bluuebunny/crossref_metadata_2025 huggingface dataset:
Flash photolytic generation and study of p‐quinone α‐phenylmethide and p‐quinone α,α‐diphenylmethide in aqueous solution
Authors: Chang J. A. , Kresge A. J. , Zhan H.‐Q. , Zhu Y.
Published: May 2004

p‐Quinone α‐phenylmethide (7) and p‐quinone α,α‐diphenylmethide (8) were generated by flash photolytic dehydration of p‐hydroxy‐α‐phenylbenzyl alcohol (9, R1 = Ph, R2 = H) and p‐hydroxy‐α,α‐diphenylbenzyl alcohol (9, R1 = R2 = Ph) respectively, and rates of their decay were measured in aqueous perchloric acid and sodium hydroxide solutions and also as in acetic acid, biphosphate ion, tris(hydroxymethyl)methylammonium ion, ammonium ion and bicarbonate ion buffers. The rate profiles for the hydration of these quinone methides that these data provide show hydronium ion and hydroxide ion‐catalyzed regions and also ‘uncatalyzed’ water reactions, with saturation of hydronium ion catalysis in dilute solution for the diphenyl‐substituted substrate but only in concentrated acid solution for the less basic monophenyl substrate. Both substrates also give inverse hydronium ion isotope effects (kH+/kD+ < 1). These results show that the hydronium ion‐catalyzed reactions occur by rapid pre‐equilibrium protonation of the quinone methide on its carbonyl oxygen atom followed by rate‐determining capture of the benzyl‐type carbocation thus formed by water. Phenyl substitution retards the rate of hydration and also reduces the acidity constant of the quinone methide conjugate acid. The molecular basis of these substituent effects is discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Strong hydrogen bonding in chymotrypsin and other serine proteases
Authors: Frey Perry A.
Published: May 2004

The hydrogen bond linking His57‐Nδ1 and Asp102‐Oδ1 in chymotrypsin (Cht) at low pH and in transition state analogue complexes of Cht with peptide trifluoromethylketones (peptide‐TFKs) at pHs up to 12 has been assigned as a low barrier hydrogen bond (LBHB). The hydrogen bonds in these species of Cht display the physicochemical properties of LBHBs, as follows: 1) The proton NMR signals are far downfield, 18.1 ppm for Cht at low pH and 18.6–18.9 ppm for peptide‐TFK complexes. 2) The D/H fractionation factors are low, 0.3–0.4 for the peptide‐TFK complexes. 3) The deuterium and tritium isotope shifts (δD–δH, δT–δH) are negative. 4) The enthalpies of activation for solvent exchange (ΔHex) are high, 10–19 kcal mol−1. The LBHB is postulated to increase the base strength of His57 in the transition state for the nucleophilic addition of Ser195 to the peptide acyl group of a substrate. This property of His57 is displayed by His57 in the complexes of Cht with peptide‐TFKs, in which its pKa lies between 10.6 and 12 depending on the structure of the peptide. These values are optimal for an acid/base catalyst that both abstracts a proton from Ser195 in the formation of the tetrahedral intermediate and donates a proton to the leaving N‐terminal amino group in the decomposition of the tetrahedral intermediate. Strong hydrogen bonds in simple molecules can be studied in both aqueous and nonaqueous solutions, and the conditions for their existence are discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Vibrational analysis of the chorismate rearrangement: relaxed force constants, isotope effects and activation entropies calculated for reaction in vacuum, water and the active site of chorismate mutase
Authors: Ruggiero Giuseppe D. , Guy Sara J. , Martí Sergio , Moliner Vicent , Williams Ian H.
Published: May 2004

We present results derived from vibrational Hessians calculated for the reactant complex, transition structure and product complex of the rearrangement of chorismate to prephenate under different conditions. The AM1 semiempirical MO and B3LYP/6–31G* density functional methods were employed for calculations in vacuum, whereas a hybrid QM/MM method AM1/CHARMM/TIP3P was used for calculations in water and within the active site of B. subtilis chorismate mutase. Kinetic and equilibrium isotope effects and entropies of activation and reaction were investigated as a function of the increasing size of the Hessian, as the system is expanded to include not only the atoms of chorismate/prephenate itself but also an increasing number of surrounding water molecules (up to 99) or active‐site residues (up to 225 atoms). Primary 13C and 18O isotope effects are not sensitive to the size of the Hessian, but secondary 3H–C5 and 3H2–C9 effects require the inclusion of at least those atoms directly involved in hydrogen bonds to the substrate or, better, a complete first solvation shell or cage of active‐site amino acid residues. Pauling bond orders for the breaking CO and making CC bonds are remarkably similar for the transition structures in all three media. Relaxed force constants for stretching of these bonds (which allow meaningful comparisons to be made along a reaction path) give a significantly different picture of the bonding changes in the transition structures. The ratio of logarithms of kinetic and equilibrium isotope effects does not agree with measures of transition‐state structure derived from Pauling bond orders or from relaxed force constants. There is no simple relationship between kinetic isotope effects and transition‐state structure for this Claisen rearrangement. The calculated vibrational entropy of activation for the enzymic reaction agrees well with an experimental value for E. coli chorismate mutase. Vibrational entropy reduces the free energy barrier for the catalysed reaction by about 1 kJ mol−1 at 333 K. Copyright © 2004 John Wiley & Sons, Ltd.
Correlating biological activity with calculated geometric motifs in cyclolinopeptide A analogs
Authors: Zubrzak P. , Leplawy M. T. , Kowalski M. L. , Szkudlińska B. , Paneth P. , Silberring J. , Suder P. , Zabrocki J.
Published: May 2004

Three linear and three cyclic analogs of cyclolinopeptide A, with phenylalanine residues in position 8 and/or 9 replaced by N‐benzylglycine, were synthesized using the SPPS method and cyclization with TBTU reagent. The peptides were examined for their immunosuppressive activity in a lymphocyte proliferation test. In order to test the importance of the edge‐to‐face interactions between Phe8–Phe9 aromatic rings, molecular modeling studies were carried out. The results support its importance of the edge‐to‐face interactions for the biological activity of these compounds and indicate that the distance between the two rings also plays an essential role. Copyright © 2004 John Wiley & Sons, Ltd.
Hydrolysis of 2‐(p‐nitrophenoxy)tetrahydropyran: solvent and α‐deuterium secondary kinetic isotope effects and relationships with the solvolysis of simple secondary alkyl arenesulfonates and the enzyme‐catalyzed hydrolysis of glycosides
Authors: Ahmad Imran A. , Birkby Sara L. , Bullen Claire A. , Groves Patrick D. , Lankau Timm , Lee Won Heui , Maskill Howard , Miatt Peter C. , Menneer Iain D. , Shaw Katherine
Published: May 2004

The effect of solvent composition in aqueous ethanol, trifluoroethanol and hexafluoropropan‐2‐ol on the rate constant and activation parameters for the uncatalysed hydrolysis of 2‐(p‐nitrophenoxy)tetrahydropyran (1) was investigated, and the m(YOTs) value is 0.60. This appreciable but less than maximal value is in accordance with an SN1 mechanism with rate‐limiting ionization. The α‐deuterium secondary kinetic isotope effect (α‐kie) for the uncatalysed hydrolysis of 1 is 1.17 in water (46°C), 1.15 in aqueous trifluoroethanol (50% mole fraction, 70.6°C) and 1.13 in aqueous ethanol (50% mole fraction, 70.6°C). These values correspond to about 1.19 at 25°C, which is characteristic of rate‐limiting ionization in an SN1 reaction and appreciably higher than values for enzyme‐catalysed glycolysis. The α‐kie is smaller under aqueous acidic conditions (1.07, 0.1 mol dm−3 hydrochloric acid, 20.2°C) when 1 hydrolyses with acid catalysis. The previously reported α‐kie for the hydrolysis of 1 in buffered aqueous dioxan (1.063, 25°C) is now seen to correspond to acid‐catalysed hydrolysis. These new results for 1 indicate that transition structures in enzyme‐catalysed glycolyses with α‐kie values of less than about 1.15 at 25°C involve a lower degree of carbenium ion character than has hitherto been assumed. Copyright © 2004 John Wiley & Sons, Ltd.
Dual temperature‐ and pH‐sensitive hydrogels from interpenetrating networks and copolymerization of N‐isopropylacrylamide and sodium acrylate
Authors: Chen Hong , Hsieh You‐Lo
Published: May 2004

Hydrogels responsive to both temperature and pH have been synthesized in the forms of sequential interpenetrating networks (IPNs) of N‐isopropylacrylamide (NIPAAm) and sodium acrylate (SA) and compared with the crosslinked random copolymers of N‐isopropylacrylamide and SA. Whereas the stimuli‐sensitive behaviors of copolymer hydrogels were strongly dependent on the ionic SA contents, the IPN hydrogels exhibited independent swelling and thermal behaviors of each network component. The sequences and media in the synthesis of IPNs influenced the swelling capacities of the IPNs, but not the temperature or pH ranges at which the swelling changes occurred. In IPNs, a more expanded primary gel network during the synthesis of the secondary network contributed to the better swelling of the final IPNs. Both the swelling and thermal behaviors of the IPNs suggest that poly(N‐isopropylacrylamide) and poly(sodium acrylate) are phase separated regardless of their synthesis conditions. The presence of the poly(sodium acrylate) network did not influence the temperature or the extent of phase transition of the poly(N‐isopropylacrylamide) network in the IPNs, but did improve the thermal stability of the IPNs. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 3293–3301, 2004
Two‐Phase Flow Characterization by Automated Digital Image Analysis. Part 2: Application of PDIA for Sizing Sprays
Authors: Kashdan Julian T. , Shrimpton John S. , Whybrew Adam
Published: May 2004

A series of experiments were conducted in order to assess the robustness and accuracy of a recently developed digital image analysis technique (PDIA). This paper investigates the application of the PDIA technique to the sizing of relatively small fuel droplets of diameters in the range 5 to 30 μm produced by a pressure‐swirl atomizer. The measurement performance of the PDIA system has been assessed in terms of individual object diameters and also number and volume probability density functions of diameter in comparison to phase Doppler anemometry (PDA) data obtained under identical conditions. PDIA measurements revealed good agreement with spray data obtained by PDA at a measurement location 36 diameters downstream from the nozzle orifice with differences in the arithmetic mean diameter, D10 and volume mean diameter, D30 of approximately 5 and 3% respectively. The PDIA technique was shown to detect the presence of very large, predominantly non‐spherical droplets whose diameters were in excess of 100 μm. These droplets, although few in number constitute a significant proportion of the total spray volume and would have otherwise been either erroneously measured or have passed through the probe volume undetected using PDA due to non‐sphericity. Smaller objects may also be measured correctly by both methods although sensitivity to signal‐to‐noise ratio, for both methods can generate spurious and contradictory errors.
Thermal effects in stretching of Go‐like models of titin and secondary structures
Authors: Cieplak Marek , Hoang Trinh Xuan , Robbins Mark O.
Published: May 2004

The effect of temperature on mechanical unfolding of proteins is studied using a Go‐like model with a realistic contact map and Lennard–Jones contact interactions. The behavior of the I27 domain of titin and its serial repeats is contrasted to that of simple secondary structures. In all cases, thermal fluctuations accelerate the unraveling process, decreasing the unfolding force nearly linearly at low temperatures. However, differences in bonding geometry lead to different sensitivity to temperature and different changes in the unfolding pattern. Due to its special native‐state geometry, titin is much more thermally and elastically stable than the secondary structures. At low temperatures, serial repeats of titin show a parallel unfolding of all domains to an intermediate state, followed by serial unfolding of the domains. At high temperatures, all domains unfold simultaneously, and the unfolding distance decreases monotonically with the contact order, that is, the sequence distance between the amino acids that form the native contact. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Absence of kinetic thermal stabilization in a hyperthermophile rubredoxin indicated by 40 microsecond folding in the presence of irreversible denaturation
Authors: LeMaster David M. , Tang Jianzhong , Hernández Griselda
Published: May 2004

The striking kinetic stability of many proteins derived from hyperthermophilic organisms has led to the proposal that such stability may result from a heightened activation barrier for unfolding independent of a corresponding increase in the thermodynamic stability. This in turn implies a corresponding retardation of the folding reaction. A commonly cited model for kinetic thermal stabilization is the rubredoxin fromPyrococcus furiosus(Pf), which exhibits an irreversible denaturation lifetime at 100°C of nearly a week. Utilizing protein resonances shifted well outside of the random coil chemical shift envelope, nuclear magnetic resonance (NMR) chemical exchange measurements onPfrubredoxin as well as on the mesophileClostridium pasteurianum(Cp) rubredoxin demonstrate reversible thermal transition temperatures of 144°C (137°C for the N‐terminal modified A2K variant) and 104°C, respectively, with similar (un)folding rates of ≈25,000 s−1, only modestly slower than the diffusion controlled rate. The absence of a substantial activation barrier to rubredoxin folding as well as the similar folding kinetics of the mesophile protein indicate that kinetic stabilization has not been utilized by the hyperthermophile rubredoxin in achieving its extreme thermal stability. The two‐state folding kinetics observed forPfrubredoxin contradict a previous assertion of multiphasic folding based on hydrogen exchange data extrapolated to an estimated midpoint of transition temperature (Tm) of nearly 200°C. This discrepancy is resolved by the observation that the base‐catalyzed hydrogen exchange of the model dipeptide (N‐acetyl‐L‐cysteine‐N‐methylamide)4‐Cd2+is 23‐fold slower than that of the free cysteine model dipeptide used to normalize thePfrubredoxin hydrogen exchange data. Proteins 2004. © 2004 Wiley‐Liss, Inc.
The protective effect of film metallization against oxidative deterioration and discoloration of sensitive foods
Authors: Piergiovanni L. , Limbo S.
Published: May 2004

The importance of the optical properties of packaging materials is often underestimated and little attention is generally given to the shelf‐life of light‐sensitive food products. In this paper, the effects of the light barrier of different metallized films in delaying chemical degradative reactions, which occur in dry lasagna made with eggs and spinach, were investigated. The array of films evaluated in the experiment accounted for a large distribution of optical properties. Pouches prepared from the different films were filled with dry lasagna and stored at room temperature for about 4 months under a fluorescent light source. Sensory evaluations, CIE‐L*, a*, b* colour measurements and hexanal formation were evaluated during storage. The shelf‐life of lasagna packed in metallized films was 2.5 times greater than the same product packed in non‐metallized films. A correlation between transmittance values of the packaging films and shelf‐life reduction was obtained. Because of the fat and the pigments of lasagna and also its shape (large surface area), lasagna seems to be a good model system when studying the protective performance of packaging materials against degradative reactions that involve oxygen and are very sensitive to light exposure. Copyright © 2004 John Wiley & Sons, Ltd.
The evolution of methods for female sterilization
Authors: Wilson E.W.
Published: May 2004

Methods for the sterilization of women by occlusion of the Fallopian tubes have evolved by changes in the approaches to the tubes and trials of various methods for occluding the tubal lumen. Approaches to the tube have included: the anterior abdominal wall routes by laparotomy, minilaparotomy and laparoscopy; a vaginal approach through the posterior vaginal fornix; and transcervical approaches, either blind, or via the hysteroscope. Methods for obtaining tubal occlusion have included: excision and suture techniques; electrocautery; clips and rings; intratubal occlusive devices and chemicals introduced into the tubal lumen. The development of each of the approaches to the tube and of the methods for obtaining tubal occlusion are discussed.
Specifications for new technologies for female sterilization for use in developing countries
Authors: Dusitsin N.
Published: May 2004

The difficulties in providing readily accessible sterilization services for women in rural settings in developing countries are described; they include: problems with personnel; problems with training; anesthesia difficulties; and cost. For a new method of sterilization to be useful in such situations several criteria concerned with overcoming the perceived problems must be met. Any new procedure should be simple, easily learned, capable of being completed with a single visit, and should require only local anesthesia.
Postmenopausal hormone therapy into the 21st century
Authors: Speroff L.
Published: May 2004

At the time of the menopause, a review of the major health issues can be especially rewarding. Besides the general issues of good health, particular attention is now being focused on prevention of cardiovascular disease and osteoporosis because of the potentially beneficial effects of postmenopausal hormone therapy. Hormone therapy should be offered to most women as they consider their paths for successful aging. However, as for any pharmacological intervention, the benefits of treatment must outweigh the risk. The available data would appear to indicate that, for most women, this is in fact the case with current research into future hormonal therapies aimed at further improving the benefit:risk ratio.
HRT and the risk of deep vein thrombosis
Authors: Barlow D.H.
Published: May 2004

Venous thromboembolism (VTE) has long been recognized as a risk of oral contraceptive use in women, but until recently hormone replacement therapy (HRT) was not thought to be associated with a similar risk; the epidemiological literature having been reassuring. The recent publication of four independent epidemiological studies has changed our perspective on VTE risk on HRT. These studies suggest that the risk of VTE may be increased by up to three‐fold during HRT. However, the absolute risk remains low at approximately one occurrence in 5000 woman‐years and appears greatest in the early years of HRT use. However, given that mortality from VTE is low, it seems unlikely that these new findings will substantially change the overall balance of benefits and risks associated with long‐term HRT.
POPULAR ICONOCLASM AND THE POLITICS OF THE PARISH IN EASTERN ENGLAND, 1640–1642
Authors: WALTER JOHN
Published: May 2004

This article explores the extent of popular iconoclasm in England in the period immediately before the start of civil war and for a region – eastern England – thought to lie at the heart of these events. It explores systematically the evidence for the extent of destruction (and the problems in its recording and recovery), the nature of the targets attacked, and the identities of the iconoclasts. The article argues that this first phase of iconoclasm was directed largely against Laudian innovations. Claiming an agency to police sacred space, iconoclasts derived legitimation from the public condemnation of Laudianism in parliament, print, and pulpit. Narrowing the focus, the article moves on to explore the occurrence of iconoclasm through a series of case studies of the complex process of conflict and negotiation within the politics of the parish that preceded, accompanied, and sometimes pre-empted popular destruction. The evidence of iconoclasm is used to show how the implementation of the Laudian programme might politicize local churches as sites of conflict and the potential therefore inherent in its aggressive enforcement for a wider political conflict.
NETWORKING: TRADE AND EXCHANGE IN THE EIGHTEENTH-CENTURY BRITISH EMPIRE
Authors: GLAISYER NATASHA
Published: May 2004

Historians face the problem of how to write the history of the eighteenth-century British empire. How can the history of Britain and the history of its empire be brought together? Recent research has demonstrated the value of employing the idea of networks to describe the interrelatedness of empire. In the history of science and economic history such a notion has been quite thoroughly articulated, particularly in relation to the exchange of botanical knowledge and the transaction of goods. Here it is argued that conceiving of empire as a set of networks through which knowledge and ideas were exchanged, trust was negotiated, goods were traded, and people travelled is an avenue worth pursuing in the project to write the history of the eighteenth-century British empire.
Mapping seabed biotopes at Hastings Shingle Bank, eastern English Channel. Part 1. Assessment using sidescan sonar
Authors: Brown Craig J. , Hewer Alison J. , Meadows William J. , Limpenny David S. , Cooper Keith M. , Rees Hubert L.
Published: May 2004

A multi-technique approach was used to map the spatial distribution of seabed biotopes (i.e. physical habitats and their associated benthic assemblages) in the vicinity of Hastings Shingle Bank in the eastern English Channel, part of which is licensed for the extraction of marine aggregates for the construction industry. An area of seabed, approximately 12×4 km in size, was surveyed using a high-resolution sidescan sonar system, and a mosaic of the output was produced, covering 100% of the survey area. The area was then divided into acoustically distinct regions based on the sidescan sonar data, and the benthic communities and sediment types within each of the regions were ground-truthed using a Hamon grab fitted with a video camera, and using a heavy duty 2-m beam trawl. Additional information concerning the seabed was obtained through the application of video and photographic techniques. Sediments within the survey area ranged from cobbles and coarse gravels on the Shingle Bank, to various grades of sands to the north and south. Analysis of faunal data revealed the presence of statistically distinct biological assemblages within each acoustic region. Using all available data, four discrete biotopes were identified and their spatial distribution mapped across the survey area.
The spatial distribution of plankton communities in a Slope Water anticyclonic Oceanic eDDY (SWODDY) in the southern Bay of Biscay
Authors: Fernández Emilio , Álvarez Florentina , Anadón Ricardo , Barquero Susana , Bode Antonio , García Ana , García-Soto Carlos , Gil Julio , González Nicolás , Iriarte Arantza , Mouriño Beatriz , Rodríguez Francisco , Sánchez Ricardo , Teira Eva , Torres Silvia , Valdés Luis , Varela Manuel , Varela Ramiro , Zapata Manuel
Published: May 2004

Slope Water anticyclonic Oceanic eDDIES (SWODDIES) are typical mesoscale features of open-ocean waters of the southern Bay of Biscay which usually develop in winter by shedding from the seasonal poleward current flowing along the northern Spanish slope. These eddies have been intensively studied from the physical perspective. However, their effect on the distribution of biological properties and on the functioning of the pelagic ecosystem has not been assessed so far. To this aim, a sea-truth, multidisciplinary and comprehensive study of a SWODDY was carried out in summer 1998. The eddy, radius of ≈50 km, was initially centred at 45·5°N 6·0°W, being characterized by a relatively homogeneous core of water in the centre of the eddy extending from 80 to about 200 dbar. In the central region of the core, temperature (12·55–12·75°C) and salinity (≈35·70) values were higher than outside the eddy. The optical properties of the eddy also differed from those of the surrounding waters. A distinct biological signature was found associated with the eddy. Depth-integrated chlorophyll-a concentrations were 25% higher at the eddy centre where upward doming of the seasonal pycnocline (up to 30 dbar) occurred. Enhanced phytoplankton biomass was related to a higher contribution of >10 μm cells, mainly represented by diatoms and chrysophyceans. Phytoplankton and mesozooplankton species composition in and outside the eddy differed significantly reflecting the coastal origin of the water parcel trapped by the eddy. The sharp modification of the planktonic community composition, biomass and associated size-structure caused by slope water oceanic eddies are likely to exert a significant effect upon the upper trophic levels of the pelagic ecosystem of the southern Bay of Biscay.
Spatio-temporal changes of the near-bottom mesozooplankton from the English Channel
Authors: Vallet Carole , Dauvin Jean-Claude
Published: May 2004

The near-bottom mesozooplankton was caught by a four net suprabenthic sledge on six sites in the English Channel during both spring and autumn. Taxa richness showed no significant difference between seasons, nevertheless diversity (H′), evenness (J) and normalized rarefaction number of taxa E(S91) were higher in autumn than in spring at each site except at Site 2 offshore Plymouth, where Calanus helgolandicus dominated at both seasons. Copepods dominated in abundance at each site in spring while crustacean larvae were dominant in autumn except at Site 2 offshore Plymouth, where copepods remained dominant and, at Site 6 in the Dover Strait, where no significant difference occurred between copepod and crustacean larvae abundances. Four assemblages were distinguished depending on the season. Abundance was higher during the day than at night as a result of a mesozooplankton concentration in the near-bottom layer during the daytime. Moreover, three vertical patterns of suprabenthic mesozooplankton were identified according to their distribution above the near-bottom layer: taxa distributed homogeneously in the four nets; taxa concentrated in nets 2 and 4, and taxa concentrated in the three upper nets.
Benthic assemblages in two Mediterranean caves: species diversity and coverage as a function of abiotic parameters and geographic distance
Authors: Martí Ruth , Uriz Maria J. , Ballesteros Enric , Turon Xavier
Published: May 2004

Benthic assemblages of two Mediterranean submarine caves were compared. Species coverage and number of species were lower in internal (dark) communities than external. This feature was specially marked in the less illuminated cave. Ordination analyses performed on species coverage per community for each cave separately, distinguished several benthic communities from the outermost to the innermost zone of each cave. Cluster analyses on species coverage, taking into account all communities in both the caves, established similarities among communities: algal-dominated communities clustered according to the level of light received independently of the cave they inhabited, while animal-dominated communities were more similar within each cave than between the caves. Moreover, among the abiotic parameters measured irradiance was the only factor that clearly diminished from the entrance to the innermost zone in both the caves. In contrast, water movement and particulate organic matter varied differently in each cave. Results indicate that the different topography, depth and geographic location of the two caves determine water movement, light penetration and nutrient availability along the caves. These factors are responsible for determining species abundance and diversity, as well as species growth habit in each community.
Diel changes in vertical distribution of copepods community in Tanabe Bay, Japan
Authors: Shimode Shinji , Shirayama Yoshihisa
Published: May 2004

Diel vertical migration (DVM) and distributional patterns of copepods collected in the water column at shallow water site (Station M) in Tanabe Bay, Japan were investigated. Twenty-one taxa of zooplankton and 48 species of copepods at Station M had positive ΔZ values (subtraction of night-time weighted mean depth from daytime value) and performed normal DVM. The highest ΔZ value was 4·3 observed in Ambunguipes rufocincta. Three taxa and 39 species collected only at night also had high WMD (weighted mean depth) values (4·0∼7·5), which were previously considered hyperbenthic species. Statistically significant differences were found only in Myodocopina spp., Calocalanus plumulosus and Clausocalanus spp. Myodocopina spp. and Clausocalanus spp. showed downward migration at low to high and high tidal phases. Calocalanus plumulosus and some copepods performed downward migration during high and high to low tidal phases. Four distributional patterns of copepod species in Tanabe Bay were found. The groups are as follows: (A) true planktonic group; (B) swarming and night emerging group; (C) night emerging meiobenthic and hyperbenthic group; (D) symbiotic and night emerging group.
Abundances of Metridia lucens in the western Irish Sea
Authors: Rowlands William Ll. , Dickey-Collas Mark , Geffen Audrey J. , Nash Richard D.M.
Published: May 2004

Interannual and spatial differences in the abundance of Metridia lucens are reported from the Irish Sea from 1996 to 2001. In most years the abundance in spring is very low (<50 m2), however in 2001 the abundance was high and this enabled a rare study of the vertical distribution of M. lucens in coastal waters. The vertical distribution differs with time of day and water column structure. Abundances were always higher in stratified deeper waters compared with mixed or coastal waters.
Occurrence of the epizoic barnacle Octolasmis angulata on the crab Charybdis feriatus from Daya Bay, China
Authors: Yan Yan , Huang Liangmin , Miao Suying
Published: May 2004

This is the first record of the epizoic barnacle (Octolasmis angulata) on the crab Charybdis feriatus. Prevalence of O. angulata was 85·7% and mean intensity of infestation was 59±64·5 (range 3–239). Prevalence and mean intensity of infestation increased with host size in the range 55–120 mm carapace width. Barnacles occurred most frequently on the gills, anterior branchial chamber wall in the epibranchial space, occasionally on the wall of the branchial chambers beneath the gills and on the scaphognathite within the branchial chambers. Most barnacles were observed on the hypobranchial surface of the gills.
The impact of two species of bioturbating shrimp (Callianassa subterranea and Upogebia deltaura) on sediment denitrification
Authors: Howe Rebecca L. , Rees Andrew P. , Widdicombe Stephen
Published: May 2004

In a benthic mesocosm experiment, the effects of two species of burrowing Thalassinidean shrimps (Callianassa subterranea and Upogebia deltaura) on rates of sediment denitrification were determined using the isotope pairing technique. Denitrification rate (Dtot) and coupled nitrification–denitrification (Dn) were shown to be significantly enhanced by the presence of U. deltaura by 2·9 and 3·3 times respectively, relative to control measurements. For U. deltaura the stimulation of the denitrification rate was found to be significantly related to the size of the animal (F=5·81, P=0·042). No deviation from the rates determined in control cores for either Dtot or Dn was observed for those cores inhabited by C. subterranea. The increase in Dtot with U. deltaura was considered to be the result of a combination of different factors, including; the direct extension of the sediment–water interface and an increase in oxygenation of the sediments and solute transport, as a result of the ventilating activities of the animal itself.
Selective resorption in nutritive phagocytes of the sea urchin Anthocidaris crassispina
Authors: Reunov Arkadiy A. , Kalachev Alexander V. , Yurchenko Olga V. , Au Doris W.T.
Published: May 2004

Phagocytic resorption during spermatogenesis was studied in the sea urchin Anthocidaris crassispina. Nutritive phagocytes in gonad absorbed both waste sperm cells and residual bodies discarded from maturing spermatids, and these materials were subsequently compartmented in heterophagosomes. Based on 180 heterophagosomes examined by transmission electron microscopy, over 99% of heterophagosomes contained either residual bodies or sperm cells only. Simultaneous resorption of sperm cells and residual bodies in a heterophagosome was uncommon, with only ∼0.56% occurrence, suggesting that heterophagosomes have a selective resorption ability in nutritive phagocytes.
Investigations of oocyte in vitro maturation within a mouse model
Authors: Heng Boon Chin Alexis , Chye Ng Soon
Published: May 2004

This study attempted to develop a ‘less meiotically competent’ murine model for oocyte in vitro maturation (IVM), which could more readily be extrapolated to human clinical assisted reproduction. Oocyte meiotic competence was drastically reduced upon shortening the standard duration of in vivo gonadotrophin stimulation from 48 h to 24 h, and by selecting only naked or partially naked germinal vesicle oocytes, instead of fully cumulus enclosed oocyte complexes. With such a less meiotically competent model, only porcine granulosa coculture significantly enhanced the oocyte maturation rate in vitro, whereas no significant enhancement was observed with macaque and murine granulosa coculture. Increased serum concentrations and the supplementation of gonadotrophins, follicular fluid and extracellular matrix gel within the culture medium did not enhance IVM under either cell-free or coculture conditions. Culture medium conditioned by porcine granulosa also enhanced the maturation rate, and this beneficial effect was not diminished upon freeze–thawing. Enhanced IVM in the presence of porcine granulosa coculture did not, however, translate into improved developmental competence, as assessed by in vitro fertilization and embryo culture to the blastocyst stage.
Patterns of expression of cyclins A, B1, D, E and cdk 2 in preimplantation mouse embryos
Authors: Waclaw Ronald R. , Chatot Clare L.
Published: May 2004

Cell cycle regulatory proteins have been characterized in somatic cells and exhibit phase-specific expression patterns. Changes in expression of these regulatory proteins have not been clearly characterized in early preimplantation mouse embryos. This study utilized indirect immunofluorescence to determine the expression pattern of G1/S phase cyclins D and E; S, G2/M phase cyclins A and B1, and cdk 2 during the first three cell cycles of mouse embryo development. Cyclin D demonstrated low expression throughout the first cell cycle but had a somatic-like pattern of expression in cycles 2 and 3 with peak expression at G1 declining through S phase to a low during G2. Cyclin E was present at peak levels in G1 declining through S to a low in G2 during both the first and third cell cycles, but remained at moderate levels during the entire second cell cycle. Cyclin A was maintained at moderate levels throughout the first two cell cycles but showed a somatic-like pattern with a low level in G1 increasing during S phase with peak levels during G2 of the third cell cycle. Cyclin B consistently demonstrated a pattern opposite to a somatic G2/M cyclin, with peak levels in G1 declining through S phase to a low in G2 during each of the three cell cycles examined. Cdk 2 was present at consistent levels during G1 and S phases of all three cell cycles declining slightly in G2.
Estrogen receptor β localization in the lizard (Podarcis s. sicula) testis
Authors: Chieffi Paolo , Varriale Bruno
Published: May 2004

There is increasing evidence that 17β-estradiol is necessary for normal male fertility. The aim of the present study was to characterize estrogen receptor β (ERβ) expression in a non-mammalian vertebrate model, the lizard (Podarcis s. sicula) testis. Immunocytochemical analysis shows that ERβ proteins are present among germ cells in the nucleus of the spermatogonia, in primary spermatocytes and spermatids. Western blot analysis with antibodies against the ERβ gene product revealed an isoform with a specific weight of 55 kDa. In conclusion, the widespread expression of ERβ in the Podarcis s. sicula testis is consistent with a role for estrogens in modulating spermatogenesis in the male.
Juvenile Sandhoff disease—Nine new cases and a review of the literature
Authors: Hendriksz C. J. , Corry P. C. , Wraith J. E. , Besley G. T. N. , Cooper A. , Ferrie C. D.
Published: May 2004

Summary: Juvenile Sandhoff disease (McKusick 268800) is a rare lysosomal storage disorder with only 12 cases recorded in the literature. This condition is also referred to as the subacute form of hexosaminidase deficiency. We describe 9 new cases of Pakistani origin and compare these with the other published cases. Ataxia and speech abnormalities were the commonest presentation. Constipation and urinary incontinence were frequent and may be due to autonomic neuropathy. Cherry‐red spot was not noted in any of our cases. Increased lower limb reflexes were the commonest physical finding. Significant delay in diagnosis may be due to the nonspecific presentation of this condition. Diagnosis was on the basis of hexosaminidase deficiency. Residual enzyme activity did not correlate with the clinical picture. Emerging therapies make early diagnosis of this disorder important.
Low‐protein diet and progression of retinal degeneration in gyrate atrophy of the choroid and retina: A twenty‐six‐year follow‐up
Authors: Santinelli R. , Costagliola C. , Tolone C. , D'Aloia A. , D'Avanzo A. , Prisco F. , Perrone L. , del Giudice E. Miraglia
Published: May 2004

Summary: Gyrate atrophy of the choroid and retina is an autosomal recessive chorioretinal dystrophy which leads to a slowly progressive loss of vision. The primary defect is due to a deficiency of the enzyme ornithine δ‐aminotransferase, which is responsible for markedly elevated levels of ornithine in plasma and other body fluids. Although several therapeutic regimens have been proposed, the reduction in ornithine accumulation obtained by reducing the intake of its precursor arginine (semisynthetic low‐arginine diet) is the one most practised. In this clinical and molecular study we report a patient with hyperornithinaemia and gyrate atrophy of the choroid and retina who had been diagnosed when she was 3 years 9 months old. She also presented mild mental retardation, delayed language development and speech defects. The patient has recently been found to be homozygous for the new Gly91Arg amino acid substitution of the enzyme ornithine δ‐aminotransferase. This mutation lies in a region of the mature protein that is considered crucial for the mitochondrial targeting activity. In this patient, a 28‐year treatment with a completely natural low‐protein diet (0.8 g/kg per day of natural protein) has been able to significantly reduce ornithine plasma levels, and to greatly delay the natural progression of the chorioretinal changes. This study suggests that, in the long‐term treatment of gyrate atrophy, the efficacy in slowing the progression of chorioretinal changes and the palatability of a completely natural low‐protein diet make this treatment a potentially viable alternative in patients refusing the semisynthetic diet.
Discordant PKU phenotype in one family due to disparate genotypes and a novel mutation
Authors: Johnston J. J. , Lichter‐Konecki U. , Wilson E. , Cobb B. R. , Evans B. M. , Schnur R. E. , Wong L ‐J. C.
Published: May 2004

Summary: Classical phenylketonuria (PKU) and mild hyperphenylalaninaemia (MHP) are two ends of the broad diagnostic spectrum in phenylalanine hydroxylase (PAH) deficiency. We have analysed a family in which classical PKU, MHP and a normal phenotype occurred in family members with different mutations. Sequence analysis revealed three mutations segregating in the family. The individual with classical PKU had two previously reported deleterious mutations. A third novel mutation was identified in the other two individuals. This report demonstrates that when discordant phenotypes occur in a family, without protein loading or phenylalanine tolerance test, complete analysis of the PAH gene may be performed in order to support the diagnosis and assist in accurate genetic counselling and patient management.
Impacts of atmospheric variability on a coupled upper‐ocean/ecosystem model of the subarctic Northeast Pacific
Authors: Monahan Adam Hugh , Denman Kenneth L.
Published: May 2004

The biologically‐mediated flux of carbon from the upper ocean to below the permanent thermocline (the biological pump) is estimated to be ∼10 PgC/yr [Houghton et al., 2001], and plays an important role in the global carbon cycle. A detailed quantitative understanding of the dynamics of the biological pump is therefore important, particularly in terms of its potential sensitivity to climate change and its role in this change via feedback processes. Previous studies of coupled upper‐ocean/planktonic ecosystem dynamics have considered models forced by observed atmospheric variability or by smooth annual and diurnal cycles. The second approach has the drawback that environmental variability is ubiquitous in the climate system, and may have a nontrivial impact on the (nonlinear) dynamics of the system, while the first approach is limited by the fact that observed time series are generally too short to obtain statistically robust characterizations of variability in the system. In the present study, an empirical stochastic model of high‐frequency atmospheric variability (with a decorrelation timescale of less than a week) is estimated from long‐term observations at Ocean Station Papa in the northeast subarctic Pacific. This empirical model, the second‐order statistics of which resemble those of the observations to a good approximation, is used to produce very long (1000‐year) realizations of atmospheric variability which are used to drive a coupled upper‐ocean/ecosystem model. It is found that fluctuations in atmospheric forcing do not have an essential qualitative impact on most aspects of the dynamics of the ecosystem when primary production is limited by the availability of iron, although pronounced interannual variability in diatom abundance is simulated (even in the absence of episodic iron fertilization). In contrast, the impacts of atmospheric variability are considerably more significant when phytoplankton growth is limited in the summer by nitrogen availability, as observed closer to the North American coast. Furthermore, the high‐frequency variability in atmospheric forcing is associated with regions in parameter space in which the system alternates between iron and nitrogen limitation on interannual to interdecadal timescales. Both the mean and variability of export production are found to be significantly larger in the nitrogen‐limited regime than in the iron‐limited regime.
Relationship between Measurements of Pollution in the Troposphere (MOPITT) and in situ observations of CO based on a large‐scale feature sampled during TRACE‐P
Authors: Crawford J. H. , Heald C. L. , Fuelberg H. E. , Morse D. M. , Sachse G. W. , Emmons L. K. , Gille J. C. , Edward D. P. , Deeter M. N. , Chen G. , Olson J. R. , Connors V. S. , Kittaka C. , Hamlin A. J.
Published: May 2004

During Transport and Chemical Evolution over the Pacific (TRACE‐P), there were several opportunities to perform in situ sampling coincident with overpasses of the Measurements of Pollution in the Troposphere (MOPITT) instrument on board the EOS Terra satellite. This sampling consisted of in situ vertical profiles of CO by NASA's DC‐8 aircraft intended to provide data useful for validating MOPITT observations of CO column. One particular profile conducted over the central North Pacific revealed a layer of pollution characterized by CO mixing ratios more than double background values. Sampling of the surrounding region by both the NASA DC‐8 and P‐3B aircraft showed this layer to have a considerable geographic extent, at least 25° longitude (∼2500 km) and 4° latitude (∼400 km). Using back trajectory analysis, this polluted layer is followed back in time and compared with four consecutive MOPITT overpasses. MOPITT observations during these four overpasses agree well with the location of the layer as inferred by the trajectories; however, the detected CO column amount increases backward in time by just over 20%. Further analysis shows that the majority of this change in detected column abundance is consistent with two factors: (1) changes in the thickness of the polluted layer over time (9 ± 3%) and (2) changes in retrieved column abundance due to the altitude of the layer (7 ± 3%). This demonstrates that there are both real and artificial sources of variability that must be understood before MOPITT observations can be quantitatively useful. An unexpected finding was the difference in the variance of MOPITT observations depending on whether observations were taken under daylight or nighttime conditions. The variance in daytime observations of the polluted layer was approximately double that for nighttime data. The results of this analysis indicate that targeted in situ sampling of large‐scale pollution events can provide insight leading to more realistic interpretation of MOPITT observations. Strategies for sampling such events repeatedly during their evolution could also provide more interesting opportunities for validation.
Using ionospheric scintillation observations for studying the morphology of equatorial ionospheric bubbles
Authors: Dandekar B. S. , Groves K. M.
Published: May 2004

For a study of the equatorial ionosphere, ionospheric scintillation data at VHF and L‐band frequencies have been routinely collected by ground‐based receivers at Ancon, Peru, Antofagasta, Chile, and Ascension Island, UK, since May 1994. The receivers routinely monitor VHF transmissions from two geosynchronous satellites located at 100°W longitude and 23°W longitude, and L‐band signals from satellites located at 75°W longitude and 15°W longitude. This combination provides a network of seven usable, reasonably separated links for monitoring ionospheric equatorial bubble activity in the South American longitude sector. A data set of seven years covering the period from 1995 to 2001 was studied to determine the temporal, diurnal, and seasonal behavior of equatorial bubbles. The results of our statistical study are presented here. In general the equatorial ionospheric bubble activity shows a strong systematic and primary dependence in temporal, diurnal, and seasonal variation, and a secondary weak dependence on geomagnetic and solar flux activity. At present, the dependence on solar and magnetic activity is not usable for near‐time and short‐term prediction of the equatorial bubble activity. Equatorial bubbles usually start 1 hour after sunset, the activity peaks before local midnight, and vanishes by early morning. The activity peaks in the months of November and January–February and is practically absent (weak) from May to August. On a daily basis on the average one sees 1 to 3 bubbles. The duration of bubbles is about 70 min, and the time spacing between the bubbles is 1 to 2 hours. The bubble activity in general follows the phase of solar cycle activity. The observed systematic behavior of the equatorial bubbles allows for a now cast and short‐term forecast of the bubble activity in the South American sector.