bluuebunny/crossref_metadata_2025 huggingface dataset:
Correction to “Control of fossil‐fuel particulate black carbon and organic matter, possibly the most effective method of slowing global warming”
Authors: Jacobson Mark Z.
Published: July 2005

This document describes two updates and a correction that affect two figures (Figures 1 and 14) in “Control of fossil‐fuel particulate black carbon and organic matter, possibly the most effective method of slowing global warming” by Mark Z. Jacobson (Journal of Geophysical Research, 107(D19), 4410, doi:10.1029/2001JD001376, 2002). The modifications have no effect on the numerical simulations in the paper, only on the postsimulation analysis. The changes include the following: (1) The overall lifetime of CO2 is updated to range from 30 to 95 years instead of 50 to 200 years, (2) the assumption that the anthropogenic emission rate of CO2 is in equilibrium with its atmospheric mixing ratio is corrected, and (3) data for high‐mileage vehicles available in the U.S. are used to update the range of mileage differences (15–30% better for diesel) in comparison with one difference previously (30% better mileage for diesel). The modifications do not change the main conclusions in J2002, namely, (1) “any emission reduction of fossil‐fuel particulate BC plus associated OM may slow global warming more than may any emission reduction of CO2 or CH4 for a specific period,” and (2) diesel cars emitting continuously under the most recent U.S. and E.U. particulate standards (0.08 g/mi; 0.05 g/km) may warm climate per distance driven over the next 100+ years more than equivalent gasoline cars. Toughening vehicle particulate emission standards by a factor of 8 (0.01 g/mi; 0.006 g/km) does not change this conclusion, although it shortens the period over which diesel cars warm to 13–54 years,” except as follows: for conclusion 1, the period in Figure 1 of J2002 during which eliminating all fossil‐fuel black carbon plus organic matter (f.f. BC + OM) has an advantage over all anthropogenic CO2 decreases from 25–100 years to about 11–13 years and for conclusion 2 the period in Figure 14 of J2002 during which gasoline vehicles may have an advantage broadens from 13 to 54 years to 10 to >100 years. On the basis of the revised analysis, the ratio of the 100‐year climate response per unit mass emission of f.f. BC + OM relative to that of CO2‐C is estimated to be about 90–190.
Estimation of groundwater consumption by phreatophytes using diurnal water table fluctuations: A saturated‐unsaturated flow assessment
Authors: Loheide Steven P. , Butler James J. , Gorelick Steven M.
Published: July 2005

Groundwater consumption by phreatophytes is a difficult‐to‐measure but important component of the water budget in many arid and semiarid environments. Over the past 70 years the consumptive use of groundwater by phreatophytes has been estimated using a method that analyzes diurnal trends in hydrographs from wells that are screened across the water table (White, 1932). The reliability of estimates obtained with this approach has never been rigorously evaluated using saturated‐unsaturated flow simulation. We present such an evaluation for common flow geometries and a range of hydraulic properties. Results indicate that the major source of error in the White method is the uncertainty in the estimate of specific yield. Evapotranspirative consumption of groundwater will often be significantly overpredicted with the White method if the effects of drainage time and the depth to the water table on specific yield are ignored. We utilize the concept of readily available specific yield as the basis for estimation of the specific yield value appropriate for use with the White method. Guidelines are defined for estimating readily available specific yield based on sediment texture. Use of these guidelines with the White method should enable the evapotranspirative consumption of groundwater to be more accurately quantified.
Spring‐neap tide‐induced beach water table fluctuations in a sloping coastal aquifer
Authors: Jeng D.-S. , Mao X. , Enot P. , Barry D. A. , Li L.
Published: July 2005

Predictions of water table fluctuations in coastal aquifers are needed for numerous coastal and water resources engineering problems. Most previous investigations have been based on the Boussinesq equation for the case of a vertical beach. In this note an analytical solution based on shallow water expansion for the spring‐neap tide‐induced water table fluctuations in a coastal aquifer is presented. Unlike most previous investigations, multitidal signals are considered with a sloping coastal aquifer. The new solution is verified by comparing with field observations from Ardeer, Scotland. On the basis of the analytical approximation the influences of higher‐order components on water table elevation are examined first. Then, a parametric study has been performed to investigate the effects of the amplitude ratio (?), frequency ratio (?), and phases (d1 and d2) on the tide‐induced water table fluctuations in a sloping sandy beach.
Scalable recovery of plasmid DNA based on aqueous two‐phase separation
Authors: Frerix Andreas , Müller Markus , Kula Maria‐Regina , Hubbuch Jürgen
Published: July 2005

Future developments in gene therapy and DNA vaccination depend on cost‐effective large‐scale production of pharmaceutical‐grade pDNA (plasmid DNA). Given the large amount of impurities present in the feedstock, purification processes that have high specificity and capacity at a moderate cost are required. In the present study, we describe a non‐chromatographic procedure based on aqueous two‐phase extraction allowing a fast and simply scalable capture step. PEG [poly(ethylene glycol)] in combination with potassium citrate or potassium phosphate was tested as phase component for extraction. By increasing either PEG or salt concentration, the partitioning of nucleic acids changed from bottom to top phase. Phase systems with a composition of 15% PEG 800 and 20% potassium phosphate at pH 7.0 showed a strong partitioning of pDNA to the bottom phase, linked to a clear decrease in open circular pDNA, while proteins, genomic DNA and RNA remain at the top or at the interphase. A great advantage of the current process is that the complete procedure of lysis, precipitation, clarification and extraction can be performed in a single vessel. The number of denatured and sheared genomic DNAs in a spiking experiment was found to be depleted by more than 99%.
Fed‐batch pediocin production by Pediococcus acidilactici NRRL B‐5627 on whey
Authors: Pérez Guerra Nelson , Bernárdez Paula Fajardo , Agrasar Ana Torrado , López Macías Cristina , Castro Lorenzo Pastrana
Published: July 2005

Cell growth and pediocin production by Pediococcus acidilactici NRRL B‐5627 on whey were compared by using batch fermentation and re‐alkalized fed‐batch fermentation. The batch fermentations were performed on DWG [DW (diluted whey) supplemented with 1% (w/v) glucose], DWYE [DW supplemented with 2% (w/v) yeast extract] and DWGYE (DW supplemented with 1% glucose plus 2% yeast extract) media. The fed‐batch culture on DWYE medium was fed with a mixture of concentrated whey (48 g of total sugars/l) supplemented with 2% yeast extract and 400 g/l concentrated glucose. The re‐alkalized fed‐batch culture was characterized by higher biomass (6.57 g/l) and pediocin [517.6 BU (bacteriocin activity units)/ml] concentrations compared with the batch processes on MRS (de Man, Rogosa and Sharpe) broth (1.76 g/l and 493.2 BU/ml), DW (0.17 g/l and 57.7 BU/ml), DWG (0.14 g/l and 53.6 BU/ml), DWYE (1.43 g/l and 187.6 BU/ml) and DWGYE (1.28 g/l and 167.3 BU/ml) media. A mixed acid fermentation was observed during the growth of P. acidilactici NRRL B‐5627 in the fed‐batch culture on DWYE medium, and other products (acetic acid and ethanol) in addition to lactic acid accumulated in the medium. Mathematical models were set up to describe fed‐batch production of biomass and pediocin by P. acidilactici. The models developed offer a better fit and a more realistic description of the experimental biomass and pediocin production data when compared with the logistic and Luedeking and Piret [(1959) J. Biochem. Microbiol. Technol. Eng. 1, 431–459] model.
Periodic formation and propagation of double layers in the expanding chamber of an inductive discharge operating in Ar∕SF6 mixtures
Authors: Plihon N. , Corr C. S. , Chabert P. , Raimbault J.-L.
Published: July 2005

It has previously been shown [Tuszewski et al., Plasma Sources Sci. Technol. 12, 396 (2003)] that inductive discharges in electronegative gases are subject to two types of instability: the source instability related to the E to H transition and a transport instability, occurring downstream when an expanding chamber is present. These two types of instability are observed in our “helicon” reactor operated without a static magnetic field in low-pressure Ar∕SF6 mixtures. Temporally and spatially resolved measurements show that, in our experiment, the downstream instability is a periodic formation and propagation of a double layer. The double layer is born at the end of the source tube and propagates slowly to the end of the expansion region with a velocity of 150ms−1.
Effect of micellar environment on Marcus correlation curves for photoinduced bimolecular electron transfer reactions
Authors: Kumbhakar Manoj , Nath Sukhendu , Mukherjee Tulsi , Pal Haridas
Published: July 2005

Photoinduced electron transfer (ET) between coumarin dyes and aromatic amine has been investigated in two cationic micelles, namely, cetyltrimethyl ammonium bromide (CTAB) and dodecyltrimethyl ammonium bromide (DTAB), and the results have been compared with those observed earlier in sodium dodecyl sulphate (SDS) and triton-X-100 (TX-100) micelles for similar donor-acceptor pairs. Due to a reasonably high effective concentration of the amines in the micellar Stern layer, the steady-state fluorescence results show significant static quenching. In the time-resolved (TR) measurements with subnanosecond time resolution, contribution from static quenching is avoided. Correlations of the dynamic quenching constants (kqTR), as estimated from the TR measurements, show the typical bell-shaped curves with the free-energy changes (ΔG0) of the ET reactions, as predicted by the Marcus outersphere ET theory. Comparing present results with those obtained earlier for similar coumarin-amine systems in SDS and TX-100 micelles, it is seen that the inversion in the present micelles occurs at an exergonicity (−ΔG0>∼1.2–1.3eV) much higher than that observed in SDS and TX-100 micelles (−ΔG0>∼0.7eV), which has been rationalized based on the relative propensities of the ET and solvation rates in different micelles. In CTAB and DTAB micelles, the kqTR values are lower than the solvation rates, which result in the full contribution of the solvent reorganization energy (λs) towards the activation barrier for the ET reaction. Contrary to this, in SDS and TX-100 micelles, kqTR values are either higher or comparable with the solvation rates, causing only a partial contribution of λs in these cases. Thus, Marcus inversion in present cationic micelles is inferred to be the true inversion, whereas that in the anionic SDS and neutral TX-100 micelles are understood to be the apparent inversion, as envisaged from two-dimensional ET theory.
Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations
Authors: Heinz Tim N. , Hünenberger Philippe H.
Published: July 2005

A new scheme, the lattice-sum-emulated reaction-field (LSERF) method, is presented that combines the lattice-sum (LS) and reaction-field (RF) approaches for evaluating electrostatic interactions in molecular simulations. More precisely, the LSERF scheme emulates a RF calculation (based on an atomic cutoff) via the LS machinery. This is achieved by changing the form of the electrostatic interactions in a standard LS calculation (Coulombic) to the form corresponding to RF electrostatics (Coulombic plus quadratic reaction-field correction term, truncated at the cutoff distance). It is shown (both analytically and numerically) that in the limit of infinite reciprocal-space accuracy, (i) the LSERF scheme with a finite reaction-field cutoff and a given reaction-field permittivity is identical to the RF scheme with the same parameters (and an atomic cutoff), and (ii) the LSERF scheme is identical to the LS scheme in the limit of an infinite reaction-field cutoff, irrespective of the reaction-field permittivity. This new scheme offers two key advantages: (i) from a conceptual point of view, it shows that there is a continuity between the RF and LS schemes and unifies them into a common framework; (ii) from a practical point of view, it allows us to perform RF calculations with arbitrarily large reaction-field cutoff distances for the same computational costs as a corresponding LS calculation. The optimal choice for the cutoff will be the one that achieves the best compromise between artifacts arising from the dielectric heterogeneity of the system (short cutoff) and its artificial periodicity (long cutoff). The implementation of the LSERF method is extremely easy, requiring only very limited modifications of any standard LS code. For practical applications to biomolecular systems, the use of the LSERF scheme with large reaction-field cutoff distances is expected to represent a significant improvement over the current RF simulations involving comparatively much shorter cutoffs.
Low target power wafer sputtering regime identified during magnetron tantalum barrier physical vapor deposition
Authors: Stout Phillip J. , Denning Dean J. , Michaelson Lynne M. , Bagchi Sandeep , Zhang Da , Ventzek Peter L. G.
Published: July 2005

A wafer sputtering regime has been identified during tantalum barrier deposition using a magnetron physical vapor deposition (MPVD) tool. The MPVD tools are designed to operate at high target powers (tens of kW) where the highly directed energetic metal (athermal metal) is the dominant metal species incident on the wafer. Although athermal metal gives better coverage than neutral metal (thermal) due to the narrower range of incident strike angles to the wafer, shadowing by the feature geometries is still a concern. Having available a wafer sputter regime or “resputter” regime in a PVD tool allows for redistribution of metal from horizontal surfaces in the feature exposed to the plasma to vertical surfaces in the feature. The key in obtaining a wafer sputter regime is the operation of the plasma source in a range that the wafer bias power is effective at generating a sufficient self-bias for sputtering to occur. Discussed are modeling results which predict the wafer sputtering regime and the experimental confirmation that the low target power wafer sputter regime exists. The identified sputter regime in MPVD is such that there is a net deposition of metal at the field. Metal thickness reduction does occur at the trench and via bottoms where much of the unionized metal is being shadowed yielding a lower deposition to sputtering ratio compared to the field.
Mechanisms of imprint effect on ferroelectric thin films
Authors: Zhou Y. , Chan H. K. , Lam C. H. , Shin F. G.
Published: July 2005

We have developed a single/double layer model to explain horizontal shifting of measured D-E hysteresis loops (imprint) for ferroelectric thin films. Such phenomenon can be explained by considering three mechanisms or their multiple effects: (1) stress induced by film/electrode lattice mismatch or clamping, (2) domain pinning induced by, e.g., oxygen vacancies, or (3) degradation of ferroelectric properties in film/electrode surface layers. First, it is found that hysteresis loops under the influence of stress exhibit large horizontal shifts with magnitudes comparable to those observed in experiments. Second, a pseudo-non-switching layer with a large coercive field is assumed to be present at the film/electrode interface in an otherwise homogeneous ferroelectric thin film, and in this case our simulation also shows a large imprint effect. Third, it is also found that time-dependent space-charge-limited conduction is likely to be one origin for the occurrence of imprint.
Parametric study of a highly efficient chemical oxygen-iodine laser with supersonic mixing of iodine and oxygen
Authors: Rybalkin V. , Katz A. , Barmashenko B. D. , Rosenwaks S.
Published: July 2005

We report on a detailed parametric study of the extremely efficient supersonic chemical oxygen-iodine laser recently developed in our laboratory [V. Rybalkin, A. Katz, B. D. Barmashenko, and S. Rosenwaks, Appl. Phys. Lett. 85, 5851 (2004)]. At the early stage of operation, 40.0% efficiency was measured for 1 s followed by a sustained 35.5% chemical efficiency for 20 s. The power and spatial distributions of the gain and temperature across the flow were measured for different supersonic nozzles with both staggered and nonstaggered iodine injection holes, different injection locations along the flow and nozzle throat heights. The effects of the partial pressure of O2 and the residence time of the flow in the generator, as well as the heating of the nozzle, are discussed and shown to be crucial in attaining this high efficiency. By carefully studying and optimizing the operation of the chemical generator, 0.73 yield of singlet oxygen was obtained for conditions corresponding to the highest efficiency.
Carrier recombination and differential diode quality factors in the dark forward bias current-voltage characteristics of a-Si:H solar cells
Authors: Deng J. , Wronski C. R.
Published: July 2005

A careful study has been carried out on dark forward bias current-voltage characteristics in high-quality well-controlled a-Si:H solar cell structures. Contributions of potential barriers in the intrinsic layers adjacent to the p and n contacts on carrier injection have been clearly identified and carrier recombination in the p∕i regions systematically controlled and clearly separated from that in the bulk of the intrinsic layers. It is found that the recombination in the p∕i regions results in voltage-independent diode quality factor, n, with values very close to 1 whereas recombination in the bulk results in bias-dependent differential diode quality factors, n(V). These n(V) characteristics are consistent with Shockley-Read-Hall recombination through a continuous distribution of gap states in the intrinsic layers which have spatially uniform distributions of gap states and electric field. Based on an analytical model the n(V) characteristics are interpreted in terms of Gaussian-like energy distributions of gap states in both undiluted and diluted protocrystalline a-Si:H intrinsic layers. Gaussian-like distributions are identified centered around as well as ∼0.3eV away from midgap with differences in their distributions for the two materials in the annealed states and their evolution upon introducing light-induced defects. These results demonstrate that forward bias dark currents and, in particular, n(V) characteristics offer a reliable probe for characterizing the gap states of the native- and light-induced defect states in a-Si:H solar cells as well as mechanisms limiting their performance.
Electromagnetic field of fractal distribution of charged particles
Authors: Tarasov Vasily E.
Published: July 2005

Electric and magnetic fields of fractal distribution of charged particles are considered. The fractional integrals are used to describe fractal distribution. The fractional integrals are considered as approximations of integrals on fractals. Using the fractional generalization of integral Maxwell equation, the simple examples of the fields of homogeneous fractal distribution are considered. The electric dipole and quadrupole moments for fractal distribution are derived.
Actinometry of inductively coupled Cl2∕N2 plasmas for dry etching of GaAs
Authors: Brückl Tobias , Zull Heribert
Published: July 2005

Inductively coupled plasma dry etching of GaAs with Cl2∕N2-containing plasmas and investigations of these plasmas with optical emission spectroscopy and actinometry are presented. The results of actinometry were revised to allow the comparison of relative ground-state densities at different pressures. The obtained relative ground-state densities of N2, Cl2, and Cl (I) are presented as functions of the process parameters [rf power, pressure, and Cl2∕(Cl2+N2) ratio]. Cl (I) relative ground-state densities were found to be linearly connected to the pressure and the Cl2∕(Cl2+N2) ratio. GaAs etch rates up to 3μm∕min were obtained, while etch rates of the photoresist mask did not exceed 0.95μm∕min. The impact of the rf power changes on the etch rates was negligible. Plotting the etch rates against the process parameters revealed a linear relationship between the etch rates and the pressure and between the etch rates and the Cl2∕(Cl2+N2) ratio. Therefore a correlation between the Cl (I) relative ground-state density measured in plasmas without wafer and GaAs and the photoresist mask etch rate was found. All GaAs dry etching examined in this investigation was found to take place in a reactant-limited regime with Cl (I) as the rate-limiting species.
Formation of ZrTiCuNiBe bulk metallic glass by shock-wave quenching
Authors: Yang C. , Liu R. P. , Zhan Z. J. , Sun L. L. , Zhang J. , Gong Z. Z. , Wang W. K.
Published: July 2005

Zr 41 Ti 14 Cu 12.5 Ni 10 Be 22.5 bulk metallic glass (BMG) was prepared by shock-wave quenching. Differences in property, structure, and thermal stability were found between the BMGs prepared by the shock-wave quenching and water quenching. The glass transition temperature of the shock-wave-quenched BMG is about 13K higher than that of the water-quenched one. Although the density of the shock-wave-quenched BMG is decreased, the acoustic velocities in it are increased. Shock-wave quenching is possibly a promising method for preparing BMG.
Atomic-layer-deposited Al2O3–HfO2–Al2O3 dielectrics for metal-insulator-metal capacitor applications
Authors: Ding Shi-Jin , Zhu Chunxiang , Li Ming-Fu , Zhang David Wei
Published: July 2005

Atomic-layer-deposited Al2O3–HfO2–Al2O3 dielectrics have been investigated to replace conventional silicon oxide and nitride for radio frequency and analog metal-insulator-metal capacitors applications. In the case of 1-nm-Al2O3, sufficiently good electrical performances are achieved, including a high dielectric constant of ∼17, a small dissipation factor of 0.018 at 100kHz, an extremely low leakage current of 7.8×10−9A∕cm2 at 1MV∕cm and 125°C, perfect voltage coefficients of capacitance (74ppm∕V2 and 10ppm∕V). The quadratic voltage coefficient of capacitance decreases with the applied frequency due to the change of relaxation time with different carrier mobility in insulator, and correlates with the dielectric composition and thickness, which is of intrinsic property owing to electric field polarization. Furthermore, the conduction mechanism of the AHA dielectrics is also discussed, indicating the Schottky emission dominated at room temperature.
The Recycling of Container and Packaging Waste in the Spanish Retail Distribution Sector
Authors: Alcalde Nuria , Garcés Concepción , Pedraja Marta , Rivera Pilar
Published: July 2005

The authors analyse the determinants of the commercial container recycling behaviour of small and medium-sized companies in the retail-distribution sector of a representative Spanish city. A conceptual model is proposed, based on the literature on the incentives for and barriers to participation in selective collection programmes. By application of structural equation model methodology to a sample of 245 retail-distribution establishments, the main determinants of recycling were ascertained to be the perceived importance of the environmental problems and the perception of good management by public authorities. However, the free-rider attitude represents a barrier to participation.
Neighbourhood Social Capital and Neighbourhood Effects
Authors: Johnston Ron , Propper Carol , Sarker Rebecca , Jones Kelvyn , Bolster Anne , Burgess Simon
Published: July 2005

Recent research has provided very strong circumstantial evidence of the existence of neighbourhood effects in voting patterns at recent UK general elections. The usual reason adduced to account for these spatial variations is the neighbourhood effect. This hypothesises that people are influenced in their decisionmaking and behavioural patterns by their neighbours, with interpersonal conversation being the main means of transmitting such influence. Although there is an increasing body of evidence showing the impact of such conversations—that people who talk together, vote together—relatively little of this has grounded the geography of such conversations in the individuals' local neighbourhoods. Those who interact locally should show more evidence of ‘neighbourhood-effect-like’ patterns than those who do not. To inquire whether this is indeed so, this paper extends recent work on voting patterns in the United Kingdom by investigating the behaviour of individuals with different levels of participation in their local milieux—what we define below as neighbourhood social capital.
Possible role of the 11-cis-retinyl conformation in controlling the dual decay processes of excited rhodopsin
Authors: Liu Robert S. H. , Hammond George S. , Mirzadegan Taraneh
Published: July 2005

In this work, we examine how the reported dual decay processes of rhodopsin and binding site stereospecificity can be accounted for by the recently available crystal structure of rhodopsin. Arguments are presented for possible presence of two rhodopsin “rotamers” that fit within the binding cavity. Directed pathways of decay could account for the observed excited decay processes. We summarize evidence for the possible existence of two different ground-state configurations that give rise to two different excited species.
Functional cavitands: Chemical reactivity in structured environments
Authors: Purse Byron W. , Rebek Julius
Published: July 2005

Container-shaped molecules provide structured environments that impart geometric bounds on the motions and conformations of smaller molecular occupants. Moreover, they provide “solvation” that is constrained in time and space. When inwardly directed functional groups are present, they can interact chemically with the occupants. Additionally, the potential for reactivity and catalysis is greatly enhanced. Deep cavitands, derived from resorcinarenes, nearly surround smaller molecules and have been one of the most successful platforms for elaboration with functional groups. Derivatives bearing organic and metal-binding functional groups have been shown to affect recognition properties and selectively accelerate diverse reactions. In this review, we examine recent examples of these systems with an emphasis on how and why ordered nanoenvironments impart changes in the properties and reactivity of their occupants.
Recombinant AAV2 transduction of primitive human hematopoietic stem cells capable of serial engraftment in immune-deficient mice
Authors: Santat Leah , Paz Helicia , Wong Christie , Li Lijing , Macer James , Forman Stephen , Wong K. K. , Chatterjee Saswati
Published: July 2005

A recombinant AAV2 (rAAV2) vector encoding antisense RNA to HIV-1 transactivating region (TAR) was evaluated for transduction of human cord blood CD34
+
CD38
-
hematopoietic stem cells (HSC) capable of serial engraftment in nonobese diabetic (NOD)/severe combined immunodeficient (SCID) mice. Results revealed long-term multilineage marking in primary and secondary recipients, and significantly, an enrichment of transduced cells in secondary hosts, indicating efficient transduction of multipotential self-renewing HSC. These results were confirmed by the persistence of rAAV marking of clonogenic progenitors in serial analyses of recipient marrow. Upon HIV-1 challenge, the macrophage progeny of transduced CD34
+
cells expressed antisense RNA and exhibited sustained and significant inhibition of virus replication as compared with controls in every donor tested, without selective pressure. This study represents a clear
in vivo
demonstration of efficient rAAV2 transduction of human HSC.
Activationless electron transfer through the hydrophobic core of cytochrome
c
oxidase
Authors: Jasaitis Audrius , Rappaport Fabrice , Pilet Eric , Liebl Ursula , Vos Marten H.
Published: July 2005

Electron transfer (ET) within proteins occurs by means of chains of redox intermediates that favor directional and efficient electron delivery to an acceptor. Individual ET steps are energetically characterized by the electronic coupling
V
, driving force Δ
G
, and reorganization energy λ. λ reflects the nuclear rearrangement of the redox partners and their environment associated with the reactions; λ ≈ 700–1,100 meV (1 eV = 1.602 × 10
-19
J) has been considered as a typical value for intraprotein ET. In nonphotosynthetic systems, functional ET is difficult to assess directly. However, using femtosecond flash photolysis of the CO-poised membrane protein cytochrome
c
oxidase, the intrinsic rate constant of the low-Δ
G
electron injection from heme
a
into the heme
a
3
-Cu
B
active site was recently established at (1.4 ns)
-1
. Here, we determine the temperature dependence of both the rate constant and Δ
G
of this reaction and establish that this reaction is activationless. Using a quantum mechanical form of nonadiabatic ET theory and common assumptions for the coupled vibrational modes, we deduce that λ is <200 meV. It is demonstrated that the previously accepted value of 760 meV actually originates from the temperature dependence of Cu
B
–CO bond breaking. We discuss that low-Δ
G
, low-λ reactions are common for efficiently channeling electrons through chains that are buried inside membrane proteins.
Iron and
Pseudomonas aeruginosa
biofilm formation
Authors: Banin Ehud , Vasil Michael L. , Greenberg E. Peter
Published: July 2005

Iron serves as a signal in
Pseudomonas aeruginosa
biofilm development. We examined the influence of mutations in known and putative iron acquisition-signaling genes on biofilm morphology. In iron-sufficient medium, mutants that cannot obtain iron through the high-affinity pyoverdine iron acquisition system form thin biofilms similar to those formed by the parent under low iron conditions. If an iron source for a different iron acquisition system is provided to a pyoverdine mutant, normal biofilm development occurs. This enabled us to identify iron uptake gene clusters that likely serve in transport of ferric citrate and ferrioxamine. We suggest that the functional iron signal for
P. aeruginosa
biofilm development is active transport of chelated iron or the level of internal iron. If the signal is internal iron levels, then a factor likely to be involved in iron signaling is the cytoplasmic ferric uptake regulator protein, Fur, which controls expression of iron-responsive genes. In support of a Fur involvement, we found that with low iron a Fur mutant was able to organize into more mature biofilms than was the parent. The two known Fur-controlled small regulatory RNAs (PrrF1 and F2) do not appear to mediate iron control of biofilm development. This information establishes a mechanistic basis for iron control of
P. aeruginosa
biofilm formation.
Disabling TNF receptor signaling by induced conformational perturbation of tryptophan-107
Authors: Murali Ramachandran , Cheng Xin , Berezov Alan , Du Xiulian , Schön Arnie , Freire Ernesto , Xu Xiaowei , Chen Youhai H. , Greene Mark I.
Published: July 2005

We have disabled TNF receptor (TNFR) function by inducing allosteric modulation of tryptophan-107 (W107) in the receptor. The allosteric effect operates by means of an allosteric cavity found a short distance from a previously identified loop involved in ligand binding. Occupying this cavity by small molecules leads to perturbation of distal W107 and disables functions of the TNFR, a molecule not known to undergo conformational change upon binding TNF-α. TNF-α-induced NF-κB and p38 kinase activities and clinical symptoms of collagen-induced arthritis in mice were all diminished. Thus, disabling receptor function by induced conformational changes of active binding surfaces represents an innovative paradigm in structure-based drug design.
Alterations in the α2 isoform of Na,K-ATPase associated with familial hemiplegic migraine type 2
Authors: Segall Laura , Mezzetti Alessandra , Scanzano Rosemarie , Gargus J. Jay , Purisima Enrico , Blostein Rhoda
Published: July 2005

A number of missense mutations in the Na,K-ATPase α2 catalytic subunit have been identified in familial hemiplegic migraine with aura. Two alleles (L764P and W887R) showed loss-of-function, whereas a third (T345A) is fully functional but with altered Na,K-ATPase kinetics. This study describes two additional mutants, R689Q and M731T, originally identified by Vanmolkot
et al.
[Vanmolkot, K. R.,
et al.
(2003)
Ann. Neurol.
54, 360-366], which we show here to also be functional and kinetically altered. Both mutants have reduced catalytic turnover and increased apparent affinity for extracellular K
+
. For both R689Q and M731T, sensitivity to vanadate inhibition is decreased, suggesting that the steady-state E
1
↔ E
2
poise of the enzyme is shifted toward E
1
. Whereas the K′
ATP
is not affected by the R689Q replacement, the M731T mutant has an increase in apparent affinity for ATP. Analysis of the structural changes effected by T345A, R689Q, and M731T mutations, based on homologous replacements in the known crystal structure of the sarcoplasmic reticulum Ca-ATPase, provides insights into the molecular bases for the kinetic alterations. It is suggested that the disease phenotype is the consequence of lowered molecular activity of the α2 pump isoform due to either decreased K
+
affinity (T345A) or catalytic turnover (R689Q and M731T), thus causing a delay in extracellular K
+
clearance and/or altered localized Ca
2+
handling/signaling secondary to reduced activity in colocalized Na
+
/Ca
2+
exchange.
Redundant control of the
Caenorhabditis elegans
sperm/oocyte switch by PUF-8 and FBF-1, two distinct PUF RNA-binding proteins
Authors: Bachorik Jennifer L. , Kimble Judith
Published: July 2005

PUF proteins control both growth and differentiation in the
C. elegans
germ line. These conserved RNA-binding proteins inhibit expression of target mRNAs, either by repressing translation or promoting degradation. Previous studies showed that PUF-8, a PUF protein with striking similarity to human Pumilio, prevents return of primary spermatocytes to the mitotic cell cycle [Subramaniam, K. & Seydoux, G. (2003)
Curr. Biol.
13, 134–139]. We now report that PUF-8 is also critical for the hermaphrodite sperm/oocyte switch. Most
puf-8
mutant hermaphrodites make both sperm and oocytes and are self-fertile, but some make a vast excess of sperm and fail to switch into oogenesis. This
puf-8
defect is dramatically enhanced by removal of another
puf
gene called
fbf-1
: all
fbf-1 puf-8
double mutants fail in the hermaphrodite sperm/oocyte switch. Therefore,
puf-8
and
fbf-1
act redundantly to control this decision. Epistasis analyses place
puf-8
and
fbf-1
upstream of
fog-2
, a gene near the top of the germ-line sex determination pathway. Furthermore, the abundance of FOG-2 increases dramatically in the distal region of
fbf-1 puf-8
double mutants. We suggest that PUF-8 and FBF-1 may control
fog-2
expression, and that the sperm/oocyte decision occurs in the distal germ line.
The psychrophilic lifestyle as revealed by the genome sequence of
Colwellia psychrerythraea
34H through genomic and proteomic analyses
Authors: Methé Barbara A. , Nelson Karen E. , Deming Jody W. , Momen Bahram , Melamud Eugene , Zhang Xijun , Moult John , Madupu Ramana , Nelson William C. , Dodson Robert J. , Brinkac Lauren M. , Daugherty Sean C. , Durkin Anthony S. , DeBoy Robert T. , Kolonay James F. , Sullivan Steven A. , Zhou Liwei , Davidsen Tanja M. , Wu Martin , Huston Adrienne L. , Lewis Matthew , Weaver Bruce , Weidman Janice F. , Khouri Hoda , Utterback Terry R. , Feldblyum Tamara V. , Fraser Claire M.
Published: July 2005

The completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium
Colwellia psychrerythraea
34H, a model for the study of life in permanently cold environments, reveals capabilities important to carbon and nutrient cycling, bioremediation, production of secondary metabolites, and cold-adapted enzymes. From a genomic perspective, cold adaptation is suggested in several broad categories involving changes to the cell membrane fluidity, uptake and synthesis of compounds conferring cryotolerance, and strategies to overcome temperature-dependent barriers to carbon uptake. Modeling of three-dimensional protein homology from bacteria representing a range of optimal growth temperatures suggests changes to proteome composition that may enhance enzyme effectiveness at low temperatures. Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition.
Cohesins are required for meiotic DNA breakage and recombination in
Schizosaccharomyces pombe
Authors: Ellermeier Chad , Smith Gerald R.
Published: July 2005

In preparation for the unique segregation of homologs at the first meiotic division, chromosomes undergo dramatic changes. The meiosis-specific sister chromatid cohesins Rec8 and Rec11 of
Schizosaccharomyces pombe
are recruited around the time of premeiotic replication, and Rec10, a component of meiosis-specific linear elements, is subsequently added. Here we report that Rec10 is essential for meiosis-specific DNA breakage by Rec12 (Spo11 homolog) and for meiotic recombination. DNA breakage and recombination also depend on the Rec8 and Rec11 cohesins, strictly in some genomic intervals but less so in others. Thus, in addition to their previously recognized role in meiotic chromosome segregation, cohesins have a direct role, as do linear element components, in meiotic recombination by enabling double-strand DNA break formation by Rec12. Our results reveal a pathway, whose regulation is significantly different from that in the distantly related yeast
Saccharomyces cerevisiae
, for meiosis-specific chromosome differentiation and high-frequency recombination.
Space–time thermodynamics of the glass transition
Authors: Merolle Mauro , Garrahan Juan P. , Chandler David
Published: July 2005

We consider the probability distribution for fluctuations in dynamical action and similar quantities related to dynamic heterogeneity. We argue that the so-called “glass transition” is a manifestation of low action tails in these distributions where the entropy of trajectory space is subextensive in time. These low action tails are a consequence of dynamic heterogeneity and an indication of phase coexistence in trajectory space. The glass transition, where the system falls out of equilibrium, is then an order–disorder phenomenon in space–time occurring at a temperature
T
g
, which is a weak function of measurement time. We illustrate our perspective ideas with facilitated lattice models and note how these ideas apply more generally.
Effect of temperature and host plant leaf morphology on the efficacy of two entomopathogenic biocontrol agents of Thrips palmi (Thysanoptera: Thripidae)
Authors: Cuthbertson A.G.S. , North J.P. , Walters K.F.A.
Published: July 2005

The efficacy of two entomopathogenic biocontrol agents, Steinernema feltiae (Filipjev) and Verticillium lecanii (Zimmerman) Viégas (reclassified now as Lecanicillium muscarium (Petch) Zare & Gams), against Thrips palmi Karny was investigated. Assessments of the effect of temperature on the efficacy of S. feltiae indicated that higher mortality of T. palmi was recorded at 20°C compared to either 15 or 25°C, whereas significantly higher T. palmi mortality followed application of L. muscarium at 25°C. Testing the control agents efficacy on three host plants; chrysanthemum, sweet pepper and cucumber, under constant temperature and high humidity conditions produced no significant difference in the level of T. palmi larval mortality on each host plant. Incorporating the chemical insecticide imidacloprid with both biological agents in a combined control strategy increased T. palmi juvenile mortality. The potential role of S. feltiae and L. muscarium within integrated pest management programmes for the control of T. palmi is discussed.
Molecular and biochemical characterization of a sand fly population from Sri Lanka: evidence for insecticide resistance due to altered esterases and insensitive acetylcholinesterase
Authors: Surendran S.N. , Karunaratne S.H.P.P. , Adamsn Z. , Hemingway J. , Hawkes N.J.
Published: July 2005

With an increasing incidence of cutaneous leishmaniasis in Sri Lanka, particularly in northern provinces, insecticide-mediated vector control is under consideration. Optimizing such a strategy requires the characterization of sand fly populations in target areas with regard to species composition and extant resistance, among other parameters. Sand flies were collected by human bait and cattle-baited net traps on Delft Island, used as an illegal transit location by many refugees returning to the north of Sri Lanka from southern India where leishmaniasis is endemic. For species identification, genomic DNA was extracted and a fragment of the ribosomal 18S gene amplified. The sequence from all flies analysed matched that of Phlebotomus argentipes Annandale & Brunetti, the primary vector in India and the most likely vector in Sri Lanka. Independent morphological analysis also identified P. argentipes. To establish the current susceptibility status of vector species, data were obtained at the biochemical level, from which potential cross-resistance to alternative insecticides can be predicted. The Delft Island collection was assayed for the activities of four enzyme systems involved in insecticide resistance (acetylcholinesterase, non-specific carboxylesterases, glutathione-S-transferases and cytochrome p450 monooxygenases), establishing baselines against which subsequent collections can be evaluated. There was preliminary evidence for elevated esterases and altered acetylcholinesterase in this population, the first report of these resistance mechanisms in sand flies to our knowledge, which probably arose from the malathion-based spraying regimes of the Anti-Malarial Campaign.
The metabolic syndrome: the crossroads of diet and genetics
Authors: Roche Helen M. , Phillips Catherine , Gibney Michael J.
Published: July 2005

The metabolic syndrome is a very common disease associated with an increased risk of type 2 diabetes mellitus (T2DM) and CVD. The clinical characteristics of the metabolic syndrome include insulin resistance, dyslipidaemia, abdominal obesity and hypertension. The diverse clinical characteristics illustrate the complexity of the disease process, which involves several dysregulated metabolic pathways. Thus, multiple genetic targets must be involved in the pathogenesis and progression of the metabolic syndrome. Nevertheless, the human genome has not changed markedly in the last decade but the prevalence of the metabolic syndrome has increased exponentially, which illustrates the importance of gene–environmental interactions. There is good evidence that nutrition plays an important role in the development and progression of the metabolic syndrome. Indeed, obesity is a key aetiological factor in the development of the metabolic syndrome. Understanding the biological impact of gene–nutrient interactions will provide a key insight into the pathogenesis and progression of diet-related polygenic disorders, including the metabolic syndrome. The present paper will explore the interactions between genetic background and dietary exposure or nutritional therapy, focusing on the role of dietary fatty acids within the context of nutrient regulation of gene expression and individual responsiveness to dietary therapy. Only with a full understanding of gene–gene, gene–nutrient and gene–nutrient–environment interactions can the molecular basis of the metabolic syndrome be solved to minimise the adverse health effects of obesity and reduce the risk of the metabolic syndrome, and subsequent T2DM and CVD.
The role of animal nutrition in improving the nutritive value of animal-derived foods in relation to chronic disease
Authors: Givens D. I.
Published: July 2005

Foods derived from animals are an important source of nutrients in the diet; for example, milk and meat together provide about 60 and 55% of the dietary intake of Ca and protein respectively in the UK. However, certain aspects of some animal-derived foods, particularly their fat and saturated fatty acid (SFA) contents, have led to concerns that these foods substantially contribute to the risk of CVD, the metabolic syndrome and other chronic diseases. In most parts of Europe dairy products are the greatest single dietary source of SFA. The fatty acid composition of various animal-derived foods is, however, not constant and can, in many cases, be enhanced by animal nutrition. In particular, milk fat with reduced concentrations of the C12–16SFA and an increased concentration of 18:1 MUFA is achievable, although enrichment with very-long-chainn-3 PUFA is much less efficient. However, there is now evidence that some animal-derived foods (notably milk products) contain compounds that may actively promote long-term health, and research is urgently required to fully characterise the benefits associated with the consumption of these compounds and to understand how the levels in natural foods can be enhanced. It is also vital that the beneficial effects are not inadvertently destroyed in the process of reducing the concentrations of SFA. In the future the role of animal nutrition in creating foods closer to the optimum composition for long-term human health is likely to become increasingly important, but production of such foods on a scale that will substantially affect national diets will require political and financial incentives and great changes in the animal production industry.
Costly but worthless gifts facilitate courtship
Authors: Sozou Peter D , Seymour Robert M
Published: July 2005

What are the characteristics of a good courtship gift? We address this question by modelling courtship as a sequential game. This is structured as follows: the male offers a gift to a female; after observing the gift, the female decides whether or not to accept it; she then chooses whether or not to mate with the male. In one version of the game, based on human courtship, the female is uncertain about whether the male intends to stay or desert after mating. In a second version, there is no paternal care but the female is uncertain about the male's quality. The two versions of the game are shown to be mathematically equivalent. We find robust equilibrium solutions in which mating is predominantly facilitated by an ‘extravagant’ gift which is costly to the male but intrinsically worthless to the female. By being costly to the male, the gift acts as a credible signal of his intentions or quality. At the same time, its lack of intrinsic value to the female serves to deter a ‘gold-digger’, who has no intention of mating with the male, from accepting the gift. In this way, an economically inefficient gift enables mutually suitable partners to be matched.
On the performance of molecular dynamics applications on current high-end systems
Authors: Hein Joachim , Reid Fiona , Smith Lorna , Bush Ian , Guest Martyn , Sherwood Paul
Published: July 2005

The effective exploitation of current high performance computing (HPC) platforms in molecular simulation relies on the ability of the present generation of parallel molecular dynamics code to make effective utilisation of these platforms and their components, including CPUs and memory. In this paper, we investigate the efficiency and scaling of a series of popular molecular dynamics codes on the UK's national HPC resources, an IBM p690+ cluster and an SGI Altix 3700.

Focusing primarily on the
Amber
,
Dl_Poly
and
Namd
simulation codes, we demonstrate the major performance and scalability advantages that arise through a distributed, rather than a replicated data approach.