bluuebunny/crossref_metadata_2025 huggingface dataset:
THE BROAD APPLICATION OF A DEPTH INVERSION ALGORITHM BASED ON THE DYNAMIC MODE DECOMPOSITION
Authors: Gawehn Matthijs , Vries Sierd de , Aarninkhof Stefan
Published: January 2021

The technological boost of drones and satellites offers new and more flexible platforms for video-based depth inversion. It signals a desire to generate depth estimates on-the-fly, requiring more flexibility and high computational speeds. For this purpose, a novel algorithm was developed, which is based on the Dynamic Mode Decomposition. The analysis of video from three different field-sites in the Netherlands, Australia and US, suggests that 32 s of video are sufficient to correctly capture the significant wave components in the wave-field. It means that DMD-based depth inversion is suited for fast coastal reconnaissance.Recorded Presentation from the vICCE (YouTube Link): https://youtu.be/TcE13C1oTKw
CHALLENGES OF BOUNDARY CONDITIONS IN OPEN OCEAN MODELS
Authors: Herold Judith , Lemont Eric , Bettington Stuart , Couriel Edward
Published: January 2021

The development and calibration of coastal numerical models to support engineering design and environmental impact studies is a challenging process and one that requires professional judgement and continual assessment of all aspects of the model makeup. Fundamental to the integrity of the model are appropriate boundary conditions and quality observational data for calibration. Open ocean boundary conditions are typically the most complex and important aspect of a model build. They represent the influence of dynamics occurring beyond the model extent, bridging large-scale dynamics to the small-scale processes in the model. This study discusses the challenges of open ocean boundaries and how we utilised data to achieve an effective model.Recorded Presentation from the vICCE (YouTube Link): https://youtu.be/evL7f_17wZg
NUMERICAL EXPERIMENTS ON RESONANT WAVE AMPLIFICATION OVER A FRINGING REEF
Authors: Lasserre Camila Gaido , Tissier Marion , Reniers Ad , Pearson Stuart , Bricker Jeremy
Published: January 2021

Waves are important drivers for reef hydrodynamics, and therefore strongly contribute to flooding over reef-lined coasts. While high-frequency waves are largely dissipated when they propagate over the reef flat due to breaking and friction, low-frequency (LF) waves are generally able to reach the back-reef beach. There, they can reflect and form (quasi-) standing wave patterns, which under resonant conditions can lead to disproportionally high run-up on the beach (e.g., Pequignet et al., 2009; Gawehn et al., 2016). The probability of this phenomenon is expected to increase due to sea-level rise (e.g., Pequignet et al., 2009). In this study, we numerically investigate long wave resonance and the processes enhancing or limiting the resonant amplification of long waves over the reef flat. Besides the role of frictional dissipation (e.g., Pomeroy et al. 2012), we investigate how the nonlinear transformation of long waves influences the amplification rate.Recorded Presentation from the vICCE (YouTube Link): https://youtu.be/caZcI8YYs0I
TRANSIENT DAM-BREAK WAVE LOADING ON PIPELINES NEAR SLOPING BED
Authors: Ghodoosipour Behnaz , Takabatake Tomoyuki , Nistor Ioan , Mohammadian Majid , Hamano Go , Ishii Hidenori , Imura Kotaro , Shibayama Tomoya
Published: January 2021

Extreme events such as tsunamis and floods have caused massive damaging consequences to nearshore infrastructures. This has been more significant recently due to a changing climate. Transmission pipelines are among such infrastructures and need to be protected against potential extreme events. Design of pipelines requires comprehensive understanding of the exerting hydrodynamic forces. Such pipelines are often placed on sloping beds in coastal areas. Therefore, to address the uncertainties and parameters involved in extreme hydrodynamic loading on pipelines near sloping bed, an experimental program was conducted at the hydraulic laboratory in WASEDA University, Tokyo, Japan. This study is a complement of another experimental research conducted by Ghodoosipour et al., 2019a and b to investigate loadings from tsunami-like dam-break waves on pipelines located on flat bed.Recorded Presentation from the vICCE (YouTube Link): https://youtu.be/y6nSfe34SAw
NUMERICAL SIMULATION OF WAVE-DRIVEN FLOWS ON A MORPHOLOGICALLY EVOLVING BEACH
Authors: Marmoush Ramy , Mulligan Ryan
Published: January 2021

Wave-driven flows in the nearshore zone are responsible for the erosion and transport of beach sediments, causing a continuous cycle of bathymetric change that is linked with changes to wave transformation and nearshore hydrodynamics. Numerical models have been used to investigate the evolving nearshore wave field corresponding to beach morphology change in field studies (e.g., Ruiz de Alegria-Arzaburu et al., 2013). In the present study, the non-hydrostatic wave-flow SWASH model (Zijlema et al., 2011) is applied to five laboratory cases to investigate the change in wave and flow fields corresponding to evolving beach morphology during a simulated storm event.Recorded Presentation from the vICCE (YouTube Link): https://youtu.be/LZQQuuiqsPY
WAVE AND SEAFLOOR SPECTRA PREDICTIONS WITH THE COUPLED SWAN-NSEA MODELING SYSTEM
Authors: Penko Allison , Rogers Erick , Calantoni Joseph
Published: January 2021

The existence and evolution of bedforms on the seafloor have significant effects in the areas of oceanography, marine geophysics, and underwater acoustics including the transport of sediment, wave energy attenuation, and seabed sonar scattering and penetration. Here, we present a wave-seafloor modeling system that couples a spectral seafloor boundary layer model (NSEA) with an operational wave model (SWAN) that includes the dynamic feedback between the predicted wave spectra and the wave generated bedforms on the seafloor through a bottom roughness parameter. NSEA is a seafloor spectral model that uses hydrodynamic input forcing forecasted by the wave model SWAN to predict the evolving seafloor spectra given a sediment grain diameter and an estimation of the biologic activity. The system can be used to determine the spatially and temporally varying bottom roughness under given wave forcing important for coastal morphology and acoustic applications.Recorded Presentation from the vICCE (YouTube Link): https://youtu.be/u66k6lZbEbw
NONHYDROSTATIC MODELING OF FLOW INTERACTIONS WITH HIGHLY FLEXIBLE VEGETATION
Authors: Tahvildari Navid , Familkhalili Ramin , Ma Gangfeng
Published: January 2021

Improving our understanding of the interactions between gravity waves, currents, and coastal vegetation, which are nonlinear in nature, enables coastal engineers and managers to better estimate hydrodynamic forces on coastal infrastructure and utilize natural elements to mitigate their impacts. Aquatic vegetation is ubiquitous in coastal waters and it is well-known that flow loses energy over vegetation. Computational modeling of wave-vegetation interaction has been the subject of numerous recent studies and many improvements have been achieved in reducing limitations applied on wave and vegetation behavior in these models. Mechanisms for highly flexible vegetation have been incorporated in a Boussinesq-type model and Reynolds-Averaged Navier-Stokes (RANS) models. Flow dynamics over flexible vegetation and vegetation dynamics in response to hydrodynamic forcing are important for predicting wave and surge dissipation by vegetation, storm impacts on vegetation canopies, ecological processes, and sediment transport in estuaries, and require further investigation. In this study, we implement a numerical model for highly flexible vegetation in an open-source RANS model NHWAVE to address some of these questions.Recorded Presentation from the vICCE (YouTube Link): https://youtu.be/oAwb8nu4RSs
BOUSSINESQ MODELING OF COMBINED STORM SURGE AND WAVES OVER WETLANDS FORCED BY WIND
Authors: Chen Qin , Zhu Ling , Shi Fengyan , Brandt Steve
Published: January 2021

Coastal wetlands protect the shoreline and infrastructure by attenuating wind waves and reducing storm surge. It is of importance to accurately quantify the flood protection provided by vegetation. Existing numerical models for hurricane waves and storm surge are based on the phase-averaged wave action balance equation and the nonlinear shallow water equations, respectively, with the wind forcing and vegetal drag as the free surface and bottom boundary conditions. To consider the interaction of waves and surge, the phase-averaged short wave and long wave (storm surge) models can be coupled in a staggered fashion. If the time step of the wave model and storm surge model are 30 minutes and 1 s, respectively, both models would exchange information every 30 minutes. There is no iteration between the wave and surge models at each coupling interval. An alternative to this state-of-the-practice of hurricane wave and storm surge modeling is to simulate the combined wave and surge motion driven by wind and attenuated by wetland vegetation using a phase-resolving Boussinesq model. The objective of this study is threefold: 1) to demonstrate the capability of modeling wave growth by wind, wave reduction by vegetation, and the total water level (wave setup, wind setup and wave runup) using the extended FUNWAVE-TVD model; 2) to analyze the energy balance of the combined wave and surge motion; 3) to examine the momentum balance with an emphasis on the vegetal drag owing to the combined wave orbital velocity and wind-driven current velocity.Recorded Presentation from the vICCE (YouTube Link): https://youtu.be/-o_kx4hPvC8
PREDICTING INFRAGRAVITY WAVES IN HARBOURS - AN EVALUATION OF PUBLISHED EQUATIONS AND THEIR USE IN FORECASTING OPERATIONAL THRESHOLDS
Authors: McComb Peter , Zyngfogel Remy , Gomez Begona Perez
Published: January 2021

Infragravity (IG) waves have received considerable study since the 1950s (Munk, 1949, Bertin, 2018), allowing their generation, propagation and impacts to be more effectively quantified. Here, we are concerned with the frequencies that directly excite motion in moored ships, thereby creating problematic and often unsafe conditions. Operational knowledge gained in surge-affected ports in Australia and New Zealand revealed IG height thresholds common to all locations (McComb, 2011), with wave periods from 25 to 120-150s being causative. A further observation that the IG spectral shapes at berths remain relatively constant regardless of the incident short wave spectra (McComb, 2014) allows robust predictive methodologies to be developed to forecast the onset and the passing of these empirically-derived values. The governing IG height thresholds are: Hsless than 0.10m is safe and manageable for a well-tendered vessel; at Hs 0.10-0.15m caution is advised and additional management is recommended, and at Hsgreater than 0.15m active management is required. Management options include shore moorings, pneumatic fendering, ShoreTension, MoorMaster etc. Without intervention, IG conditions greater than 0.20m are universally considered dangerous. Further, IG heights are strongly modulated by tide at certain locations (Thomson, 2006), which creates rapidly changing conditions that compound the difficulties ensuring safe and effective operations. We selected five published methods to predict nearshore IG height (Lara 2004, McComb 2005, Okihiro 1992, Arduin 2014 and Cuomo 2017) and undertook an evaluation of their efficacy at two energetic ports on opposite sides of the Earth. The ports of Gijon in Spain and Taranaki in New Zealand both experience problematic moored ship motions and have been subject to numerous studies of their wave dynamics over previous decades. Consequently, there is a body of knowledge, operational experience and local data to make an evaluation. The purpose of this work is to offer pragmatic guidance to the developers of operational forecasting systems on the optimal method to predict IG heights for safe mooring of ships at berth. Recorded Presentation from the vICCE (YouTube Link): https://youtu.be/8oCRQkMdcIo
SOLITARY-WAVE-INDUCED BOUNDARY LAYER FLOWS OVER PERMEABLE BEDS
Authors: Pujara Nimish , Meza-Valle Claudio , Liu Philip L.-F.
Published: January 2021

In the nearshore environment, viscous effects of wave- induced boundary layer flows above sea beds are important in evaluating sediment fluxes and wave damping. These effects need to be included in phase- resolved nearshore models for accurate determination of quantities such as the bed shear stress and the decrease in wave height due to frictional dissipation. In this work, we analyze the boundary layers induced by a solitary wave on permeable sea beds (extending previous work of wave-induced boundary layers on an impermeable bed). We find that the velocity profiles and bed shear stress are sensitive to the hydraulic conductivity of the bed, but not extremely sensitive to the precise boundary condition at the bed-fluid interface.
L'acide N‐glycolyl‐muramique, constituant des parois de Mycobacterium smegmatis: Identification par spectrometrie de masse
Authors: Adam A. , Petit J.F. , Wietzerbin-Falszpan J.
Published: July 2002

The repeating disaccharide unit of the mucopeptide of the cell wall of Mycobacterium smegmatis contains N‐acetyl‐glucosamine linked to N‐glycolyl‐muramic acid. This first identification of N‐glycolyl‐muramic acid as a natural product has been performed by mass spectrometry of the permethylated disaccharide. N‐glycolyl muramic acid has been synthesized: the natural and synthetic products are identical.
The emission of chlorophyll in vivo
Authors: Breton Jacques
Published: July 2002

Low temperature photosystem 2 emission (F685,F695) of chloroplasts may originate from a small pool of pigments. However, the excitons reaching the reaction center have been generated in a much larger pool of chlorophylls constituting the almost non‐fluorescent light‐harvesting complex. Based upon structural information an interpretation for the molecular origin of theF695emission of variable yield was proposed [FEBS Lett. (1982) 147, 17–20]: in reaction centers having the quinone acceptor reduced, a charge recombination occurring between the primary donor P680+and Phe−(the pheophytin primary acceptor) can generate a singlet excited state of Phe which deactivates by emittingF695. Here, an analogous process is discussed forF685with the emission occurring either from P680 directly or from the small pool of core antenna chlorophylls surrounding the reaction center. Furthermore, the presence ofF695in the low temperature emission spectra of dark‐adapted chloroplasts leads us to propose that charge recombination also takes place in open reaction centers when the quinone acceptor is oxidized. In this case the short lifetime (130 ± 20 ps) observed for the singlet exciton in the intact membrane suggests that the rate‐limiting step in conditions of active photosynthesis is more probably determined by the stabilization of the negative charge on the quinone than by either the rate of energy transfer among antenna or the rate of trapping by the reaction center.
Platelet activating factor (PAF‐acether) promotes an early degradation of phosphatidylinositol‐4,5‐biphosphate in rabbit platelets
Authors: Mauco Gérard , Hugues Chap , Louis Douste-Blazy
Published: July 2002

32P‐Labelled washed rabbit platelets were incubated with 0.6 nM platelet activating factor (PAF‐acether), giving a full aggregation and release response within 30–60 s. The major phospholipid changes observed under these conditions were: (1) An increased labelling of phosphatidic acid (PA) within 10 s and of phosphatidylinositol (MPI) at 30 s, reflecting the activation of the MPI cycle via the cytosolic phospholipase C; (2) an enhancement of phosphatidylinositol‐4‐phosphate (DPI) and phosphatidylinositol‐4,5‐bisphosphate (TPI) labelling at later incubation times; (3) an early degradation of TPI with a counterbalancing formation of DPI. The latter changes suggest a receptor‐mediated stimulation of TPI‐phosphomonoesterase, the role of which in the mechanism of platelet activation is discussed.
Ca2+, calmodulin‐dependent phosphorylation of glycogen synthase by a brain protein kinase
Authors: Iwasa Takafumi , Fukunaga Kohji , Yamamoto Hideyuki , Tanaka Etsuro , Miyamoto Eishichi
Published: July 2002

A Ca2+, calmodulin‐dependent protein kinase from brain with aMrof 640 000 is capable of phosphorylating glycogen synthase from skeletal muscle. The reaction was inhibited by the addition of 1 mM EGTA and 50 μM trifluoperazine, but not by protein kinase inhibitor and heparin. The amount of phosphate incorporated into glycogen synthase was 1.4 mol/mol subunit. The phosphorylation sites of glycogen synthase were cyanogen bromide‐treated peptides CB‐1 and CB‐2 and only the seryl residue was phosphorylated.
Human liver mitochondrial aldehyde dehydrogenase: a C‐terminal segment positions and defines the structure corresponding to the one reported to differ in the Oriental enzyme variant
Authors: Hempel John , Kaiser Rudolf , Jörnvall Hans
Published: July 2002

Mitochondrial isoenzymeAmino acid sequenceIsoenzyme differenceStructure‐function relationship
Site‐specific cleavage of double‐strand DNA by hydroperoxide of linoleic acid
Authors: Inouye Satoshi
Published: July 2002

The breakage of double‐strand (ds) DNA by 13‐L‐hydroperoxy‐cis‐9, trans‐11‐octadecadienoic acid (LAHPO) was investigated by agarose gel electrophoresis of supercoiled pBR322 DNA and the site of cleavage on the DNA molecule was determined by the method of DNA sequence analysis using 3'‐end and 5'‐end‐labeled DNA fragments as substrates. LAHPO caused cleavage at the position of guanine nucleotide in dsDNA. LAHPO caused dsDNA breaks at specific sites, but linoleic acid (LA) and 13‐L‐hydoxy‐cis‐9,trans‐11‐octadecadienoic acid (LAHO) have no such effects on dsDNA. The active oxygen atom of the hydroperoxy group of LAHPO was perhaps responsible for the site‐specific cleavage of dsDNA.
Tightly bound adenosine diphosphate, which inhibits the activity of mitochondrial F1‐ATPase, is located at the catalytic site of the enzyme
Authors: Drobinskaya I.Ye. , Kozlov I.A. , Murataliev M.B. , Vulfson E.N.
Published: July 2002

The binding of one ADP molecule at the catalytic site of the nucleotide depleted F1‐ATPase results in a decrease in the initial rate of ATP hydrolysis. The addition of an equimolar amount of ATP to the nucleotide depleted F1‐ATPase leads to the same effect, but, in this case, inhibition is time dependent. The half‐time of this process is about 30 s, and the inhibition is correlated with Pi dissociation from the F1‐ATPase catalytic site (uni‐site catalysis). The F1‐ATPase‐ADP complex formed under uni‐site catalysis conditions can be reactivated in two ways: (i) slow ATP‐dependent ADP release from the catalytic site (τ½ 20 s) or (ii) binding of Pi in addition to MgADP and the formation of the triple F1‐ATPase‐MgADP‐Pi complex. GTP and GDP are also capable of binding to the catalytic site, however, without changes in the kinetic properties of the F1‐ATPase. It is proposed that ATP‐dependent dissociation of the F1‐ATPase‐GDP complex occurs more rapidly, than that of the F1‐ATPase‐ADP complex.
Cooperative calcium binding and calmodulin regulation in the calcium‐dependent adenosine triphosphatase purified from the erythrocyte membrane
Authors: Kosk-Kosicka Danuta , Inesi Giuseppe
Published: July 2002

Erythrocyte membrane Ca2+‐ATPase
Calmodulin
Purified Ca2+‐ATPase
Intrinsic fluorescence
Cooperativity
Exploration of nucleotide binding sites in the mitochondrial membrane by 2‐azido‐[α‐32P]ADP
Authors: Dalbon Pascal , Boulay François , Vignais Pierre V.
Published: July 2002

The ADP/ATP carrier of beef heart mitochondria is able to bind 2‐azido‐[α‐32P]ADP in the dark with a K
d value of ∼ 8 μM. 2‐Azido ADP is not transported and it inhibits ADP transport and ADP binding. Photoirradiation of beef heart mitochondria with 2‐azido‐[α‐32P]ADP results mainly in photolabeling of the ADP/ATP carrier protein; photolabeling is prevented by carboxyatractyloside, a specific inhibitor of ADP/ATP transport. Upon photoirradiation of inside‐out submitochondrial particles with 2‐azido‐[α‐32P]ADP, both the ADP/ATP carrier and the β subunit of the membrane‐bound F1‐ATPase are covalently labeled. The binding specificity of 2‐azido‐[α‐32P]ADP for the β subunit of F1‐ATPase is ascertained by prevention of photolabeling of isolated F1 by preincubation with an excess of ADP.
A proteolipid in cancer cells is the origin of their high‐resolution NMR spectrum
Authors: Wright Lesley C. , May George L. , Dyne Marlen , Mountford Carolyn E.
Published: July 2002

High‐resolution proton nuclear magnetic resonance studies show that the spectrum of a proteolipid complex, isolated from the serum of patients with malignant diseases, is directly comparable with that obtained from intact cancer cells and solid tumours. These NMR signals have previously been shown to reveal differences between cancer cells with various biological characteristics such as metastatic capacity and drug sensitivity. The proteolipid contains cholesterol, phospholipid, triglyceride, glycolipids, ether‐linked lipids, and an apoprotein of unusual electrophoretic mobility. We have yet to confirm the presence of the mRNA reported by others. NMR spectroscopy could be used as a rapid method of identifying the presence of this proteolipid complex in human serum and aiding the diagnosis of malignant disease.
Sequence‐imposed structural constraints in the TonB protein of E. coli
Authors: Evans J.S. , Levine B.A. , Trayer I.P. , Dorman C.J. , Higgins C.F.
Published: July 2002

The solution conformation of a 33‐residue peptide segment derived from the TonB protein which is implicated in bacterial membrane transport processes, has been investigated using high‐resolution proton magnetic resonance techniques. This proline‐rich peptide possesses sequence‐imposed sections of elongated secondary structure that must be retained in the native protein configuration. These structural constraints provide elements of stiffness that imply a purely structural role for TonB and are relevant to the subcellular location and biological role of the protein. On the basis of these data we suggest that this protein spans the periplasmic space linking the inner and outer membrane components of TonB‐dependent transport systems.
The activated human met gene encodes a protein tyrosine kinase
Authors: Tempest Philip R. , Cooper Colin S. , Major Glenn N.
Published: July 2002

We have raised antibodies against a synthetic dodecapeptide corresponding to the carboxyl terminus of the predicted met gene product. Phosphorylation of 60 kDa and 65 kDa proteins on tyrosine residues was observed when immunoprecipitates of cells containing the activated human met gene were incubated with [γ‐32P]ATP. Phosphoproteins with the same molecular masses could be immunoprecipitated from cells metabolically labelled with [32P]orthophosphate. When considered together, these observations indicate that the activated human met gene encodes 60 kDa and 65 kDa proteins that can catalyse autophosphorylation on tyrosine residues.
Calcium‐binding proteins in rat skin
Authors: Schelling Claude P. , Didierjean Liliane , Rizk Marthe , Pavlovitch Jana H. , Takagi Takashi , Heizmann Claus W.
Published: July 2002

Skin Ca2+‐binding protein (SCaBP) was reported to be distinct from the Ca2+‐binding parvalbumin (PV), however, more recently its amino acid sequence was shown to be identical to PV. We purified a protein (Mr12 000; pI4.5) from isolated epidermis (free of other cell layers) of adult rats and whole skin (containing no PV) of newborn rats. This protein is referred to as epidermal protein (EP‐12), distinct from PV in its hydrophobicity, amino acid composition and immunological properties. Previously isolated SCaBP was shown to be a mixture of EP‐12 and PV. The localization and possible functions of EP‐12 and of PV in skin of adult and newborn rat are discussed.
Complete amino acid sequence of human intestinal aminopeptidase N as deduced from cloned cDNA
Authors: Olsen Jørgen , Cowell Gillian M. , Kønigshøfer Elaine , Danielsen E.Michael , Møller Jette , Laustsen Liselotte , Hansen Ole C. , Welinder Karen G. , Engberg Jan , Hunziker Walter , Spiesst Martin , Sjöström Hans , Norén Ove
Published: July 2002

The complete primary structure (967 amino acids) of an intestinal human aminopeptidase N (EC 3.4.11.2) was deduced from the sequence of a cDNA clone. Aminopeptidase N is anchored to the microvillar membrane via an uncleaved signal for membrane insertion. A domain constituting amino acid 250–555 positioned within the catalytic domain shows very clear homology to E. coli aminopeptidase N and contains Zn2+ ligands. Therefore these residues are part of the active site. However, no homology of the anchor/junctional peptide domain is found suggesting that the juxta‐ and intra‐membraneous parts of the molecule have been added/preserved during development. It is speculated that this part carries the apical address.
Lipoxins stimulate prostacyclin generation by human endothelial cells
Authors: Brezinski Mark E. , Gimbrone Michael A. , Nicolaou K.C. , Serhan Charles N.
Published: July 2002

Cultured human umbilical endothelial cells were incubated with lipoxins and their ability to generate prostacyclin (PGI2) was assessed and compared to that induced by either leukotriene C4 or an ionophore of divalent cations (A‐23,187). When exposed to either lipoxin A4, lipoxin B4, or 7‐cis, 11‐trans‐lipoxin A4, endothelial cells generated prostacyclin detected as 6‐keto‐PGF1α. Of the lipoxins examined, 7‐cis, 11‐trans‐lipoxin A4 proved to be the most effective with PGI2 production twice that induced by equimolar amounts of A‐23,187 (5 μM). On a molar basis, lipoxin A4 and lipoxin B4 were less potent than leukotriene C4 although they were more efficacious. When either lipoxin A4 or lipoxin B4 was added to cells simultaneously with leukotriene C4, the formation of prostacyclin was greater than that induced by leukotriene C4 alone. During the time course of exposure to lipoxins (0–20 min, 37°C), cultured endothelial cells did not further transform these compounds via ω‐oxidation as determined by reverse‐phase HPLC. These data indicate that lipoxins can stimulate PGI2 generation by human endothelial cells. Moreover, they suggest a role for these lipoxygenase products of arachidonic acid in the regulation of hemostasis, inflammation and vascular reactivity.
Purification and partial characterization of a lectin from the seeds of Trichosanthes kirilowii Maximowicz
Authors: Falasca Anna Ida , Abbondanza Ada , Barbieri Luigi , Bolognesi Andrea , Rossi Carlo Alfonso , Stirpe Fiorenzo
Published: July 2002

A lectin was purified from the seeds of Trichosanthes kirilowii, belonging to the family Cucurbitaceae, growing in China. The lectin is a glycoprotein of 57 kDa, consists of two subunits with apparent molecular masses of 37 and 25 kDa, is specific for galactose, and is not mitogenic for human lymphocytes.
Carnitine cycle in brown adipose tissue mitochondria as a tool for studying the regulatory role of fatty acids in the uncoupling protein function
Authors: Ježek Petr , Krasinskaya Inna P. , Smirnova Ira , Drahota Zdenék
Published: July 2002

A concerted function of purine nucleotide (PN) binding and fatty acid (FA) release from the uncoupling protein (UP) resulting in the maximum coupling (potential) of brown adipose tissue (BAT) mitochondria was demonstrated. The uncoupling effect of FA was studied (at 4 mM MgCl2): 17 nmol oleate per mg protein caused a slight uncoupling with 8.9 mM ATP but with ATP below 3.6 mM almost total uncoupling was achieved. This shows that the PN‐controlled gate can be stabilized in the closed conformation (with 8.9 mM ATP), also when FA is bound to UP. The sensitivity of the FA effect to ATP proves that oleate directly interacts with UP. The closed conformation of the H+ channel of UP is then abolished by oleate when a lower free ATP concentration is maintained outside.
Stimulation of protein synthesis by raised extracellular pH in cardiac myocytes and perfused hearts
Authors: Gaitanaki Catherine J. , Sugden Peter H. , Fuller Stephen J.
Published: July 2002

Protein synthesis was stimulated in freshly‐isolated rat cardiac myocytes by increasing the extracellular pH of Hepes‐buffered Tyrode's solutions over the range pH 7.4–8.4. The maximal stimulation was about 45%. Protein synthesis in anterogradely‐perfused rat hearts was stimulated by 11% by increasing the pH of the bicarbonate‐containing perfusion medium from pH 7.4 to 7.8. This manoeuvre increased intracellular pH by 0.12 units. A concomitant increase in phosphocreatine concentration was observed. These findings are consistent with the hypothesis that intracellular pH may exert profound effects on tissue protein synthesis rates.
Fluoride is a strong and specific inhibitor of (asymmetrical) Ap4A hydrolases
Authors: Guranowski Andrzej
Published: July 2002

Fluoride acts as a noncompetitive, strong inhibitor of (asymmetrical) Ap4A hydrolases (EC 3.6.1.17). The K
i values estimated for the enzymes isolated from seeds of some higher plants (yellow lupin, sunflower and marrow) are in the range of 2–3 μM and I
50 for the hydrolase from a mammalian tissue (beef liver) is 20 μM. The anion, up to 25 mM, does not affect the following other enzymes which are able to degrade the bis(5'‐nucleosidyl)‐oligophosphates: Escherichia coli (symmetrical) Ap4A hydrolase (EC 3.6.1.41), yeast Ap4A phosphorylase (EC 2.7.7.53), yellow lupin Ap3A hydrolase (EC 3.6.1.29) and phosphodiesterase (EC 3.1.4.1). None of halogenic anions but fluoride affects the activity of (asymmetrical) Ap4A hydrolases. Usefulness of the fluoride effect for the in vivo studies on the Ap4A metabolism is shortly discussed.
Activation of a complex of ATPase with the natural protein inhibitor in submitochondrial particles
Authors: Khodjaev E.Yu. , Komarnitsky F.B. , Capozza G. , Dukhovich V.F. , Chernyak B.V. , Papa S.
Published: July 2002

Almost all ATPase molecules in submitochondrial particles, isolated from beef heart mitochondria in the presence of MgATP, are in an inactive complex with the natural protein inhibitor (IF1). In de‐energized particles at high ionic strength a slow and irreversible ATPase activation is found to occur due to a dissociation of the enzyme‐inhibitor complex. The pH‐dependence of this process points out that deprotonation of IF1 molecule is an essential step in the dissociation of the complex. Zn2+ sharply accelerates ATPase activation, probably via binding with the deprotonated form of IF1. ATPase activation is completely prevented by MgATP, indicating the formation of a transient enzyme‐inhibitor complex retaining ATPase activity
Inhibition of protein phosphatases‐1 and ‐2A with acanthifolicin
Authors: Holmes Charles F.B. , Luu Hue A. , Carrier France , Schmitz Francis J.
Published: July 2002

Acanthifolicin (9,10‐epithio‐okadaic acid from Pandoras acanthifolium) inhibited protein phosphatase‐1 (PP1) similarly to okadaic acid (IC50 = 20 nM and 19 nM, respectively) but was slightly less active against protein phosphatase‐2A (PP2A) (IC50 1 nM and 0.2 nM, respectively). Methyl esterification of acanthifolicin sharply reduced its activity. PP2A was inhibited with an IC50 = 5.0 μM, whilst PP1 was inhibited < 10% at 250 μM toxin. Okadaic acid methyl ester was similarly inactive whereas dinophysistoxin‐1 (35‐methyl okadaic acid) inhibited PP1/2A almost as potently as okadaic acid. Pure acanthifolicin/okadaic acid methyl ester may be useful as specific inhibitors of PP2A at 1–10 μM concentrations in vitro and perhaps in vivo. The data also indicate that a region on these toxins important for PP1/2A inhibition comprises the single carboxyl group.
Tumor necrosis factor Characterization at the molecular, cellular and in vivo level
Authors: Fiers Walter
Published: July 2002

TNF was originally characterized as an antitumor agent and a factor cytotoxic for many malignant cells. It is now clear that it plays an important role in the defense against viral, bacterial and parasitic infections, — and in (auto‐)immune responses. Natural induction of TNF is protective, but its overproduction may be detrimental and even lethal to the host. The structure of TNF and its interaction with the two types of cellular receptor are becoming better understood. TNF elicits a variety of events in different cell types. It subverts the electron transport system or the mitochondria into production of oxygen radicals, which can kill the (malignant) cells when these do not contain or produce protective enzymes. Furthermore, TNF induces a set of genes and at least part of this transcriptional activation is mediated by NFkB. The prospects of TNF as an antitumor drug can be improved on the one hand by agents such as LI+, which synergizes, and on the other hand by inhibitors of the systemic toxicity which do not interfere with the antitumor efficacy. Also, in tumor‐bearing animals which have been rendered tolerant by administration of small doses of TNF, an effective and complete elimination of the tumors can be obtained by the combined action of TNF plus interferon.
Characterization of the interaction of doxorubicin with (poly)phosphoinositides in model systems Evidence for specific interaction with phosphatidylinositol‐monophosphate and ‐diphosphate
Authors: de Wolf Frits A. , Demel Rudy A. , Bets Danny , van Kats Carlos , de Kruijff Ben
Published: July 2002

The anticancer drug doxorubicin penetrates into Langmuir monolayers containing phosphoinositides. Upon binding of doxorubicin to phosphoinositide‐containing SUV, its fluorescence is self‐quenched due to self‐association. As compared to other anionic phospholipids, as much as 2‐ to 3‐fold larger effects were obtained with PIP and PIP2, in mixtures of these lipids with DOPC. Doxorubicin competes efficiently with the non‐penetrating antibiotic neomycin for binding to PIP2. According to its penetration, specific binding of doxorubicin was half‐maximal at 5–15 μM. It is likely that also in biological membranes doxorubicin binds specifically to PIP and PIP2.
Two proteins act as the IUF1 insulin gene enhancer binding factor
Authors: Scott Valerie , Clark Andrew R. , Hutton John C. , Docherty Kevin
Published: July 2002

IUF1 is a pancreatic β cell‐specific factor which binds to the sequence 5′‐CPyCTAATG‐3′ (CT box) within the human insulin gene enhancer. Here we show that IUF1 is composed of 2 binding activities that can be separated by DEAE ion exchange chromatography. South Western blot analysis indicates that these distinct binding activities have apparent molecular weights of 115 kDa and 46 kDa.
Ca2+/calmodulin is involved in growth factor‐induced retinoblastoma gene product phosphorylation in human vascular endothelial cells
Authors: Takuwa Noriko , Zhou Wei , Kumada Mamoru , Takuwa Yoh
Published: July 2002

In human vascular endothelial cells, both growth factor‐induced DNA synthesis and retinoblastoma gene product (RB) phosphorylation are absolutely dependent on extracellular Ca2+, and are potently inhibited by an active calmodulin antagonits, W‐7, but not an inactive analogue, W‐12. A reduction in the extracellular Ca2+ or an addition of W‐7 as late as 8 h after growth factor stimulation still inhibits both RB phosphorylation and DNA synthesis to the full extent. However, once RB phosphorylation occurs 12–16 h after addition of the growth factors, it is not reversed by subsequent Ca2+ reduction or W‐7. These results suggest the existence of a Ca2+/calmodulin‐dependent process relatively late in the mitogenic signalling cascade, at a step proximal to RB phosphorylation reaction itself.
A predicted three‐dimensional structure for the carcinoembryonic antigen (CEA)
Authors: Bates Paul A. , Luo Jingchu , Sternberg Michael J.E.
Published: July 2002

A three‐dimensional model for the carcinoembryonic antigen (CEA) has been constructed by knowledge‐based computer modelling. Each of the seven extracellular domains of CEA are expected to have immunoglobulin folds. The N‐terminal domain of CEA was modelled using the first domain of the recently solved NMR structure or rat CD2, as well as the first domain of the X‐ray crystal structure of human CD4 and an immunoglobulin variable domain REI as templates. The remaining domains were modelled from the first and second domains or CD4 and REI. Link conformations between the domains were taken from the elbow region of antibodies. A possible packing model between each of the seven domains is proposed. Each residue of the model is labelled as to its suitability for site‐directed mutagenesis.
Molecular cloning and developmental expression of a human kidney S‐adenosylmethionine synthetase
Authors: Horikawa Saburo , Tsukada Kinji
Published: July 2002

cDNA clones encoding the human kidney S‐adenosylmethionine synthetase (kidney‐type isozyme) were isolated. The amino acid sequence deduced from the cDNA indicates that this enzyme contains 395 amino acids and has a molecular mass of 43,660 Da. The predicted amino acid sequence of this protein shares 84% similarity with that of human liver S‐adenosylmethionine synthetase (liver‐type isozyme). In addition, the developmental expression of these two isozyme mRNAs has been studied in the human liver using the reverse transcription—polymerase chain reaction (RT‐PCR).
pH changes associated with cytochrome c oxidase reaction with H2O2 Protonation state of the peroxy and oxoferryl intermediates
Authors: Konstantinov A.A. , Capitanio N. , Vygodina T.V. , Papa S.
Published: July 2002

pH changes associated with the mitochondrial cytochrome oxidase reaction with H2O2 have been studied. In the presence of forricyanide or Tris‐phenanthroline complex of CoIII as electron acceptors, reaction or H2O2 with the oxidized cytochrome oxidase is accompanied by a steady proton release with a rate constant of ca. 3 M−1 s−1 at pH 6.8. The acidification is completely inhibited by superoxide dismutase and its pro‐steady‐state kinetics correlates with that of the oxoferryl compound (F) accumulation. Apparently, the proton release is linked to superoxide generation by cytochrome oxidase under these conditions. In the presence of superoxide dismutase and without the electron acceptors, the H2O2‐induced transitions of cytochrome oxidase from the oxidized to the peroxy (P) and from the peroxy to the oxoferryl state are not associated with any significant proton release or uptake. The results point to the following mechanism of O−
2 generation and protonation states of the cytochrome oxidase compounds P and F:
Structure of tubulin C‐terminal domain obtained by subtilisin treatment The major α and β tubulin isotypes from pig brain are glutamylated
Authors: Redeker Virginie , Melki Ronald , Promé Danielle , Le Caer Jean-Pierre , Rossier Jean
Published: July 2002

Limited subtilisin digestion of the tubulin α, β heterodimer has been used in this work to reduce the total number of tubulin isotypes from 20 for native to 9 for subtilisin‐cleaved tubulin. This indicates that the major part of tubulin heterogeneity is located at the C‐terminus of the molecule. The C‐terminal peptides of both α and β subunits of tubulin were purified by anion‐exchange HPLC. Combined use of Edman degradation chemistry and mass spectrometry on the isolated peptides shows that subtilisin cleavage occurs at position Asp‐438 and His‐406 of α and Gln‐433 and His‐396 of β tubulin chains. Quantitative analysis of our data show that cleavage at positions His‐406 (α) and His‐396 (β) occurs with a low efficiency and indicates that the major isotypes of pig brain tubulin are modified by sequential attachment of 1 to 5 glutamic acid residues at positions Glu‐445 or −435 of α and β tubulin, respectively.
Design, synthesis and functional characterization of a pentameric channel protein that mimics the presumed pore structure of the nicotinic cholinergic receptor
Authors: Montal Myrta Oblatt , Iwamoto Takeo , Tomich John M. , Montal Mauricio
Published: July 2002

Nicotinic cholinergic receptors are membrane proteins composed of five subunits organized around a central aqueous pore. A pentameric channel protein, T5M2δ, that emulates the presumed pore‐forming structure of this receptor was generated by assembling five helix‐forming peptide modules at the lysine ϵ‐amino groups of the 11‐residue template [K∗AK∗KK∗PGK∗EK∗G], where ∗ indicates attachment sites. Helical modules represent the sequence of the M2 segment of the Torpedo californica acetylcholine receptor (AChR) δ subunit; M2 segments are considered involved in pore‐lining. Purified T5M2δ migrates in SDS‐PAGE with an apparent M
r~14,000, concordant with a protein of 126 residues. T5M2δ forms cation‐selective channels when reconstituted in planar lipid bilayers. The single channel conductance in symmetric 0.5 M K.C1 is 40 pS. This value approximates the 45 pS single channel conductance characteristic of authentic purified Torpedo AChR, recorded under otherwise identical conditions. These results, together with conformational energy calculations, support the notion that a bundle of five amphipathic a‐helices is a plausible structural motif underlying the inner bundle that forms the pore of the pentameric AChR channel.
Active increase in cardiolipin synthesis in the stationary growth phase and its physiological significance in Escherichia coli
Authors: Hiraoka Shuichi , Matsuzaki Hiroshi , Shibuya Isao
Published: July 2002

Activity of the Escherichia coli cardiolipin synthase, encoded by cls, increased about 10‐fold in the stationary growth phase, while other committedstep enzymes in phospholipid biosynthesis rather decreased. A null cls mutant lost viability to 10−4 of the wild‐type cells during the prolonged incubation for 5 days. Cardiolipin was most stable among membrane phospholipids during the incubation. Accordingly, cardiolipin should play a role in survival of the cell and E. coli employs a sophisticated way to form cardiolipin according to need even under non‐growing conditions.
NADH‐cytochrome b5 reductase and cytochrome b5 isoforms as models for the study of post‐translational targeting to the endoplasmic reticulum
Authors: Borgese Nica , D'Arrigo Antonello , De Silvestris Marcella , Pietrini Grazia
Published: July 2002

Cytochrome b
5 and NADH‐cytochrome b
5, reductase are integral membrane proteins with cytosolic active domains and short membrane anchors, which are inserted post‐translationally into their target membranes. Both are produced as different isoforms, with different localizations, in mammalian cells. In the rat, the reductase gene generates two transcripts by an alternative promoter mechanism: a ubiquitous mRNA coding for the myristylated membrane‐bound form, and an erythroid mRNA which generates both the soluble form and a nonmyristylated membrane‐binding form. The available evidence indicates that the ubiquitous myristylated form binds to the cytosolic face of both outer mitochondrial membranes and ER. In contrast, two genes code for two homologous forms of cytochrome b
5, one of which is found on outer mitochondrial membranes, the other on the ER. The gene specifying the ER form probably also generates an erythroid‐specific mRNA by alternative splicing, which codes for soluble cytochrome b
5. Possible molecular mechanisms responsible for the observed localizations of these different enzyme isoforms are discussed.
The role of the stalk in the coupling mechanism of F1F0‐ATPases
Authors: Walker John E. , Collinson Ian R.
Published: July 2002

The extrinsic and intrinsic membrane sectors of F1F0‐ATPases are linked by a slender stalk 40–50 Å in length. The stalk transmits the energy produced by oxidative or photosynthetic phosphorylation from the intrinsic sector, F0, to the catalytic sites in the extrinsic F1 sector. How this is achieved is unknown, but long‐range conformational changes linked to transmembrane proton transport may be involved. In bacterial and chloroplast F1F0‐ATPases, the stalk is probably a composite of subunits δ and ε, part of the γ‐subunit, and the extrinsic membrane domains of 2 subunits (identical or non‐identical according to the species) that are bound to the membrane by their N‐terminal regions. The stalk in the bovine mitochondrial enzyme appears to be more complex, and the γ, δ, ε, OSCP, F6, b and d subunits all contribute to it. A bovine stalk complex has been assembled in vitro from bacterially expressed OSCP, F6, b and d, both in the presence and in the absence of F1‐ATPase. One molecule of each of these subunits is present in the assembled complexes, as there is also in each native F1F0‐ATPase assembly. Providing that suitable crystals can be obtained, the stalk complex and the F1·stalk complex may permit the high resolution structure of bovine F1‐ATPase to be extended into the stalk domain.
Presence of protein phosphatase type 1 and its involvement in temperature‐dependent flagellar movement of fowl spermatozoa
Authors: Ashizawa Koji , Wishart Graham J. , Tomonaga Hiroshi , Nishinakama Kohfumi , Tsuzuki Yasuhiro
Published: July 2002

Even in the presence of ATP, the motility of demembranated fowl spermatozoa was negligible at the avian body temperature of 40°C. Motility could be restored by the addition of calyculin A, okadaic acid, specific inhibitors of phosphatase type 1 (PP1) and PP‐2A, and inhibitor 1 or inhibitor 2, which are specific inhibitors of protein phosphatase type 1 (PP1). Demembranated spermatozoa, stimulated by calyculin A or okadaic acid, lost their motility following the addition of 1 mM CaCl2, but this was restored gradually by the stepwise addition of EGTA. Immunoblotting of sperm extract using an antibody to PP1 revealed a major cross‐reacting protein of 36–37 kDa, which corresponded to the molecular weight of the known catalytic subunit of PP1. These results suggest that PP1 present in the fowl sperm axoneme may be involved in the inhibition of fowl sperm motility at 40°C via Ca2+‐dependent regulatory systems.
Molecular mechanisms of damage by excess nitrogen oxides: Nitration of tyrosine by gas‐phase cigarette smoke
Authors: Eiserich Jason , Vossen Veronique , O'Neill Charles A. , Halliwell Barry , Cross Carroll E. , van der Vliet Albert
Published: July 2002

Nitric oxide (nitrogen monoxide, •NO) plays important physiological roles, but an excess can be toxic. •NO is present in cigarette smoke (CS) at up to 500 ppm, and probably represents one of the greatest erogenous sources of •NO to which humans are exposed. We show here that gas‐phase CS is capable of converting tyrosine to 3‐nitrotyrosine (3‐NO2‐Tyr) and dityrosine, to an extent dependent on time of exposure and pH. Glutathione, ascorbic acid and uric acid decreased the CS‐induced formation of 3‐NO2‐Tyr and dityrosine. We suggest that nitrogen oxides in CS can modify proteins in the respiratory tract and may contribute to CS toxicity.
Cloning and expression of mRNA encoding prepro‐gonad‐inhibiting hormone (GIH) in the lobster Homarus americanus
Authors: de Kleijn Dominique P.V. , Sleutels Frank J.G.T. , Martens Gerard J.M. , Van Herp François
Published: July 2002

The gonad‐inhibiting hormone (GIH) is produced in the eyestalk X‐organ sinus gland complex of male and female lobsters, and plays a prominent role in the regulation of reproduction, e.g. inhibition of vitellogenesis in female animals. To study this neurohormone at the mRNA level, we cloned and sequenced a cDNA which encodes GIH in the lobster Homarus americanus. The structure of preproGIH consists of a signal peptide and the GIH peptide itself. A comparative analysis revealed that lobster GIH, together with crab molt‐inhibiting hormone, belongs to a separate group of the crustacean hyperglycemic hormone (CHH) peptide family which seems to be unique for crustaceans. Expression studies showed that GIH mRNA is expressed in the eyestalk, indicating that the neuroendocrine center in this optic structure is the only source of GIH. As this center modulates the other (neuro)endocrine organs in crustaceans, it is postulated that GIH regulates production and release of hormones involved in reproduction/molting processes.