH2CH3)5 is forced to adopt a two-shell coordination structure. This is consistent with neutron diffraction studies of concentrated lithium/methylamine solutions, which also suggest that the first solvation shell around the lithium atom can contain a maximum of four methylamine molecules.
Rational R-matrices, centralizer algebras and tensor identities for e6 and e7 exceptional families of Lie algebras
Authors: MacKay N. J. , Taylor A.
Published: October 2007

We use Cvitanović’s [Group Theory (Princeton University Press, Princeton, NJ, in press) (http://www.nbi.dk/GroupTheory/); Phys. Rev. D 14, 1536 (1976)] diagrammatic techniques to construct the rational solutions of the Yang-Baxter equation [Yang-Baxter Equation in Integrable Systems, edited by M. Jimbo, Advanced Series in Mathematical Physics Vol. 10 (World scientific, Singapore, 1990)] associated with the e6 and e7 families of Lie algebras, and thus explain Westbury’s [J. Phys. A 36, 2857 (2003)] observations about their uniform spectral decompositions. In doing so, we explore the extensions of the Brauer and symmetric group algebras to the centralizer algebras of e7 and e6 on their lowest-dimensional representations and (up to threefold) tensor products thereof, giving bases for them and a range of identities satisfied by the algebras’ defining invariant tensors.
Spontaneous emission of Weibel fluctuations by anisotropic distributions
Authors: Tautz R. C. , Schlickeiser R.
Published: October 2007

Recently [Yoon, Phys. Plasmas 14, 064504 (2007)], the spontaneous emission of magnetic field fluctuations in isotropic particle distribution functions was investigated. Here, the question is addressed as to how these fluctuations develop for an anisotropic distribution function that supports the Weibel instability. It is shown that, depending on the parameters, either electromagnetic or aperiodic magnetic fluctuations are dominant.
Grain and grain boundary vortex dynamics in YBa2Cu3O7-δ coated conductor by ac susceptibility
Authors: Palau A. , Puig T. , Obradors X.
Published: October 2007

ac-susceptibility measurements have been performed on YBa2Cu3O7−δ (YBCO) epitaxial thin films and coated conductors (CCs) in order to determine and compare the vortex motion regimes and dynamic responses induced at different temperatures and magnetic fields. A general phase diagram in the (Hac,T) plane has been built up, where three different dynamic regimes could be identified and compared for epitaxial films and CCs with different textures. Moreover, we have performed a comprehensive study of the dc-magnetic field and current density dependencies of the vortex activation energies associated with Abrikosov vortices inside the grains and Abrikosov-Josephson vortices at the grain boundaries and have built up a complete magnetic phase diagram valid for CCs in the (Hdc-T) plane. We present a full description of the different vortex motion regimes identified in the diagram. With this study we have been able to analyze and describe the general behavior of vortex dynamics at high temperatures, close to the irreversibility line, for YBCO thin films and CCs.
Photoluminescence of Ga-doped ZnO film grown on c-Al2O3 (0001) by plasma-assisted molecular beam epitaxy
Authors: Park H. C. , Byun D. , Angadi B. , Hee Park D. , Choi W. K. , Choi J. W. , Jung Y. S.
Published: October 2007

High quality gallium doped ZnO (Ga:ZnO) thin films were grown on c-Al2O3(1000) by plasma-assisted molecular beam epitaxy, and Ga concentration NGa was controlled in the range of 1×1018–2.5×1020∕cm3 by adjusting∕changing the Ga cell temperature. From the low-temperature photoluminescence at 10K, the donor bound exciton I8 related to Ga impurity was clearly observed and confirmed by comparing the calculated activation energy of 16.8meV of the emission peak intensity with the known localization energy, 16.1meV. Observed asymmetric broadening with a long tail on the lower energy side in the photoluminescence (PL) emission line shape could be fitted by the Stark effect and the compensation ratio was approximately 14–17% at NGa⩾1×1020∕cm3. The measured broadening of photoluminescence PL emission is in good agreement with the total thermal broadening and potential fluctuations caused by random distribution of impurity at NGa lower than the Mott critical density.
Strikingly different luminescent properties arising from single crystals grown from solution or from the vapor phase in a diketo-pyrrolo-pyrrole analog
Authors: Imoda Tomohiko , Mizuguchi Jin
Published: October 2007

The title compound di-cyano-pyrrolo-pyrrole (DCPP) is an analog of diketo-pyrrolo-pyrrole (DPP) known as a red pigment on the market. Brilliant orange photoluminescence has been observed in crystals of DCPP recrystallized from solution (crystal I); whereas the luminescence was quite weak in single crystals grown from the vapor phase (crystal II). To elucidate the difference in luminescent properties, a series of structural analysis together with thermal analysis has been carried out on crystals I and II at −180 °C, RT, 150 °C, and 200 °C. However, no difference in structure is recognized between crystals I and II within the precision of the x-ray analysis. Nevertheless, a slight difference in sublimation temperature of about 5° is observed between crystals I and II. Since the sublimation temperature depends on the cohesion in the solid state and the cohesion, in turn, governs the extent of lattice vibration (i.e., nonradiative process), a slight difference in sublimation temperature appears to determine the fraction between the radiative and nonradiative processes in crystals I and II.
Wall effects in microchannel-based macromolecular separation under electromagnetohydrodynamic influences
Authors: Paul Dibyadeep , Chakraborty Suman
Published: October 2007

The present paper aims to develop a theoretical model to highlight the influences of the near-wall interaction potentials and the consequent migrative fluxes on the size-based separation of macromolecules in microchannels subject to combined electromagnetohydrodynamic influences. It is established that the speed of traverse and the extent of spreading (dispersion) of the macromolecular bands is effectively determined on the basis of the macromolecular size relative to the channel height and the extent of near-wall interactions. It is demonstrated that because of the near-wall effects, macromolecular pairs with less disparities in sizes give rise to higher values of resolution.
Characterization of stickiness by means of recurrence
Authors: Zou Yong , Thiel Marco , Romano M. Carmen , Kurths Jürgen
Published: October 2007

We propose recurrence plots (RPs) to characterize the stickiness of a typical area-preserving map with coexisting chaotic and regular orbits. The difference of the recurrence properties between quasiperiodic and chaotic orbits is revisited, which helps to understand the complex patterns of the corresponding RPs. Moreover, several measures from the recurrence quantification analysis are used to quantify these patterns. Among these measures, the recurrence rate, quantifying the percentage of black points in the plot, is applied to characterize the stickiness of a typical chaotic orbit. The advantage of the recurrence based method in comparison to other standard techniques is that it is possible to distinguish between quasiperiodic and chaotic orbits that are temporarily trapped in a sticky domain, from very short trajectories.
Interaction of magnetic field and magnetic history in high-temperature superconductors
Authors: Grilli Francesco , Ashworth Stephen P. , Civale Leonardo
Published: October 2007

Yttrium barium copper oxide (YBCO) coated conductors are now the most promising high-temperature superconducting tapes in terms of current capacity and price. One form of these conductors utilizes YBCO films on Ni–W metallic tapes and is being considered for a number of power engineering applications. In these applications, the conductor will carry an ac current, leading to energy losses, which are the focus of significant technical and experimental efforts. Our measurements of the ac losses of YBCO/Ni–W conductors carrying ac currents in applied dc magnetic fields have revealed a complex interaction between the magnetic materials present, the geometry of the conductor, the ac and dc magnetic fields, and the electromagnetic “history” of the sample. The investigation of this interaction is the main subject of this paper.