bluuebunny/crossref_metadata_2025 huggingface dataset:
Biophysical and kinetic analysis of wild‐type and site‐directed mutants of the isolated and native dehydroquinate synthase domain of the AROM protein
Authors: Park Alison , Lamb Heather K. , Nichols Charlie , Moore Jonathan D. , Brown Katherine A. , Cooper Alan , Charles Ian G. , Stammers David K. , Hawkins Alastair R.
Published: July 2004

Dehydroquinate synthase (DHQS) is the N‐terminal domain of the pentafunctional AROM protein that catalyses steps 2 to 7 in the shikimate pathway in microbial eukaryotes. DHQS converts 3‐deoxy‐D‐arabino‐heptulosonate‐7‐phosphate (DAHP) to dehydroquinate in a reaction that includes alcohol oxidation, phosphate β‐elimination, carbonyl reduction, ring opening, and intramolecular aldol condensation. Kinetic analysis of the isolated DHQS domains with the AROM protein showed that for the substrate DAHP the difference inKmis less than a factor of 3, that the turnover numbers differed by 24%, and that theKmfor NAD+differs by a factor of 3. Isothermal titration calorimetry revealed that a second (inhibitory) site for divalent metal binding has an approximately 4000‐fold increase inKDcompared to the catalytic binding site. Inhibitor studies have suggested the enzyme could act as a simple oxidoreductase with several of the reactions occurring spontaneously, whereas structural studies have implied that DHQS participates in all steps of the reaction. Analysis of site‐directed mutants experimentally test and support this latter hypothesis. Differential scanning calorimetry, circular dichroism spectroscopy, and molecular exclusion chromatography demonstrate that the mutant DHQS retain their secondary and quaternary structures and their ligand binding capacity. R130K has a 135‐fold reduction in specific activity with DAHP and a greater than 1100‐fold decrease in thekcat/Kmratio, whereas R130A is inactive.
The comparative study on the solution structures of the oxidized bovine microsomal cytochrome b5 and mutant V45H
Authors: Zhang Qi , Cao Chunyang , Wang Zhi‐Qiang , Wang Yun‐Hua , Wu Houming , Huang Zhong‐Xian
Published: July 2004

A comparative study on the solution structures of bovine microsomal cytochrome b5 (Tb5) and the mutant V45H has been achieved by 1D and 2D 1H‐NMR spectroscopy to clarify the differences in the solution conformations between these two proteins. The results reveal that the global folding of the V45H mutant in solution is unchanged, but the subtle changes exist in the orientation of the axial ligand His39, and heme vinyl groups. The side chain of His45 in V45H mutant extends to the outer edge of the heme pocket leaving a cavity at the site originally occupied by the inner methyl group of Val45 residue. In addition, the imidazole ring of axial ligand His39 rotates counterclockwise by ∼3° around the His‐Fe‐His axis, and the 4‐heme vinyl group turns to the space vacated by the removed side chain due to the mutation. Furthermore, the helix III of the heme pocket undergoes outward displacement, while the linkage between helix II and III is shifted leftward. These observations are not only consistent with the pattern of the pseudocontact shifts of the heme protons, but also well account for the lower stability of V45H mutant against heat and urea.
Solution structure of the RWD domain of the mouse GCN2 protein
Authors: Nameki Nobukazu , Yoneyama Misao , Koshiba Seizo , Tochio Naoya , Inoue Makoto , Seki Eiko , Matsuda Takayoshi , Tomo Yasuko , Harada Takushi , Saito Kohei , Kobayashi Naohiro , Yabuki Takashi , Aoki Masaaki , Nunokawa Emi , Matsuda Natsuko , Sakagami Noriko , Terada Takaho , Shirouzu Mikako , Yoshida Mayumi , Hirota Hiroshi , Osanai Takashi , Tanaka Akiko , Arakawa Takahiro , Carninci Piero , Kawai Jun , Hayashizaki Yoshihide , Kinoshita Kengo , Güntert Peter , Kigawa Takanori , Yokoyama Shigeyuki
Published: July 2004

GCN2 is the α‐subunit of the only translation initiation factor (eIF2α) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N‐terminus, which is termed the RWD domain after three major RWD‐containing proteins: RING finger‐containing proteins, WD‐repeat‐containing proteins, and yeast DEAD (DEXD)‐like helicases. In this study, we determined the solution structure of the mouse GCN2 RWD domain using NMR spectroscopy. The structure forms an α + β sandwich fold consisting of two layers: a four‐stranded antiparallel β‐sheet, and three side‐by‐side α‐helices, with an αββββαα topology. A characteristic YPXXXP motif, which always occurs in RWD domains, forms a stable loop including three consecutive β‐turns that overlap with each other by two residues (triple β‐turn). As putative binding sites with GCN1, a structure‐based alignment allowed the identification of several surface residues in α‐helix 3 that are characteristic of the GCN2 RWD domains. Despite the apparent absence of sequence similarity, the RWD structure significantly resembles that of ubiquitin‐conjugating enzymes (E2s), with most of the structural differences in the region connecting β‐strand 4 and α‐helix 3. The structural architecture, including the triple β‐turn, is fundamentally common among various RWD domains and E2s, but most of the surface residues on the structure vary. Thus, it appears that the RWD domain is a novel structural domain for protein‐binding that plays specific roles in individual RWD‐containing proteins.
Asymmetric amino acid compositions of transmembrane β‐strands
Authors: Chamberlain Aaron K. , Bowie James U.
Published: July 2004

In contrast to water‐soluble proteins, membrane proteins reside in a heterogeneous environment, and their surfaces must interact with both polar and apolar membrane regions. As a consequence, the composition of membrane proteins' residues varies substantially between the membrane core and the interfacial regions. The amino acid compositions of helical membrane proteins are also known to be different on the cytoplasmic and extracellular sides of the membrane. Here we report that in the 16 transmembrane β‐barrel structures, the amino acid compositions of lipid‐facing residues are different near the N and C termini of the individual strands. Polar amino acids are more prevalent near the C termini than near the N termini, and hydrophobic amino acids show the opposite trend. We suggest that this difference arises because it is easier for polar atoms to escape from the apolar regions of the bilayer at the C terminus of a β‐strand. This new characteristic of β‐barrel membrane proteins enhances our understanding of how a sequence encodes a membrane protein structure and should prove useful in identifying and predicting the structures of trans‐membrane β‐barrels.
Caspase activation, inhibition, and reactivation: A mechanistic view
Authors: Shi Yigong
Published: July 2004

Caspases, a unique family of cysteine proteases, execute programmed cell death (apoptosis). Caspases exist as inactive zymogens in cells and undergo a cascade of catalytic activation at the onset of apoptosis. The activated caspases are subject to inhibition by the inhibitor‐of‐apoptosis (IAP) family of proteins. This inhibition can be effectively removed by diverse proteins that share an IAP‐binding tetrapeptide motif. Recent structural and biochemical studies have revealed the underlying molecular mechanisms for these processes in mammals and in Drosophila. This paper reviews these latest advances.
Detecting hidden sequence propensity for amyloid fibril formation
Authors: Yoon Sukjoon , Welsh William J.
Published: July 2004

The preponderance of evidence implicates protein misfolding in many unrelated human diseases. In all cases, normal correctly folded proteins transform from their proper native structure into an abnormal β‐rich structure known as amyloid fibril. Here we introduce a computational algorithm to detect nonnative (hidden) sequence propensity for amyloid fibril formation. Analyzing sequence–structure relationships in terms of tertiary contact (TC), we find that the hidden β‐strand propensity of a query local sequence can be quantitatively estimated from the secondary structure preferences of template sequences of known secondary structure found in regions of high TC. The present method correctly pinpoints the minimal peptide fragment shown experimentally as the likely local mediator of amyloid fibril formation in β‐amyloid peptide, islet amyloid polypeptide (hIAPP), α‐synuclein, and human acetylcholinesterase (AChE). It also found previously unrecognized β‐strand propensities in the prototypical helical protein myoglobin that has been reported as amyloidogenic. Analysis of 2358 nonhomologous protein domains provides compelling evidence that most proteins contain sequences with significant hidden β‐strand propensity. The present method may find utility in many medically relevant applications, such as the engineering of protein sequences and the discovery of therapeutic agents that specifically target these sequences for the prevention and treatment of amyloid diseases.
NMR structure of CXCR3 binding chemokine CXCL11 (ITAC)
Authors: Booth Valerie , Clark‐Lewis Ian , Sykes Brian D.
Published: July 2004

CXCL11 (ITAC) is one of three chemokines known to bind the receptor CXCR3, the two others being CXCL9 (Mig) and CXCL10 (IP‐10). CXCL11 differs from the other CXCR3 ligands in both the strength and the particularities of its receptor interactions: It has a higher affinity, is a stronger agonist, and behaves differently when critical N‐terminal residues are deleted. The structure of CXCL11 was determined using solution NMR to allow comparison with that of CXCL10 and help elucidate the source of the differences. CXCL11 takes on the canonical chemokine fold but exhibits greater conformational flexibility than has been observed for related chemokines under the same sample conditions. Unlike related chemokines such as IP‐10 and IL‐8, ITAC does not appear to form dimers at millimolar concentrations. The origin for this behavior can be found in the solution structure, which indicates a β‐bulge in β‐strand 1 that distorts the dimerization interface used by other CXC chemokines.
Sensorimotor Adaptation to Violations of Temporal Contiguity
Authors: Cunningham Douglas W. , Billock Vincent A. , Tsou Brian H.
Published: July 2004

Most events are processed by a number of neural pathways. These pathways often differ considerably in processing speed. Thus, coherent perception requires some form of synchronization mechanism. Moreover, this mechanism must be flexible, because neural processing speed changes over the life of an organism. Here we provide behavioral evidence that humans can adapt to a new intersensory temporal relationship (which was artificially produced by delaying visual feedback). The conflict between these results and previous work that failed to find such improvements can be explained by considering the present results as a form of sensorimotor adaptation.
Reproductive strategies in two sympatric morphotypes of Arctic charr in Kalandsvatnet, west Norway
Authors: Telnes T. , SÆgrov H.
Published: July 2004

Differences in gonadal development and time of spawning were found in two coexisting morphotypes of Arctic charr Salvelinus alpinus in Kalandsvatnet, Norway. Spawning depth and some main life‐history variables also differed. These observations suggest that the two morphotypes do not interbreed freely.
Phylogeographic relationships within the Mediterranean turbot inferred by mitochondrial DNA haplotype variation
Authors: Suzuki N. , Nishida M. , Yoseda K. , ÜstÜndaǧ C. , Şahi̇n T. , Amaoka K.
Published: July 2004

The Mediterranean turbot Psetta maxima consists of two main genetically distinct lineages (western Mediterranean and ‘eastern secluded Mediterranean’ basins) as investigated by mitochondrial DNA analysis. Within the latter lineage, most haplotypes from the Sea of Azov were endemic and more than half of them derived from a single ancestral haplotype shared among all the eastern Mediterranean areas. There was no relation between morphotype variation in bony tubercles and mitochondrial genealogy.
The effect of temperature and acclimation period on repeat swimming performance in cutthroat trout
Authors: MacNutt M. J. , Hinch S. G. , Farrell A. P. , Topp S.
Published: July 2004

Hatchery cutthroat trout Oncorhynchus clarki clarki were used to examine the effects of 48 h and 3 week temperature acclimation periods on critical swimming speed (Ucrit). The Ucrit was determined for fish at acclimation temperatures of 7, 14 and 18° C using two consecutive ramp‐Ucrit tests in mobile Brett‐type swim tunnels. An additional group was tested at the stock's ambient rearing temperature of 10° C. The length of the temperature acclimation period had no significant effect on either the first or the second Ucrit(Ucrit‐1 and Ucrit‐2, respectively) or on the recovery ratio (the quotient of Ucrit‐2 Ucrit‐1−1). As anticipated, there was a significant positive relationship between Ucrit‐1 and temperature (P < 0·01) for both acclimation periods, and an increasing, though non‐significant, trend between Ucrit‐2 and temperature (P = 0·10). Acclimation temperature had no significant effect (P = 0·71) on the recovery ratio. These results indicate that a 48 h acclimation to experimental temperatures within the range of −3 to +8° C of the acclimation temperature may be sufficient in studies of swimming performance with this species. This ability to acclimate rapidly is probably adaptive for cutthroat trout and other species that occupy thermally variable environments.
Otolith description and age‐and‐growth ofKurtus gulliverifrom northern Australia
Authors: Berra T. M. , Aday D. D.
Published: July 2004

The sagitta ofKurtus gulliveriwas ovate, moderately thick with the following attributes: lateral surface convex, mesial surface flat; dorsal margin sinuate, posterior margin rounded ventrally, ventral margin rounded and irregular; sulcus divided into ostium and cauda by constriction of dorsal and ventral margins, heterosulcoid, colliculum heteromorph; dorsal depression large and distinct, ventral groove close to margin in larger otoliths; rostrum broad and antirostrum small, separated by wide, shallow excisural notch. Otolith size was moderate, average 4·6% standard length (LS), typical for a perciform. Annuli on 78 whole sagittae were read, and 15% of these were transversely sectioned for verification of the annuli. Males ranged from 94 to 235 mmLSand females from 95 to 284 mmLS. There was little difference in size distribution of the sample between the sexes, perhaps due to a 6 month spawning season over which young were continually added to the population. Some sexual dimorphism was noted, however, as age 2 year females were significantly larger than males of the same age. The largest fish aged was a 284 mmLS, 3 year‐old female, and the oldest age reached was 4 years by two males. It appears likely that most spawning females are ≥2 years old, but some larger 1 year old fish may attain sexual maturity.
Foraging behaviour and capture success in perch, pikeperch and pike and the effects of prey density
Authors: Turesson H. , Brönmark C.
Published: July 2004

The effect of school size on capture success in three different piscivores, perchPerca fluviatilis, pikeperchStizostedion luciopercaand pikeEsox lucius, was investigated. RoachRutilus rutiluswere used as prey in a pool experiment where individual predators were presented prey at densities of one, two, four, eight and 16 prey, respectively. Treatments were replicated seven times for each predator species. Perch was at first virtually unable to capture a prey from a school and suffered a significant confusion effect with increasing prey density. The effect, however, was limited in the long run, as the perch was a very effective predator in its hunting strategy where it singled out and repeatedly attacked single prey irrespective of prey density or school size. Pikeperch and pike were able to attack and capture prey at any prey density equally successfully and thus did not suffer from a confusion effect. Neither did these predators receive any apparent advantages from increasing prey density.
Increasing turbidity significantly alters the diet of brown trout: a multi‐year longitudinal study
Authors: Stuart‐Smith R. D. , Richardson A. M. M. , White R. W. G.
Published: July 2004

The stomach contents of adult brown trout Salmo trutta from Lake Sorell, Tasmania, were analysed during 6 years of increasing turbidity to follow changes in the diet associated with dramatic changes in water clarity. Brown trout were sampled from 1996, when turbidity was 26 NTU, to 2001 when turbidity was 141 NTU. The mean relative volume of stomach contents decreased progressively to 2001, by which time it was only one sixth of that in 1996, and the mean diversity of prey in stomachs decreased from an average of more than six species per stomach in 1996 to one species in 2001. The species composition of stomach contents shifted from domination by the phreatoicid isopod Colubotelson sp., to the galaxiid fish Galaxias auratus and the amphipod Austrochiltonia australis, and then the cladoceran Daphnia carinata. To give an indication of diet changes over a typical yearly cycle in the current turbid state of the lake, a sample was taken from each season from December 2000 to September 2001. Two basic diets were found during the year; brown trout specialized on D. carinata in summer and autumn, and G. auratus in winter and spring. Mean diversity of prey was less than two species per stomach in all samples from 2000 to 2001, except for the sample from spring 2001 when it was 2·2 species per stomach, and the mean relative volume of stomach contents was more than three times greater in winter than any other season. The ways in which high turbidity may have influenced the changes in the brown trout diet observed since 1996 and the patterns evident during the seasons of 2000–2001 are discussed.
Population structure of lake‐type and river‐type sockeye salmon in transboundary rivers of northern British Columbia
Authors: Beacham T. D. , McIntosh B. , MacConnachie C.
Published: July 2004

The population structure of ‘lake‐type’ and ‘river‐type’ sockeye salmon Oncorhynchus nerka, primarily in transboundary rivers in northern British Columbia, was examined with a survey of microsatellite variation. Variation at 14 microsatellite loci was surveyed from c. 3000 lake‐type and 3200 river‐type sockeye salmon from 47 populations in six river drainages in British Columbia. The mean FST for the 14 microsatellite loci and 47 populations was 0·068, and 0·034 over all river‐type populations. River‐type sockeye salmon were more genetically diverse than lake‐type sockeye salmon, with expected heterozygosity of river‐type sockeye salmon 0·72 and with an average 12·7 alleles observed per locus, whereas expected heterozygosity of lake‐type sockeye salmon was 0·65 with and average 10·5 alleles observed per locus. River drainage of origin was a significant unit of population structure. There was clear evidence of genetic differentiation among river‐type populations of sockeye salmon from different drainages over a broad geographic range in British Columbia.
Genetic diversity of brown trout in central Italy
Authors: Caputo V. , Giovannotti M. , Nisi Cerioni P. , Caniglia M. L. , Splendiani A.
Published: July 2004

Genetic diversity was analysed in brown trout Salmo trutta populations living in an area of central Italy using RFLP analysis of two mtDNA segments and of the nuclear locus LDH‐C1*. The data indicated a genetic structure profoundly altered by repeated stockings with allochthonous material of Atlantic origin. In fact, four and 11 of the haplotypes detected were, respectively, identical or genetically very close to haplotypes found in Danish populations, the putative source of stocked brown trout. Furthermore, the LDH‐C1*90 allele, typical of north‐western Europe, was widespread among the samples studied. Nonetheless, four populations are characterized by a high frequency of both putative autochthonous haplotypes and the LDH‐C1*100 allele, common in the Mediterranean basin. These populations, sampled in areas where S. trutta is documented historically, might represent a remnant of the species’ indigenous biodiversity, showing the scope for improving the management of brown trout in central Italy.
Morphological and genetic distinctness of rock and shell‐bed dwellingTelmatochromis(Teleostei, Cichlidae) in the south of Lake Tanganyika suggest the existence of two species
Authors: Takahashi T.
Published: July 2004

Two populations from Wonzye and Nkumbula Island, Lake Tanganyika, containing both rock and shell‐bed dwelling individuals of the genusTelmatochromiswere analysed by means of comparative morphological and DNA haplotype data from the mitochondrial control region. The data on individuals from rockv. shell‐bed habitats allowed a clear discrimination to be made between habitats, while there was no distinction among individuals of the same habitat from Wonzye and Nkumbula. The shell‐bed dwellers had small body size, including smaller size at sexual maturity and fewer eggs than rock dwellers. The existence of two distinct species that diversified according to habitat choice is suggested.
Competition for shelter among over‐wintering signal crayfish and juvenile Atlantic salmon
Authors: Griffiths S. W. , Collen P. , Armstrong J. D.
Published: July 2004

Three separate effects on refuge use by signal crayfish Pacifastacus leniusculus and Atlantic salmon Salmo salar were examined: (1) the effect on Atlantic salmon of an addition of signal crayfish (doubling the total number of animals), (2) the effect on signal crayfish of an addition of Atlantic salmon and (3) intraspecific compared with interspecific competition, compared by holding total density of animals constant and varying the proportion of signal crayfish and Atlantic salmon in trials. Observations were made during winter, when both species are nocturnal. The proportion of Atlantic salmon sheltering was significantly lower in the presence than in the absence of signal crayfish when the interspecific treatment (Atlantic salmon plus signal crayfish) effected a doubling in density compared to the intraspecific treatment (Atlantic salmon alone). The proportion of signal crayfish sheltering was independent of the presence of Atlantic salmon. When total density was constant, the proportion of Atlantic salmon sheltering was significantly higher in intraspecific (52·8%) than interspecific trials (27·3%). Atlantic salmon out of shelter during the day in winter are believed to be very vulnerable to predators and the capacity for fish to share shelters with one another is known to be very low. Therefore, competition from crayfish for winter shelters may lead to detrimental effects on Atlantic salmon populations.
Genetic divergence of sympatric resident and anadromous forms of Oncorhynchus mykiss in the Walla Walla River, U.S.A.
Authors: Narum S. R. , Contor C. , Talbot A. , Powell M. S.
Published: July 2004

Genetic structure (six microsatellites) and gene flow were examined among anadromous (steelhead; n = 326), resident (rainbow trout; n = 52), and mixed (n = 407)Oncorhynchus mykiss life‐history forms collected from the major drainages the mainstem Walla Walla River and the Touchet River within the Walla Walla River sub‐basin, Washington, U.S.A. Genetic structure was detected between the two major drainages. Exact tests, FST, multi‐locus assignment tests and a neighbour‐joining dendrogram revealed genetic divergence between sympatric reference populations of adult steelhead and resident rainbow trout in the mainstem Walla Walla River, but not in the Touchet River. Tests of Hardy‐Weinberg equilibrium indicated anadromous and resident O. mykiss reference populations were in equilibrium, but many of the mixed life‐history collections were out of equilibrium. Populations out of equilibrium in the mainstem Walla Walla River appeared to be admixtures as confirmed by multi‐locus assignment tests. This is evidence of genetic divergence probably resulting from assortative mating between life‐history forms or out‐of‐basin stocking practices.
The relationship between temperature and the size and age of larvae and peri‐metamorphic stages of Pleuronectes flesus
Authors: Hutchinson S. , Hawkins L. E.
Published: July 2004

Laboratory observations of live animals were used to describe the developmental sequence of the flounder Pleuronectes flesus. Developmental state was related to age and total length (LT) from hatching, through metamorphosis, to the juvenile form. By following animals at 7, 11 and 15° C it was found that, whilst the LT at metamorphosis was the same for all the temperature regimes and was not temperature‐dependant, the time taken to reach this stage was related to rearing temperature. It was also observed that animals could be induced to metamorphose by transfer to reduced salinity but only if they were close to the critical length for metamorphosis.
Performance of juvenile brown trout exposed to fluctuating water level and temperature
Authors: Flodmark L. E. W. , VØllestad L. A. , Forseth T.
Published: July 2004

Individual daily food intake, mass‐specific growth rate and growth efficiency in groups of juvenile brown trout Salmo trutta were compared in tank experiments with three water level regimes (fluctuating, stable high and low water levels) and two temperature regimes (fluctuating between 10 and 14° C and constant 14° C) to simulate events during hydropeaking in regulated rivers. Fish exposed to high stable water level showed higher food intake and growth rate, and higher or similar growth efficiency than fish exposed to fluctuating or stable low water level. Both groups of slow‐growing and fast‐growing individuals fed less and grew slower at stable low and fluctuating water level than at stable high water level. Furthermore, growth and growth efficiency were lower in brown trout exposed to stable low water level and fluctuating temperature, particularly for groups of fish with slow growth. Temperature did not have any effect at high water level. For groups of fast‐growing fish, there was no difference in growth efficiency between treatments. It is concluded that fluctuating water level and temperature have a potentially detrimental effect on growth in juvenile brown trout and effects are more severe in slow‐ than fast‐growing fish.
Genetic identification of Anisakis larvae in European hake from Atlantic and Mediterranean waters for stock recognition
Authors: Mattiucci S. , Abaunza P. , Ramadori L. , Nascetti G.
Published: July 2004

The occurrence of seven species of the larval parasitic nematode Anisakis, which can be used as a biological tag for hake Merluccius merluccius stocks throughout their geographical range, is reported. Hake were collected from 14 localities in the Mediterranean Sea and the Atlantic Ocean. Anisakis larvae (n = 1950), which were recovered, were identified to species by means of genetic markers (allozymes). Within Anisakis type I, the larvae of A. pegreffii, A. simplex s.s., A. typica and A. ziphidarum were detected, while within Anisakis type II, A. physeteris, A. brevispiculata and Anisakis sp. were identified. There were significant differences in the relative proportions of the various Anisakis species identified in hake samples from the Mediterranean Sea and Atlantic Ocean, suggesting the existence of different stocks of M. merluccius in European waters.
DNA‐based species identification of krill consumed by whale sharks
Authors: Jarman S. N. , Wilson S. G.
Published: July 2004

DNA was purified from whale shark Rhincodon typus faecal material that contained DNA derived from their prey. A DNA‐based krill identification method was used to determine the exact krill species upon which the whale shark was feeding, where morphological analysis had failed to make an identification.
Constraints of body size and swimming velocity on the ability of juvenile rainbow trout to endure periods without food
Authors: Simpkins D. G. , Hubert W. A. , Martinez Del Rio C. , Rule D. C.
Published: July 2004

The hypothesis that body size and swimming velocity affect proximate body composition, wet mass and size‐selective mortality of fasted fish was evaluated using small (107 mm mean total length, LT) and medium (168 mm mean LT) juvenile rainbow trout Oncorhynchus mykiss that were sedentary or swimming (c. 1 or 2 body length s−1) and fasted for 147 days. The initial amount of energy reserves in the bodies of fish varied with LT. Initially having less lipid mass and relatively higher mass‐specific metabolic rates caused small rainbow trout that were sedentary to die of starvation sooner and more frequently than medium‐length fish that were sedentary. Swimming at 2 body length s−1 slightly increased the rate of lipid catabolism relative to 1 body length s−1, but did not increase the occurrence of mortality among medium fish. Death from starvation occurred when fish had <3·2% lipid remaining in their bodies. Juvenile rainbow trout endured long periods without food, but their ability to resist death from starvation was limited by their length and initial lipid reserves.
Reproductive biology of two sympatric skates in the south‐west Atlantic: Psammobatis rudis and Psammobatis normani
Authors: Mabragaña E. , Cousseau M. B.
Published: July 2004

The total lengths (LT) at which 50% were mature of Psammobatis rudis and Psammobatis normani, in the south‐west Atlantic were: P. rudis, 428 mm for males and 414 mm for females and P. normani, 443 mm for males and 403 mm for females. Clasper length in mature males was greater in P. normani than in P. rudis, whereas oviducal gland width was not different between species. Females of P. normani with egg cases were found in every month sampled, and in January, March, April and July in P. rudis, although insufficient samples were available to identify peak oviposition times. Geographic variation in size frequency and maturity were found. The effects of oceanographic conditions and fishing pressure are discussed. Size at 50% maturity in both species was >74% of the maximum LT, indicating late sexual maturity and low potential stock recovery rate.
The Geography of Support for Open‐Space Initiatives: A Case Study of New Jersey's 1998 Ballot Measure*
Authors: Solecki William D. , Mason Robert J. , Martin Shannon
Published: July 2004

Objectives. By a two to one margin, New Jersey voters in 1998 approved a ballot measure authorizing a 10‐year, 1‐billion dollar open‐space acquisition program. This article's principal objectives are to investigate and explain the spatial character of that vote.

Methods. Our methods consists of regression and principal components analyses; we use municipal‐level data to define statewide patterns of voter support and participation in relation to a series of socioeconomic, political, and environmental variables.

Results. The analyses yielded two major findings: (1) support for the ballot measure was widespread, but exceptionally strong in the “wealth belt” area of north‐central New Jersey, and (2) voter participation, defined as those voting on the measure as a proportion of all who voted, lagged in the core urban areas.

Conclusions. Our conclusions point critically to the importance of socioeconomic status, urban residence, and presence of existing open‐space regulations—as well as rapid changes in the overall sociopolitical landscape—in explaining voter behavior.
Efficiency, Accountability, and Private Government: The Impact of Residential Community Associations on Residential Property Values*
Authors: Langbein Laura , Spotswood‐Bright Kim
Published: July 2004

Objective. This study evaluates the impact of residential community associations (RCAs) on RCA property values by testing competing theoretical expectations about the efficiency and accountability of RCAs with empirical evidence.

Method. We use pooled data on 195 units in six RCAs in one city, regressing sales price on RCA fees, a proxy for the importance of professional management compared to community involvement, previous property values, and other variables.

Results. We find that increases in RCA fees (and services) depress average property values over what they would be otherwise, and that professional management somewhat mitigates this effect by raising property values.

Conclusion. RCAs with horizontal, community controls act as if they are governed by a high‐demand, volunteer, review group by producing and charging too much, while professional management (i.e., hierarchical control) slightly reduces the tendency of RCAs to produce and charge too much. RCAs may not be the model of efficiency that proponents of private governments expect.
Options: Racial/Ethnic Identification of Children of Intermarried Couples*
Authors: Qian Zhenchao
Published: July 2004

Objective.Whites of various European ethnic backgrounds usually have weak ethnic attachment and have options to identify their ethnic identity (Waters, 1990). What about children born to interracially married couples?

Methods.I use 1990 Census data—the last census in which only one race could be chosen—to examine how African American‐white, Latino‐white, Asian American‐white, and American Indian‐white couples identify their children's race/ethnicity.

Results.Children of African American‐white couples are least likely to be identified as white, while children of Asian American‐white couples are most likely to be identified as white. Intermarried couples in which the minority spouse is male, native born, or has no white ancestry are more likely to identify their children as minorities than are those in which the minority spouse is female, foreign born, or has part white ancestry. In addition, neighborhood minority concentration increases the likelihood that biracial children are identified as minorities.

Conclusion.This study shows that choices of racial and ethnic identification of multiracial children are not as optional as for whites of various European ethnic backgrounds. They are influenced by race/ethnicity of the minority parent, intermarried couples' characteristics, and neighborhood compositions.
Fertility Changes Among Immigrants: Generations, Neighborhoods, and Personal Characteristics*
Authors: Hill Laura E. , Johnson Hans P.
Published: July 2004

Objective. To understand how adaptation/assimilation, disruption, and diffusion interact to produce changes in fertility levels among successive generations of Mexicans and Central Americans in the United States.

Method. Using restricted access data that link individual data (CPS) to neighborhood data (census tracts), we examine the role of generation, personal characteristics, and neighborhood characteristics in determining children ever born (CEB).

Results. There are significant differences in fertility across generations and, to a lesser extent, between women who live in ethnic enclaves and those who do not. Once personal characteristics are considered, the independent effect of generation on fertility is nearly eliminated. Personal characteristics dominate neighborhood characteristics in their ability to predict fertility. The most consistent predictor of CEB at the neighborhood level is the percentage of Hispanic adults.

Conclusions. Personal characteristics dominate fertility change across generation, and were it not for increases in educational attainment, fertility might be higher in successive generations rather than lower or unchanged.
Race/Ethnicity and Beliefs about Wealth and Poverty*
Authors: Hunt Matthew O.
Published: July 2004

Objective. Lay explanations for “wealth” have been neglected in research on beliefs about social stratification. This study compares the nature and determinants of beliefs about the causes of both wealth and poverty, with special focus on race/ethnic differences.

Methods. Using survey data collected from Los Angeles County residents in 2000, descriptive and multivariate procedures are used to analyze “individualistic” and “structuralist” beliefs about wealth and poverty. In addition, one “fatalistic” belief, asking about the role of “God's will” in shaping wealth and poverty, is examined. Analyses test (1) whether race/ethnicity and other social and political characteristics variables shape these stratification beliefs, and (2) whether African Americans, Latinos, and whites differ in the determinants of beliefs about wealth and poverty.

Results. Respondents favor individualistic over structuralist reasons for wealth, but favor structuralist over individualistic beliefs in explaining poverty. Fatalistic beliefs are least popular. On beliefs about wealth, African Americans, Latinos, and whites show similar levels of support for individualistic explanations; however, the race/ethnic minorities are both more structuralist than whites on this issue. On beliefs about poverty, the race/ethnic minorities are simultaneously more structuralist and more individualistic than are whites. Social‐class identification and self‐reported conservatism both significantly impact beliefs about wealth and poverty, and do so differently across race/ethnic lines.

Conclusions. Findings support the separate treatment and examination of beliefs about wealth and poverty, and reinforce recent calls for greater attention to “nonwhites” in studies of sociopolitical attitudes.
Early life stage toxicity of extracts from the African fish poison plants Tephrosia vogelii Hook. f. and Asystasia vogeliana Benth. on zebrafish embryos
Authors: Ekanem A. P. , Meinelt T. , Kloas W. , Knopf K.
Published: July 2004

Embryos of Danio rerio are highly susceptible to extracts of the plants Tephrosia vogelii and Asystasia vogeliana. The concentration of the dried extracts at which 50% of the embryos were affected (EC50) after 24 h exposure were 320 and 572 μg l−1, respectively; corresponding 50% mortality (LC50) values after 48 h exposure were 493 and 869 μg l−1. Results indicate that the use of these ichthyotoxic plants might have a severe impact on the survival of fish larvae in the field.
Cloning and Expression of the Gene for Serine–Glyoxylate Aminotransferase from an Obligate Methylotroph Hyphomicrobium Methylovorum GM2
Authors: Hagishita Tairo , Yoshida Toyokazu , Izumi Yoshikazu , Mitsunaga Toshio
Published: July 2004

The gene encoding serine–glyoxylate aminotransferase, one of key enzymes for the assimilation of one‐carbon compounds in methylotrophs, and its flanking regions were isolated from an obligate methylotrophic bacterium, Hyphomicrobium methylovorum GM2. Nucleotide sequencing of the recombinant plasmids revealed that the serine–glyoxylate aminotransferase gene encodes a 405‐amino‐acid protein with a calculated molecular mass of 43 880 Da. The amino acid sequence of the enzyme showed identity to the sequences of serine‐glyoxylate aminotransferase of Methylobacterium extorquens AM1 (57%), aspartate aminotransferase of Methanobacterium thermoformicicum (31%), human peroxisomal alanine–glyoxylate aminotransferase (27%), and serine‐pyruvate aminotransferase of rat liver mitochondria (33%). The recombinant plasmid, which was constructed by ligation of the cloned gene and an expression vector pKK223‐3, was introduced into Escherichia coli HB101. The recombinant enzyme was purified from transformed E. coli cells and analyzed by immunological and enzymological methods. The overexpressed enzyme was indistinguishable from the wild‐type enzyme isolated from H. methylovorum GM2.
Transcriptional Regulation of the Lutropin/Human Choriogonadotropin Receptor and Three Enzymes of Steroidogenesis by Growth Factors in Cultured Pig Leydig Cells
Authors: Chuzel Franck , Clark Ann M. , Avallet Odile , Saez José M.
Published: July 2004

Recent data have shown that Leydig‐cell‐specific functions, and therefore steroidogenic capacity, can be regulated by lutropin/human choriogonadotropin collectively termed gonadotropin and by several growth factors that are produced by and act within the testis. However, the molecular mechanisms by which these factors regulate Leydig cells are not understood. In the present study, we have investigated the effects of basic fibroblast growth factor (bFGF), epidermal growth factor (EGF), insulin‐like growth factor I (IGF‐I) and transforming growth factor β (TGF‐β) on mRNA for the gonadotropin receptor and three steroidogenic enzymes: cytochrome P‐450SCC, cytochrome P‐450 17α‐hydroxylase/C17–20 lyase (17α‐hydroxylase), and 3β‐hydroxysteroid dehydrogenase. IGF‐1, which can enhance testosterone production, increased gonadotropin‐receptor density after an increase in receptor mRNA levels, and it increased the level of mRNA for cytochrome P‐450SCC, and 17α‐hydrolyase. Micromolar concentrations of insulin had similar effects to those of IGF‐I. Moreover, the three factors that decreased testosterone production (EGF, bFGF and TGFβ1) decreased gonadotropin receptor density, receptor mRNA levels and the mRNA levels for 17α‐hydroxylase. The potential effects of these growth factors on the transcription of the gonadotropin genes for the receptor and these three steroidogenic enzymes were measured by means of nuclear run‐on assays. We demonstated that the long‐term inhibitory (EGF, bFGF, TGFβ1) or stimulatory (IGF‐I) effects of these growth factors are primarily due to a variation in the transcription rates of genes for the gonadotropin receptor, cytochrome P‐450SCC, and 17α‐hydroxylase. Moreover, since previous studies have shown than some of these growth factors are expressed within the testis, they may play a physiological role in the regulation of differentiated testicular functions.
Tyrosinase, the Key Enzyme in Melanin Synthesis, is Expressed in Murine Brain
Authors: Tief Kirsten , Hahne Michael , Schmidt Andrea , Beermann Friedrich
Published: July 2004

Tyrosinase is one of the key enzymes in mammalian melanin synthesis. The pigment is produced in two different cell types: the pigmented epithelial cell of the retina, and the melanocyte, a cell of neural‐crest origin. We recently showed that a fusion gene between regulatory sequences of tyrosinase gene (tyr) and the β‐galactosidase gene (IucZ), when introduced into transgenic mice, resulted in embryonic expression in presumptive pigment cells but also in cell populations along the entire neural tube. This expression in the developing brain was striking, and we therefore asked whether this would still be detectable after birth. Transgenic mice carrying the tyr‐lucZ fusion gene showed β‐galactosidase expression in adult brain. On Western blots, we detected tyrosinase‐specific bands of 65–68 kDa in brain and eye. Using an affinity‐purified antibody, we showed that detection of tyrosinase is specific and competed off by the presence of the cognate tyrosinase‐derived peptide. However, neither tyrosine hydroxylase nor Dopa oxidase activity were detected in protein extracts of brain. We therefore suggest that tyrosinase is present in brain but either not functional or catalyzing different reactions compared to pigment cells.
Molecular Identification of a Major Retinoic‐Acid‐Synthesizing Enzyme, a Retinaldehyde‐Specific Dehydrogenase
Authors: Zhao Dayao , McCaffery Peter , Ivins Kathryn J. , Neve Rachael L. , Hogan Patrick , Chin William W. , Dräger Ursula C.
Published: July 2004

Retinoic acid, a developmental signal implicated in the formation of the neural axis, is present at high levels in the early embryonic trunk region, where it is synthesized by a novel dehydrogenase. Here we show that the same enzyme is inducible by retinoic acid in P19 teratocarcinoma cells, and we report the cloning from P19 cells of a cDNA encoding a novel dehydrogenase, named retinaldehyde dehydrogenase‐2 (RALDH‐2). Expression in COS cells shows RALDH‐2 to be highly effective in oxidation of retinaldehyde, with no detectable activity on any other aldehyde tested.In situhybridization histochemistry on the embryonic trunk reveales RALDH‐2 mRNA both in mesoderm and neuroectoderm, with highest neuroectodermal expression in the ventral horn of the spinal cord at two restricted locations along the anteroposterior axis, presumably the subpopulation of motoneurons that innervate the limbs.
Cloning, Purification and Characterization of the Protein Subunit of Ribonuclease P from the Cyanobacterium Synechocystis sp. PCC 6803
Authors: Pascual Alberto , Vioque Agustín
Published: July 2004

The rnpA gene from the cyanobacterium Synechocystis sp. PCC 6803, which codes for the protein subunit of ribonuclease P (RNase P), has been cloned by functional complementation of an Escherichia coli mutant. This protein had previously been characterized only in proteobacteria and gram‐positive bacteria. rnpA and the closely linked rpmH gene, which code for the large subunit ribosomal protein L34, have been sequenced. The Synechocystis 6803 L34 protein is more similar to the homologous protein from some non‐green chloroplasts than to the L34 protein from other bacteria. The protein subunit of RNase P from Synechocystis 6803 has been overexpressed in E. coli and purified to homogeneity. Antibodies raised against the Synechocystis 6803 RNase P protein did not recognize the homologous protein from E. coli (C5 protein). Similarly, antibodies raised against the E. coli C5 protein did not recognize significantly the Synechocystis 6803 protein. In spite of the lack of immunological cross‐reactivity and the low level of sequence identity, the E. coli and Synechocystis 6803 proteins are functionally inter‐changeable. In enzymatic assays using either an E. coli precursor tRNATyr or a Synechocystis 6803 precursor tRNAGGln as substrates, we have detected RNase P activity with holoenzymes reconstituted with the RNA subunit from E. coli and the protein subunit from Synechocystis 6803 or with the RNA subunit from Synechocystis 6803 and the protein subunit from E. coli. The relative efficiency of cleavage of the different substrates is dependent on the origin of the protein subunit used to reconstitute the holoenzyme.
Locations of Functional Domains in the RecA Protein
Authors: Takahashi Masayuki , Maraboeuf Fabrice , Nordén Bengt
Published: July 2004

We review the locations of various functional domains of the RecA protein of Escherichia coli, including how they have been assigned, and discuss the potential regulatory roles of spatial overlap between different domains. RecA is a multifunctional and ubiquitous protein involved both in general genetic recombination and in DNA repair: it regulates the synthesis and activity of DNA repair enzymes (SOS induction) and catalyses homologous recombination and mutagenesis. For these activities RecA interacts with a nucleotide cofactor, single‐stranded and double‐stranded DNAs, the LexA repressor, UmuD protein, the UmuD2'C complex as well as with RecA itself in forming the catalytically active nucleofilament. Attempts to locate the respective interaction sites have been advanced in order to understand the various functions of RecA. An intriguing question is how these numerous functional sites are contained within this rather small protein (38 kDa). To assess more clearly the roles of the respective sites and to what extent the sites may be interacting with each other, we review and compare the results obtained from various biological, biochemical and physico‐chemical approaches. From a three‐dimensional model it is concluded that all sites are concentrated to one part of the protein. As a consequence there are significant overlaps between the sites and it is speculated that corresponding interactions may play important roles in regulating RecA activities.