bluuebunny/crossref_metadata_2025_split huggingface dataset:
Luminescence age and palaeoenvironmental implications of a late Pleistocene ground wedge on the Northeastern Tibetan Plateau
Authors: Porter Stephen C. , Singhvi Ashok , Zhisheng An , Zhongping Lai 
Published: August 2002

AbstractA periglacial ground wedge in bajada gravel near the northern base of the Qinghai Nan Shan underlies loess of late‐ and postglacial age. The composition and structure of the wedge fill are consistent with an ice‐wedge origin, implying former permafrost and relatively moist conditions at this locality. A luminescence date of 15,100±1600 years from the wedge fill marks the end of ice‐wedge activity, which is inferred to have been during the last glaciation. The present mean annual air temperature (MAAT) (−0.7 °C) is too high to produce frost cracking and ice‐wedge formation, but snowline depression of ca. 700–800 m in the adjacent mountains is consistent with a reduction in MAAT of at least 3.8 °C during the last glacial maximum. Such a temperature depression would reduce MAAT to values equivalent to Arctic regions now experiencing active ice‐wedge growth. The absence of loess of full‐glacial age and the presence of a weakly developed palaeosol atop the bajada gravel imply a stable, cold land surface. Qinghai Lake, although reduced in size at that time, likely raised local humidity to levels that favoured ice‐wedge growth in this low‐altitude sector (ca. 3000–3400 m) of the Tibetan Plateau. Copyright © 2001 John Wiley & Sons, Ltd.RésuméPrès de la base septentrionale de Qinghai Nan Shan, un coin périglaciaire a été observé dans le gravier d'une bahada recouverte de loess tardi‐ et postglaciaire. La composition et la structure du remplissage du coin peuvent s'expliquer par le développement d'un coin de glace, ce qui implique l'existence autrefois d'un pergélisol et de conditions relativement humides. Une date de 15.100 +/− 1600 ans a été obtenue par luminescence pour le remplissage ; cette date marquerait la fin de l'activité du coin de glace qui serait, de ce fait, apparu pendant la dernière glaciation. De nos jours, la température moyenne annuelle de l'air (MAAT) est de −0.7 °C, température trop élevée pour produire la fissuration par le gel et la formation d'un coin de glace ; toutefois, l'abaissement de la limite des neiges éternelles d'environ 700 à 800 m dans les montagnes voisines indique une réduction de la température moyenne annuelle d'au moins 3.8 °C pendant le maximum de la dernière glaciation. Une telle diminution de température aurait réduit la température à une valeur semblable à celle des régions arctiques où se développent de nos jours des coins de glace. L'absence de loess d'âge glaciaire et la présence d'un paléosol faiblement développé au sommet du gravier de la bahada implique que la surface est restée stable et froide. A cette époque, le lac Qinghai, quoique réduit en taille, a probablement augmenté l'humidité locale et favorisé la croissance de coins de glace dans ce secteur de faible altitude (vers 3000–3400 m) du Plateau tibétain. Copyright © 2001 John Wiley & Sons, Ltd.
Measurement and theory of ploughing boulder movement
Authors: Ballantyne Colin K. 
Published: August 2002

AbstractAnalysis of the characteristics, distribution and rate of movement of ploughing boulders reveals several attributes that throw light on the mechanism of boulder movement. Ploughing boulders occur only in areas of active solifluction, on frost‐susceptible soils with low plastic and liquid limits. During movement they rotate to adopt an alignment of least resistance. Excavations revealed thick ice lenses under the base of a boulder in winter, and emergent shear planes in frontal ridges. Rates of boulder movement average from zero to a few centimetres per year and are exponentially related to gradient. The differential thermal conductivity (diffusivity) of the boulder and surrounding soil implies that the seasonal freezing plane descends more rapidly through the boulder, causing ice‐lens growth at the boulder base; conversely, the thaw plane reaches the base of the boulder whilst the surrrounding soil is still frozen. A limit‐equilibrium model of boulder movement by gelifluction suggests that movement results from trapping of excess water under boulders during thaw, elevation of sub‐boulder porewater pressures to above‐hydrostatic levels and consequent reduction in shearing resistance at the base of the boulder. Movement is initiated by thaw of soil immediately downslope, but allows trapped water to escape, reducing porewater pressures and allowing stability to be regained. This model appears consistent with the observed characteristics, distribution and behaviour of ploughing boulders. Copyright © 2001 John Wiley & Sons, Ltd.
Identification of protein fold and catalytic residues of γ‐hexachlorocyclohexane dehydrochlorinase LinA
Authors: Nagata Yuji , Mori Katsuki , Takagi Masamichi , Murzin Alexey G. , Damborský Jiří 
Published: August 2002

Abstractγ‐Hexachlorocyclohexane dehydrochlorinase (LinA) is a unique dehydrochlorinase that has no homologous sequence at the amino acid‐sequence level and for which the evolutionary origin is unknown. We here propose that LinA is a member of a novel structural superfamily of proteins containing scytalone dehydratase, 3‐oxo‐Δ5‐steroid isomerase, nuclear transport factor 2, and the β‐subunit of naphthalene dioxygenase—all known structures with different functions. The catalytic and the active site residues of LinA are predicted on the basis of its homology model. Nine mutants that carry substitutions of the proposed catalytic residues were constructed by site‐directed mutagenesis. In addition to these, eight mutants that have a potential to make contact with the substrate were prepared by site‐directed mutagenesis. These mutants were expressed in Escherichia coli, and their activities in crude extract were evaluated. Most of the features of the LinA mutants could be explained on the basis of the present LinA model, indicating its validity. We conclude that LinA catalyzes the proton abstraction via the catalytic dyad H73‐D25 by a similar mechanism as described for scytalone dehydratase. The results suggest that LinA and scytalone dehydratase evolved from a common ancestor. LinA may have evolved from an enzyme showing a dehydratase activity. Proteins 2001;45:471–477. © 2001 Wiley‐Liss, Inc.
The leghemoglobin proximal heme pocket directs oxygen dissociation and stabilizes bound heme
Authors: Kundu Suman , Snyder Barry , Das Kaustuv , Chowdhury Pramit , Park Jaehun , Petrich Jacob W. , Hargrove Mark S. 
Published: August 2002

AbstractSperm whale myoglobin (Mb) and soybean leghemoglobin (Lba) are two small, monomeric hemoglobins that share a common globin fold but differ widely in many other aspects. Lba has a much higher affinity for most ligands, and the two proteins use different distal and proximal heme pocket regulatory mechanisms to control ligand binding. Removal of the constraint provided by covalent attachment of the proximal histidine to the F‐helices of these proteins decreases oxygen affinity in Lba and increases oxygen affinity in Mb, mainly because of changes in oxygen dissociation rate constants. Hence, Mb and Lba use covalent constraints in opposite ways to regulate ligand binding. Swapping the F‐helices of the two proteins brings about similar effects, highlighting the importance of this helix in proximal heme pocket regulation of ligand binding. The F7 residue in Mb is capable of weaving a hydrogen‐bonding network that holds the proximal histidine in a fixed orientation. On the contrary, the F7 residue in Lba lacks this property and allows the proximal histidine to assume a conformation favorable for higher ligand binding affinity. Geminate recombination studies indicate that heme iron reactivity on picosecond timescales is not the dominant cause for the effects observed in each mutation. Results also indicate that in Lba the proximal and distal pocket mutations probably influence ligand binding independently. These results are discussed in the context of current hypotheses for proximal heme pocket structure and function. Proteins 2002;46:268–277. © 2002 Wiley‐Liss, Inc.
Cooperative helix stabilization by complex Arg–Glu salt bridges
Authors: Olson C. Anders , Spek Erik J. , Shi Zhengshuang , Vologodskii Alexander , Kallenbach Neville R. 
Published: August 2002

AbstractAmong the interactions that stabilize the native state of proteins, the role of electrostatic interactions has been difficult to quantify precisely. Surface salt bridges or ion pairs between acidic and basic side chains have only a modest stabilizing effect on the stability of helical peptides or proteins: estimates are roughly 0.5 kcal/mol or less. On the other hand, theoretical arguments and the occurrence of salt bridge networks in thermophilic proteins suggest that multiple salt bridges may exert a stronger stabilizing effect. We show here that triads of charged side chains, Arg+–Glu−–Arg+ spaced at i,i+4 or i,i+3 intervals in a helical peptide stabilize alpha helix by more than the additive contribution of two single salt bridges. The free energy of the triad is more than 1 kcal/mol in excess of the sum of the individual pairs, measured in low salt concentration (10 mM). The effect of spacing the three groups is severe; placing the charges at i,i+4 or i,i+3 sites has a strong effect on stability relative to single bridges; other combinations are weaker. A conservative calculation suggests that interactions of this kind between salt bridges can account for much of the stabilization of certain thermophilic proteins. Proteins 2001;44:123–132. © 2001 Wiley‐Liss, Inc.
Distribution of indel lengths
Authors: Qian Bin , Goldstein Richard A. 
Published: August 2002

AbstractProtein sequence alignment has become a widely used method in the study of newly sequenced proteins. Most sequence alignment methods use an affine gap penalty to assign scores to insertions and deletions. Although affine gap penalties represent the relative ease of extending a gap compared with initializing a gap, it is still an obvious oversimplification of the real processes that occur during sequence evolution. To improve the efficiency of sequence alignment methods and to obtain a better understanding of the process of sequence evolution, we wanted to find a more accurate model of insertions and deletions in homologous proteins. In this work, we extract the probability of a gap occurrence and the resulting gap length distribution in distantly related proteins (sequence identity < 25%) using alignments based on their common structures. We observe a distribution of gaps that can be fitted with a multiexponential with four distinct components. The results suggest new approaches to modeling insertions and deletions in sequence alignments. Proteins 2001;45:102–104. © 2001 Wiley‐Liss, Inc.
Structure of rat parvalbumin with deleted AB domain: Implications for the evolution of EF hand calcium‐binding proteins and possible physiological relevance
Authors: Thépaut Michel , Strub Marie‐Paule , Cavé Adrien , Banères Jean‐Louis , Berchtold Martin W. , Dumas Christian , Padilla André 
Published: August 2002

AbstractAmong the EF‐hand Ca2+‐binding proteins, parvalbumin (PV) and calbindin D9k (CaB) have the function of Ca2+ buffers. They evolved from an ancestor protein through two phylogenetic pathways, keeping one pair of EF‐hands. They differ by the extra helix–loop–helix (AB domain) found in PV and by the linker between the binding sites. To investigate whether the deletion of AB in PV restores a CaB‐like structure, we prepared and solved the structure of the truncated rat PV (PVratΔ37) by X‐ray and NMR. PVratΔ37 keeps the PV fold, but is more compact, having a well‐structured linker, which differs remarkably from CaB. PvratΔ37 has no stable apo‐form, has lower affinity for Ca2+ than full‐length PV, and does not bind Mg2+, in contrast to CaB. Structural differences of the hydrophobic core are partially responsible for lowering the calcium‐binding affinity of the truncated protein. It can be concluded that the AB domain, like the linker of CaB, plays a role in structural stabilization. The AB domain of PV protects the hydrophobic core, and is required to maintain high affinity for divalent cation binding. Therefore, the AB domain possibly modulates PV buffer function. PVratΔ37 (Type PDB; Value 1G33; Service) Proteins 2001;45:117–128. © 2001 Wiley‐Liss, Inc.
Conserved core structure and active site residues in alkaline phosphatase superfamily enzymes
Authors: Galperin Michael Y. , Jedrzejas Mark J. 
Published: August 2002

AbstractCofactor‐independent phosphoglycerate mutase (iPGM) has been previously identified as a member of the alkaline phosphatase (AlkP) superfamily of enzymes, based on the conservation of the predicted metal‐binding residues. Structural alignment of iPGM with AlkP and cerebroside sulfatase confirmed that all these enzymes have a common core structure and revealed similarly located conserved Ser (in iPGM and AlkP) or Cys (in sulfatases) residues in their active sites. In AlkP, this Ser residue is phosphorylated during catalysis, whereas in sulfatases the active site Cys residues are modified to formylglycine and sulfatated. Similarly located Thr residue forms a phosphoenzyme intermediate in one more enzyme of the AlkP superfamily, alkaline phosphodiesterase/nucleotide pyrophosphatase PC‐1 (autotaxin). Using structure‐based sequence alignment, we identified homologous Ser, Thr, or Cys residues in other enzymes of the AlkP superfamily, such as phosphopentomutase, phosphoglycerol transferase, phosphonoacetate hydrolase, and GPI‐anchoring enzymes (glycosylphosphatidylinositol phosphoethanolamine transferases) MCD4, GPI7, and GPI13. We predict that catalytical cycles of all the enzymes of AlkP superfamily include phosphoenzyme (or sulfoenzyme) intermediates. Proteins 2001;45:318–324. © 2001 Wiley‐Liss, Inc.
Speeding protein folding beyond the Gō model: How a little frustration sometimes helps
Authors: Plotkin Steven S. 
Published: August 2002

AbstractBy perturbing a Gō model toward a realistic protein Hamiltonian by adding non‐native interactions, we find that the folding rate is in general enhanced as ruggedness is initially increased, as long as the protein is sufficiently large and flexible. Eventually, the rate drops rapidly toward zero when ruggedness significantly slows conformational transitions. Energy landscape arguments for thermodynamics and kinetics are coupled with a treatment of non‐native collapse to elucidate this effect. Proteins 2001;45:337–345. © 2001 Wiley‐Liss, Inc.
Fumigant toxicity of volatile natural products from Korean spices and medicinal plants towards the rice weevil, Sitophilus oryzae (L)
Authors: Lee Sung‐Eun , Lee Byoung‐Ho , Choi Won‐Sik , Park Byeoung‐Soo , Kim Jeong‐Gyu , Campbell Bruce C 
Published: August 2002

AbstractThe fumigant toxicity of various volatile constituents of essential oils extracted from sixteen Korean spices and medicinal plants towards the rice weevil, Sitophilus oryzae L (Coleoptera: Curculionidae), was determined. The most potent toxicity was found in the essential oil from Mentha arvensis L var piperascens (LC50 = 45.5 µl litre−1 air). GC–MS analysis of essential oil from M arvensis showed it to be rich in menthol (63.2%), menthone (13.1%) and limonene (1.5%), followed in abundance by β‐pinene (0.7%), α‐pinene (0.6%) and linalool (0.2%). Treatment of S oryzae with each of these terpenes showed menthone to be most active (LC50 = 12.7 µl litre−1 air) followed by linalool (LC50 = 39.2 µl litre−1 air) and α‐pinene (LC50 = 54.9 µl litre−1 air). Studies on inhibition of acetylcholinesterase activity of S oryzae showed menthone to have a nine‐fold lower inhibitory effect than menthol, despite menthone being 8.1‐fold more toxic than menthol to the rice weevil. Different modes of toxicity of these monoterpenes towards S oryzae are discussed.© 2001 Society of Chemical Industry
A mechanistic analysis of penetration of glyphosate salts across astomatous cuticular membranes
Authors: Schönherr Jörg 
Published: August 2002

AbstractPenetration of glyphosate salts across isolated poplar (Populus canescens (Aiton) Sm) cuticular membranes (CM) was studied using Na+, K+, NH4+, trimethylsulfonium+ (TMS) and isopropylamine+ (IPA) as cations. After droplet drying, humidity over the salt residues on the outer surfaces of the CM was kept constant, and cuticular penetration was monitored by sampling the receiver solution facing the inner surfaces of the CM. Glyphosate salts disappeared exponentially with time from the surfaces of the CM. This first‐order process could be quantitatively described using rate constants (k) or half‐times (time for 50% penetration; t1/2). Humidity strongly affected the velocity of penetration, as k increased by factors of 5.3 (K‐glyphosate), 6.9 (TMS‐glyphosate), 7.1 (NH4‐glyphosate), 8.5 (Na‐glyphosate) and 10.5 (IPA‐glyphosate) when humidity was increased from 70 to 100%. Depending on the type of cation and humidity, t1/2 varied between 4 and 70 h, but the humidity effect was statistically significant only at 100% humidity, when half‐times were highest with IPA‐glyphosate and lowest with TMS‐glyphosate. Glyphosate acid penetration was measured only at 90% humidity and found to be extremely slow (t1/2 = 866 h). Adding 0.2 g litre−1 of a wetter (alkylpolyglucoside) to the donor increased IPA‐glyphosate rate constants by about four times, but increasing concentration produced no further increase in k. When donors contained 0.2 g litre−1 wetter, further additions of 4 g litre−1 Ethomeen T25 did not change rate constants measured with IPA‐glyphosate at 90% humidity, while Genapol C‐100 and diethyl suberate increased k by only 35%. Concentration of IPA‐glyphosate (1, 2 and 4 g litre−1) did not influence k at 90% humidity, and pH of donor solutions (4.0, 7.7, 9.5) had no effect on k of K‐glyphosate at 90% humidity. Temperature (10 to 25 °C) had only a small influence on velocity of penetration of IPA‐glyphosate and K‐glyphosate, as energies of activation amounted to only 4.26 and 2.92 kJ mole−1, respectively. These results are interpreted as evidence for penetration of glyphosate salts in aqueous pores.© 2002 Society of Chemical Industry
Sea louse control in Scotland, past and present
Authors: Rae Gordon H 
Published: August 2002

AbstractMethods for farming the Atlantic salmon (Salmo salar L) in Scotland were developed at the Unilever Research Laboratory facility at Lochailort on the west coast of Scotland in the late 1960s. By the spring of 1972 a fledgling commercial company had been set up and Marine Harvest, as it was known, received its first year class of smolts at Lochailort. Sea lice (Lepeophtheirus salmonis Krøyer) from passing wild fish infected the smolts but did not cause any significant damage until the summer of 1976 when intervention was required. The Scottish industry has since grown to become a vital source of employment for fragile rural economies and produced about 130 000 tonnes of salmon in 2000. This paper gives an overview of how fish welfare has been maintained by the development of treatments and management strategies aimed at minimising the impact of sea lice.© 2002 Society of Chemical Industry
Synthesis of a membrane protein with two transmembrane regions
Authors: Sato Takeshi , Kawakami Toru , Akaji Kenichi , Konishi Hiroki , Mochizuki Koji , Fujiwara Toshimichi , Akutsu Hideo , Aimoto Saburo 
Published: August 2002

AbstractA membrane protein with two transmembrane domains was synthesized by means of the thioester method. The F1F0 ATP synthase subunit c (Sub.c), which consists of 79 amino acid residues (MW 8257), was chosen as a target. For synthetic purposes, two building blocks, Boc‐[Lys34(Boc)]‐Sub.c(1‐38)‐SCH2CH2CO‐Ala and Sub.c(39‐79), were synthesized via solid‐phase methods using Boc chemistry. RP‐HPLC purification conditions for the transmembrane peptide were examined. As a result, a combination of a mixture of formic acid, 1‐propanol and water with a phenyl column was found to be useful for separating the transmembrane peptide. The purified building blocks were condensed in DMSO in the presence of silver chloride, 3,4‐dihydro‐3‐hydroxy‐4‐oxo‐1,2,3‐benzotriazine (HOOBt), N,N‐diisopropylethylamine to give the product, Sub.c, after removal of Boc groups (yield 16%). The yield of the condensation reaction could be improved to 23% by raising the reaction temperature to 50 °C, and to 26% when a mixture of chloroform and methanol was used as a solvent. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd.
Design of structural joints in building frames
Authors: Jaspart Jean‐Pierre 
Published: August 2002

AbstractA single and unified concept for the design of structural joints in building frames made of any material has been developed in recent years, and is now widely implemented in European design codes. In the present paper, this concept is presented, its merits as far as the economy of a project are demonstrated, and practical design tools for its application in daily practice are briefly described. The paper also contains references to user's manuals and design handbooks.
The antioxidant activity of standardized extract of Ginkgo biloba (EGb 761) in rats
Authors: Bridi R. , Crossetti F. P. , Steffen V. M. , Henriques A. T. 
Published: August 2002

AbstractThe standardized extract of Ginkgo biloba (EGb 761) has been widely employed for its significant benefit in neurodegenerative disorders. Although antioxidative actions have been attributed to this extract, the mechanisms of the multiple principles involved in this pharmacological activity are not completely established. Parkinson's and Alzheimer's diseases are frequently associated with oxidative stress and defects in the cellular protective mechanisms. In this study, the lipid peroxidation (LPO) and the activity of the antioxidant enzymes, catalase (CAT) and superoxide dismutase (SOD) were evaluated in the hippocampus, striatum and substantia nigra (SN) of rats treated with EGb 761. An increase in the CAT and SOD activities in the hippocampus, striatum and SN, and a decrease of the LPO in the hippocampus were observed. These data are additional to the antioxidant properties of EGb 761 reported in the literature and indicate a possible role for the extract in the treatment of diseases involving free radicals and oxidative damage. Copyright © 2001 John Wiley & Sons, Ltd.
Protective effect of a plant formula on ethanol‐induced gastric lesions in rats
Authors: Zhu Min , Lew Katherine T. , Leung Po‐lau 
Published: August 2002

AbstractA plant formula and its five components were evaluated independently for their gastric protective effect against ethanol‐induced stomach lesions in rats. Aqueous extracts of the plant formula (0.25–2 g crude drug/kg orally) and its individual components (at the same dose) all showed significant stomach protective effects dose dependently. However, when these extracts were given to rats at a dose of 0.25 g/kg, the five single‐herb preparations did not show any activity, but the formula‐extract still exhibited a strong protective effect. These findings suggest the presence of a synergistic effect among the plant components. Chemical examination of the extracts indicated that the major ingredients of the five plants were essential oils, terpenoids, flavonoids, glycosides and saccharides and these may contribute to the stomach protective activity observed. Copyright © 2002 John Wiley & Sons, Ltd.