bluuebunny/crossref_metadata_2025 huggingface dataset:
Biochemical characterization of prephenate dehydrogenase from the hyperthermophilic bacterium Aquifex aeolicus
Authors: Bonvin Julie , Aponte Raphael A. , Marcantonio Maria , Singh Sasha , Christendat Dinesh , Turnbull Joanne L.
Published: May 2006

A monofunctional prephenate dehydrogenase (PD) from Aquifex aeolicus was expressed as a His‐tagged protein in Escherichia coli and was purified by nickel affinity chromatography allowing the first biochemical and biophysical characterization of a thermostable PD. A. aeolicus PD is susceptible to proteolysis. In this report, the properties of the full‐length PD are compared with one of these products, an N‐terminally truncated protein variant (Δ19PD) also expressed recombinantly in E. coli. Both forms are dimeric and show maximum activity at 95°C or higher. Δ19PD is more sensitive to temperature effects yielding a half‐life of 55 min at 95°C versus 2 h for PD, and values of kcat and Km for prephenate, which are twice those determined for PD at 80°C. Low concentrations of guanidine‐HCl activate enzyme activity, but at higher concentrations activity is lost concomitant with a multi‐state pathway of denaturation that proceeds through unfolding of the dimer, oligomerization, then unfolding of monomers. Measurements of steady‐state fluorescence intensity and its quenching by acrylamide in the presence of Gdn‐HCl suggest that, of the two tryptophan residues per monomer, one is buried in a hydrophobic pocket and does not become solvent exposed until the protein unfolds, while the less buried tryptophan is at the active site. Tyrosine is a feedback inhibitor of PD activity over a wide temperature range and enhances the cooperativity between subunits in the binding of prephenate. Properties of this thermostable PD are compared and contrasted with those of E. coli chorismate mutase‐prephenate dehydrogenase and other mesophilic homologs.
Interpretation of the dissolution of insoluble peptide sequences based on the acid‐base properties of the solvent
Authors: Malavolta Luciana , Pinto Marcelo R.S. , Cuvero Jamile H. , Nakaie Clóvis R.
Published: May 2006

The dissolution process of model insoluble peptide sequences was investigated in view of the electron acceptor (AN) and electron donor (DN) solvent properties. The Alzheimer's disease‐inducing (1–42) Aβ‐amyloid peptide and its (1–21) fragment, the (66–97) transmembrane bradykinin B2 receptor sequence, and the strongly aggregated VVLGAAIV were selected as models of insoluble peptides. Solvents presenting similar AN and DN values failed, despite their polarities, to dissociate peptide chains (free in solution or bound to a polymer). The maximum solubility of these aggregated sequences was attained in solvents presenting the highest possible (AN–DN) values (in positive or negative mode). The AN–DN values ranged from approximately −20 to +80 and, notably, the lowest dissociation power was ascribed to solvents presenting values of approximately +40. The strong hydrogen bond donor water is located in this region, indicating that, for dissociation of specific insoluble segments, the solvent should appropriately combine its acid/base strength with the potential for van der Waals interactions. We also observed a sequence‐dependent pH effect on peptide solubility confirmed through circular dichroism spectroscopy. This approach also revealed a complex but, in many cases, consistent influence of peptide conformation on its solubility degree, even when structure‐inducing solvents were added. In conclusion, the random method of selecting solvents to dissolve insoluble and intractable peptide sequences, still in use by some, could be partially supplanted by the strategy described herein, which may be also applicable to other solute dissociation processes.
Characterization of the unfolded state of bovine α‐lactalbumin and comparison with unfolded states of homologous proteins
Authors: Wirmer Julia , Berk Holger , Ugolini Raffaella , Redfield Christina , Schwalbe Harald
Published: May 2006

The unfolded states of three homologous proteins with a very similar fold have been investigated by heteronuclear NMR spectroscopy. Secondary structure propensities as derived from interpretation of chemical shifts and motional restrictions as evidenced by heteronuclear 15N relaxation rates have been analyzed in the reduced unfolded states of hen lysozyme and the calcium‐binding proteins bovine α‐lactalbumin and human α‐lactalbumin. For all three proteins, significant deviations from random‐coil predictions can be identified; in addition, the unfolded states also differ from each other, despite the fact that they possess very similar structures in their native states. Deviations from random‐coil motional properties are observed in the α‐ and the β‐domain in bovine α‐lactalbumin and lysozyme, while only regions within the α‐domain deviate in human α‐lactalbumin. The motional restrictions and residual secondary structure are determined both by the amino acid sequence of the protein and by residual long‐range interactions. Even a conservative single point mutation from I to L in a highly conserved region between the two α‐lactalbumins results in considerable differences in the motional properties. Given the differences in oxidative folding between hen lysozyme and α‐lactalbumin, the results obtained on the unfolded states suggest that residual long‐range interactions, i.e., those between the α‐ and the β‐domain of lysozyme, may act as nucleation sites for protein folding, while this property of residual structure is replaced by the calcium‐binding site between the domains in α‐lactalbumin.
Solution structure of the ubiquitin‐associated domain of human BMSC‐UbP and its complex with ubiquitin
Authors: Chang Yong‐Gang , Song Ai‐Xin , Gao Yong‐Guang , Shi Yan‐Hong , Lin Xiao‐Jing , Cao Xue‐Tao , Lin Dong‐Hai , Hu Hong‐Yu
Published: May 2006

Ubiquitin is an important cellular signal that targets proteins for degradation or regulates their functions. The previously identified BMSC‐UbP protein derived from bone marrow stromal cells contains a ubiquitin‐associated (UBA) domain at the C terminus that has been implicated in linking cellular processes and the ubiquitin system. Here, we report the solution NMR structure of the UBA domain of human BMSC‐UbP protein and its complex with ubiquitin. The structure determination was facilitated by using a solubility‐enhancement tag (SET) GB1, immunoglobulin G binding domain 1 of Streptococcal protein G. The results show that BMSC‐UbP UBA domain is primarily comprised of three α‐helices with a hydrophobic patch defined by residues within the C terminus of helix‐1, loop‐1, and helix‐3. The M‐G‐I motif is similar to the M/L‐G‐F/Y motifs conserved in most UBA domains. Chemical shift perturbation study revealed that the UBA domain binds with the conserved five‐stranded β‐sheet of ubiquitin via hydrophobic interactions with the dissociation constant (KD) of ∼17 μM. The structural model of BMSC‐UbP UBA domain complexed with ubiquitin was constructed by chemical shift mapping combined with the program HADDOCK, which is in agreement with the result from mutagenesis studies. In the complex structure, three residues (Met76, Ile78, and Leu99) of BMSC‐UbP UBA form a trident anchoring the domain to the hydrophobic concave surface of ubiquitin defined by residues Leu8, Ile44, His68, and Val70. This complex structure may provide clues for BMSC‐UbP functions and structural insights into the UBA domains of other ubiquitin‐associated proteins that share high sequence homology with BMSC‐UbP UBA domain.
Dichotomous versus palm‐type mechanisms of lateral assembly of amyloid fibrils
Authors: Makarava Natallia , Bocharova Olga V. , Salnikov Vadim V. , Breydo Leonid , Anderson Maighdlin , Baskakov Ilia V.
Published: May 2006

Despite possessing a common cross‐β core, amyloid fibrils are known to exhibit great variations in their morphologies. To date, the mechanism responsible for the polymorphism in amyloid fibrils is poorly understood. Here we report that two variants of mammalian full‐length prion protein (PrP), hamster (Ha) and mouse (Mo) PrPs, produced morphologically distinguishable subsets of mature fibrils under identical solvent conditions. To gain insight into the origin of this morphological diversity we analyzed the early stages of polymerization. Unexpectedly, we found that despite a highly conserved amyloidogenic region (94% identity within the residues 90–230), Ha and Mo PrPs followed two distinct pathways for lateral assembly of protofibrils into mature, higher order fibrils. The protofibrils of Ha PrP first formed irregular bundles characterized by a peculiar palm‐type shape, which ultimately condensed into mature fibrils. The protofibrils of Mo PrP, on the other hand, associated in pairs in a pattern resembling dichotomous coalescence. These pathways are referred to here as the palm‐type and dichotomous mechanisms. Two distinct mechanisms for lateral assembly explain striking differences in morphology of mature fibrils produced from closely related Mo and Ha PrPs. Remarkable similarities between subtypes of amyloid fibrils generated from different proteins and peptides suggest that the two mechanisms of lateral assembly may not be limited to prion proteins but may be a common characteristic of polymerization of amyloidogenic proteins and peptides in general.
Characterization of E. coli tetrameric aldehyde dehydrogenases with atypical properties compared to other aldehyde dehydrogenases
Authors: Rodríguez‐Zavala José Salud , Allali‐Hassani Abdellah , Weiner Henry
Published: May 2006

Aldehyde dehydrogenases are general detoxifying enzymes, but there are also isoenzymes that are involved in specific metabolic pathways in different organisms. Two of these enzymes are Escherichia coli lactaldehyde (ALD) and phenylacetaldehyde dehydrogenases (PAD), which participate in the metabolism of fucose and phenylalanine, respectively. These isozymes share some properties with the better characterized mammalian enzymes but have kinetic properties that are unique. It was possible to thread the sequences into the known ones for the mammalian isozymes to better understand some structural differences. Both isozymes were homotetramers, but PAD used both NAD+ and NADP+ but with a clear preference for NAD, while ALD used only NAD+. The rate‐limiting step for PAD was hydride transfer as indicated by the primary isotopic effect and the absence of a pre‐steady‐state burst, something not previously found for tetrameric enzymes from other organisms where the rate‐limiting step is related to both deacylation and coenzyme dissociation. In contrast, ALD had a pre‐steady‐state burst indicating that the rate‐limiting step was located after the NADH formation, but the rate‐limiting step was a combination of deacylation and coenzyme dissociation. Both enzymes possessed esterase activity that was stimulated by NADH; NAD+ stimulated the esterase activity of PAD but not of ALD. Finding enzymes that structurally are similar to the well‐characterized mammalian enzymes but have a different rate‐limiting step might serve as models to allow us to determine what regulates the rate‐limiting step.
Structure and dynamics of dark‐state bovine rhodopsin revealed by chemical cross‐linking and high‐resolution mass spectrometry
Authors: Jacobsen Richard B. , Sale Kenneth L. , Ayson Marites J. , Novak Petr , Hong Joohee , Lane Pamela , Wood Nichole L. , Kruppa Gary H. , Young Malin M. , Schoeniger Joseph S.
Published: May 2006

Recent work using chemical cross‐linking to define interresidue distance constraints in proteins has shown that these constraints are useful for testing tertiary structural models. We applied this approach to the G‐protein‐coupled receptor bovine rhodopsin in its native membrane using lysine‐ and cysteine‐targeted bifunctional cross‐linking reagents. Cross‐linked proteolytic peptides of rhodopsin were identified by combined liquid chromatography and FT‐ICR mass spectrometry with automated data‐reduction and assignment software. Tandem mass spectrometry was used to verify cross‐link assignments and locate the exact sites of cross‐link attachment. Cross‐links were observed to form between 10 pairs of residues in dark‐state rhodopsin. For each pair, cross‐linkers with a range of linker lengths were tested to determine an experimental distance‐of‐closest‐approach (DCA) between reactive side‐chain atoms. In all, 28 cross‐links were identified using seven different cross‐linking reagents. Molecular mechanics procedures were applied to published crystal structure data to calculate energetically achievable theoretical DCAs between reactive atoms without altering the position of the protein backbone. Experimentally measured DCAs are generally in good agreement with the theoretical DCAs. However, a cross‐link between C316 and K325 in the C‐terminal region cannot be rationalized by DCA simulations and suggests that backbone reorientation relative to the crystal coordinates occurs on the timescale of cross‐linking reactions. Biochemical and spectroscopic data from other studies have found that the C‐terminal region is highly mobile in solution and not fully represented by X‐ray crystallography data. Our results show that chemical cross‐linking can provide reliable three‐dimensional structural information and insight into local conformational dynamics in a membrane protein.
Structure and topology of the non‐amyloid‐β component fragment of human α‐synuclein bound to micelles: Implications for the aggregation process
Authors: Bisaglia Marco , Trolio Alessandra , Bellanda Massimo , Bergantino Elisabetta , Bubacco Luigi , Mammi Stefano
Published: May 2006

Human α‐synuclein is a small soluble protein abundantly expressed in neurons. It represents the principal constituent of Lewy bodies, the main neuropathological characteristic of Parkinson's disease. The fragment corresponding to the region 61–95 of the protein, originally termed NAC (non‐amyloid‐β component), has been found in amyloid plaques associated with Alzheimer's disease, and several reports suggest that this region represents the critical determinant of the fibrillation process of α‐synuclein. To better understand the aggregation process of α‐synuclein and the role exerted by the biological membranes, we studied the structure and the topology of the NAC region in the presence of SDS micelles, as membrane‐mimetic environment. To overcome the low solubility of this fragment, we analyzed a recombinant polypeptide corresponding to the sequence 57–102 of α‐synuclein, which includes some charged amino acids flanking the NAC region. Three distinct helices are present, separated by two flexible stretches. The first two helices are located closer to the micelle surface, whereas the last one seems to penetrate more deeply into the micelle. On the basis of the structural and topological results presented, a possible pathway for the aggregation process is suggested. The structural information described in this work may help to identify the appropriate target to reduce the formation of pathological α‐synuclein aggregation.
Structural basis for the enantiospecificities of R‐ and S‐specific phenoxypropionate/α‐ketoglutarate dioxygenases
Authors: Müller Tina A. , Zavodszky Maria I. , Feig Michael , Kuhn Leslie A. , Hausinger Robert P.
Published: May 2006

(R)‐ and (S)‐dichlorprop/α‐ketoglutarate dioxygenases (RdpA and SdpA) catalyze the oxidative cleavage of 2‐(2,4‐dichlorophenoxy)propanoic acid (dichlorprop) and 2‐(4‐chloro‐2‐methyl‐phenoxy)propanoic acid (mecoprop) to form pyruvate plus the corresponding phenol concurrent with the conversion of α‐ketoglutarate (αKG) to succinate plus CO2. RdpA and SdpA are strictly enantiospecific, converting only the (R) or the (S) enantiomer, respectively. Homology models were generated for both enzymes on the basis of the structure of the related enzyme TauD (PDB code 1OS7). Docking was used to predict the orientation of the appropriate mecoprop enantiomer in each protein, and the predictions were tested by characterizing the activities of site‐directed variants of the enzymes. Mutant proteins that changed at residues predicted to interact with (R)‐ or (S)‐mecoprop exhibited significantly reduced activity, often accompanied by increased Km values, consistent with roles for these residues in substrate binding. Four of the designed SdpA variants were (slightly) active with (R)‐mecoprop. The results of the kinetic investigations are consistent with the identification of key interactions in the structural models and demonstrate that enantiospecificity is coordinated by the interactions of a number of residues in RdpA and SdpA. Most significantly, residues Phe171 in RdpA and Glu69 in SdpA apparently act by hindering the binding of the wrong enantiomer more than the correct one, as judged by the observed decreases in Km when these side chains are replaced by Ala.
Identification of novel quaternary domain interactions in the Hsp90 chaperone, GRP94
Authors: Chu Feixia , Maynard Jason C. , Chiosis Gabriela , Nicchitta Christopher V. , Burlingame Alma L.
Published: May 2006

The structural basis for the coupling of ATP binding and hydrolysis to chaperone activity remains a central question in Hsp90 biology. By analogy to MutL, ATP binding to Hsp90 is thought to promote intramolecular N‐terminal dimerization, yielding a molecular clamp functioning in substrate protein activation. Though observed in studies with recombinant domains, whether such quaternary states are present in native Hsp90s is unknown. In this study, native subunit interactions in GRP94, the endoplasmic reticulum Hsp90, were analyzed using chemical cross‐linking in conjunction with tandem mass spectrometry. We report the identification of two distinct intermolecular interaction sites. Consistent with previous studies, one site comprises the C‐terminal dimerization domain. The remaining site represents a novel intermolecular contact between the N‐terminal and middle (M) domains of opposing subunits. This N+M domain interaction was present in the nucleotide‐empty, ADP‐, ATP‐, or geldanamycin‐bound states and could be selectively disrupted upon addition of synthetic geldanamycin dimers. These results identify a compact, intertwined quaternary conformation of native GRP94 and suggest that intersubunit N+M interactions are integral to the structural biology of Hsp90.
Free energies of protein–protein association determined by electrospray ionization mass spectrometry correlate accurately with values obtained by solution methods
Authors: Krishnaswamy Sanjay R. , Williams Evan R. , Kirsch Jack F.
Published: May 2006

The advantages of electrospray ionization mass spectrometry (ESIMS) to measure relative solution‐phase affinities of tightly bound protein–protein complexes are demonstrated with selected variants of the Bacillus amyloliquefaciens protein barstar (b*) and the RNAase barnase (bn), which form protein–protein complexes with a range of picomolar to nanomolar dissociation constants. A novel chemical annealing procedure rapidly establishes equilibrium in solutions containing competing b* variants with limiting bn. The relative ion abundances of the complexes and those of the competing unbound monomers are shown to reflect the relative solution‐phase concentrations of those respective species. No measurable dissociation of the complexes occurs either during ESI or mass detection, nor is there any evidence for nonspecific binding at protein concentrations <25 μM. Differences in ΔΔG of dissociation between variants were determined with precisions <0.1 kcal/mol. The ΔΔG values obtained deviate on average by 0.26 kcal/mol from those measured with a solution‐phase enzyme assay. It is demonstrated that information about the protein conformation and covalent modifications can be obtained from differences in mass and charge state distributions. This method serves as a rapid and precise means to interrogate protein–protein‐binding surfaces for complexes that have affinities in the picomolar to nanomolar range.
Characterization of three areas of interactions stabilizing complexes between SecA and SecB, two proteins involved in protein export
Authors: Patel Chetan N. , Smith Virginia F. , Randall Linda L.
Published: May 2006

The general secretory, Sec, system translocates precursor polypeptides from the cytosol across the cytoplasmic membrane in Escherichia coli. SecB, a small cytosolic chaperone, captures the precursor polypeptides before they fold and delivers them to the membrane translocon through interactions with SecA. Both SecB and SecA display twofold symmetry and yet the complex between the two is stabilized by contacts that are distributed asymmetrically. Two distinct regions of interaction have been defined previously and here we identify a third. Calorimetric studies of complexes stabilized by different subsets of these interactions were carried out to determine the binding affinities and the thermodynamic parameters that underlie them. We show here that there is no change in affinity when either one of two contact areas out of the three is lacking. This fact and the asymmetry of the binding contacts may be important to the function of the complex in protein export.
Crystal structure of the yeast His6 enzyme suggests a reaction mechanism
Authors: Quevillon‐Cheruel Sophie , Leulliot Nicolas , Graille Marc , Blondeau Karine , Janin Joel , Tilbeurgh Herman Van
Published: May 2006

The Saccharomyces cerevisiae His6 gene codes for the enzyme phosphoribosyl‐5‐amino‐1‐phosphoribosyl‐4‐imidazolecarboxamide isomerase, catalyzing the fourth step in histidine biosynthesis. To get an insight into the structure and function of this enzyme, we determined its X‐ray structure at a resolution of 1.30 Å using the anomalous diffraction signal of the protein's sulphur atoms at 1.77 Å wavelength. His6 folds in an (α/β)8 barrel similar to HisA, which performs the same function in bacteria and archaea. We found a citrate molecule from the buffer bound in a pocket near the expected position of the active site and used it to model the open form of the substrate (phosphoribulosyl moiety), which is a reaction intermediate. This model enables us to identify catalytic residues and to propose a reaction mechanism where two aspartates act as acid/base catalysts: Asp134 as a proton donor for ring opening, and Asp9 as a proton acceptor and donor during enolization of the aminoaldose. Asp9 is conserved in yeast His6 and bacterial or archaeal HisA sequences, and Asp134 has equivalents in both HisA and TrpF, but they occur at a different position in the protein sequence.
Stepwise disassembly and apparent nonstepwise reassembly for the oligomeric RbsD protein
Authors: Feng Yongjun , Jiao Wangwang , Fu Xinmiao , Chang Zengyi
Published: May 2006

Many cellular proteins exist as homo‐oligomers. The mechanism of the assembly process of such proteins is still poorly understood. We have previously observed that Hsp16.3, a protein exhibiting chaperone‐like activity, undergoes stepwise disassembly and nonstepwise reassembly. Here, the disassembly and reassembly of a nonchaperone protein RbsD, from Escherichia coli, was studied in vitro. The protein was found to mainly exist as decamers with a small portion of apparently larger oligomeric forms, both of which are able to refold/reassemble effectively in a spontaneous way after being completely unfolded. Disassembly RbsD intermediates including pentamers, tetramers, trimers, dimers, and monomers were detected by using urea‐containing pore gradient polyacrylamide gel electrophoresis, while only pentamers were detected for its reassembly. The observation of stepwise disassembly and apparent nonstepwise reassembly for both a chaperone protein (Hsp16.3) and a nonchaperone protein (RbsD) strongly suggests that such a feature is most likely general for homo‐oligomeric proteins.
Structure‐based function inference using protein family‐specific fingerprints
Authors: Bandyopadhyay Deepak , Huan Jun , Liu Jinze , Prins Jan , Snoeyink Jack , Wang Wei , Tropsha Alexander
Published: May 2006

We describe a method to assign a protein structure to a functional family using family‐specific fingerprints. Fingerprints represent amino acid packing patterns that occur in most members of a family but are rare in the background, a nonredundant subset of PDB; their information is additional to sequence alignments, sequence patterns, structural superposition, and active‐site templates. Fingerprints were derived for 120 families in SCOP using Frequent Subgraph Mining. For a new structure, all occurrences of these family‐specific fingerprints may be found by a fast algorithm for subgraph isomorphism; the structure can then be assigned to a family with a confidence value derived from the number of fingerprints found and their distribution in background proteins. In validation experiments, we infer the function of new members added to SCOP families and we discriminate between structurally similar, but functionally divergent TIM barrel families. We then apply our method to predict function for several structural genomics proteins, including orphan structures. Some predictions have been corroborated by other computational methods and some validated by subsequent functional characterization.
NMR structure of the first Ig module of mouse FGFR1
Authors: Kiselyov Vladislav V. , Bock Elisabeth , Berezin Vladimir , Poulsen Flemming M.
Published: May 2006

Fibroblast growth factor (FGF) receptors (FGFRs) regulate a multitude of cellular processes during embryogenesis and in the adult. The extracellular part of the prototypical FGFR consists of three Ig modules (Ig1 – Ig3), in which Ig2 and Ig3 determine affinity and specificity for FGF and heparin, while the Ig1 module is thought to have a regulatory function. The crystal structures of the Ig2 and Ig3 modules alone and in complex with FGF have previously been reported. The structure of the Ig1 module is unknown, and very little is known about the structural determinants for the regulatory function of this module. We describe here the NMR structure of the Ig1 module of mouse FGFR1. The three‐dimensional fold of the module belongs to the intermediate Ig subgroup and can be described as a β‐barrel consisting of two β‐sheets. One sheet is formed by A′, G, F, C, and C′, and the other by A, B, B′, E, and D β‐strands. The overall strand topology of the Ig1 module is similar to that of the Ig2 and Ig3 modules. However, the A/A′ loop of the Ig1 module is much longer than that of the Ig2 and Ig3 modules. It contains eight extra residues compared to the Ig3 module, and five extra residues compared to Ig2.
The assimilation efficiency of Asellus aquaticus L. (Crustacea, Isopoda)
Authors: PRUS TADEUSZ
Published: May 2006

(1) Comparative studies of the ash‐ratio and gravimetric methods of determining assimilation efficiency in Asellus aquaticus showed that the differential use of minerals by this species rendered the ash‐ratio method unreliable. Results obtained by the gravimetric method were therefore employed in the analysis of further experiments.

(2) The assimilation efficiencies estimated for A. aquaticus ranged between 26 and 44%, and varied according to population density and reproductive condition.

(3) Individual winter males had a significantly lower assimilation efficiency (26%) than grouped animals (35%), but the assimilation efficiency of summer males (33%) did not differ significantly from that of winter males at the same density. It is concluded that density affects assimilation efficiency in A. aquaticus.

(4) The assimilation efficiency of summer males (33 %) is significantly different from that of summer females (non‐ovigerous, 41 %; ovigerous, 44%). A mean assimilation efficiency of 40% is proposed for the summer period whereas an overall annual mean of 30% is suggested.

(5) Despite the various assimilation efficiencies reported within any one season consumption rate per unit weight is fairly constant (winter, 0·04–0·05 cal/24 h; summer, 0·36–0·38 cal/24 h) and it is suggested that the different assimilation rates are a mechanism whereby the additional energy and material requirements of females for breeding can be met without increasing food intake.
Growth, gas vacuolation and buoyancy in a natural population of a planktonic blue‐green alga
Authors: REYNOLDS C. S.
Published: May 2006

(1)The growth and development of a natural population of Anabaena circinalisis described in relation to physical and chemical conditions within a small, shallow eutrophic lake.

(2)Germination of resting spores took place when the lake was destratified, in response to improving conditions of light and temperature.

(3)The growth of the population was monitored for chlorophyll and nutrient content, and parallel determinations of heterocyst ratio, gas vacuole volume, turgor and buoyancy were made.

(4)Growth of the population was probably limited by phosphorus deficiency.

(5)Cessation of growth was marked by increases in gas vacuole volume and buoyancy.

(6)Gas vacuole volume is determined primarily by the rate of increase of the alga. It is modified by turgor changes, associated with photosynthetic rates.

(7)Surface blooms are the result of the redistribution of buoyant algae when turbulence currents are weak.

(8)Buoyancy is increased in algae lodged at the surface.
Studies on the genus Stenostomum O. Schmidt (Turbellaria; Catenulida).
Authors: KOLASA J. , YOUNG J. O.
Published: May 2006

Two species of Stenostomum, viz. S. glanduloswn Kepner and Carter and S. anops Nuttycombe and Waters, are recorded for the first time from Poland. Descriptions of the Polish material are given, and these are compared with published information on the structure of the species. A new sub‐species, viz. S. Corderoi Marcus s. sp. poznanensis s. sp. nov. is recorded from Poland, and fully described. Fealures which separate the new sub‐species from S. corderoi corderoi Marcus are listed.
Studies on the genus Stenostomum O. Schmidt (Turbellaria; Catenulida).
Authors: YOUNG J. O. , KOLASA J.
Published: May 2006

A new species of Stenostomum, viz. S. beryii sp. nov. is described from Kenya. It was recorded from a pool near Nairobi, in April and May. The new species resembles S. hemisphericum Nasonov.
Studies on the genus Stenostomum O. Schmidt (Turbellaria; Catenulida).
Authors: YOUNG J. O. , KOLASA J.
Published: May 2006

Stenostomum arevaloi Gieysztor, S. glandulosum Kepner and Carter, S. leucops (Duges), S. pseudoacetabtihtm Nuttycombe and Waters, and S. unicolor Schmidt are reported from E. Africa. The various localities in which each of the species were found are listed. All the species are new records for this region except S. Leucops which was recorded by Bohmig (1897) from Lake Victoria at Bukoba, Uganda. Descriptions of the species, based on the E. African material, are given.
Population dynamics of perch, Perca fluviatilis L. in Slapton Ley, Devon
Authors: CRAIG J. F.
Published: May 2006

Perch, Percafluviatilis L. were studied in Slapton Ley which is a eutrophic freshwater lagoon in south Devon, England. The perch were caught in traps from February 1970 to June 1971. The traps selected males during the spawning season. The water temperature did not affect the numbers of trapped fish directly, but the sight of perch in the traps appeared to attract others. Sex ratios were found to be equal in the first 2 years of life but older year classes were predominantly female. The population consisted of young individuals. Males were found to mature in their first year and most females matured in their second. The fecundity varied from an average of 1000 eggs in perch n i the 9.75 cm length group to 30,500 eggs in fish in the 27.75 cm group. A few shoals of perch moved throughout the Ley although the majority of fish stayed in the same area. Population estimates showed a range from 10,000 to 95,000 for fish 9.75 cm and above. The large variations in population estimates and survival rates were attributed to the necessity of using traps which had variable catches and to the harmful effects of handling the perch. Chironomids were important in the diet of perch of all sizes. Plankton and Asellus were other important foods, the latter especially during the winter months. Perch 11.5 cm to 13.9 cm selected the widest range of food organisms. Only perch 14.0 cm and above ate fish.
Population dynamics and production of Daphnia hyalina in a eutrophic reservoir
Authors: GEORGE D. G. , EDWARDS R. W.
Published: May 2006

The population dynamics and production of Daphnia hyaiina^ the dominant cladoceran i n Eglwys Nynydd, a shallow eutrophic reservoir in South Wales, were studied for 2 years against a background of limnological measurements. The appearance and development of successive generations from egg to adult could be followed from changing numbers in arbitrarily defined size classes. Seasonal variations in mean length, mean brood‐size and proportion of gravid adults were recorded and mean brood‐size was related to changing food and temperature conditions. Egg‐development times for D. hyaiina were determined in culture and the population parameters finite birth (S), instantaneous birth (b′), instantaneous population change (r′), instantaneous death (d′) and finite death rates (D) were estimated from field data. Turnover and production estimates were calculated from finite death rates and biomass. The calculated potential rate of increase (b′) was nearly always greater than the observed rate of increase (r′): seasonal changes in death rate (d′) generally parallel changes in birth rate (b′) but remain somewhat out of phase. Population oscillations are probably due t o a delay in the expression of the effects of population density upon birth and death rates.

The mean biomass of Daphnia in 1970 was 0‐57 mg dry wt/l (0‐88 g C/m2) and in 1971 0‐32 mg dry wt/l (0.49 g C/m2). Annual production for Daphnia was 11‐8 mg dry wt/l (18‐2 g C/m2) in 1970 and 8‐30 mg dry wt/l (12 8 g C/m2) in 1971. Information available on primary production in the reservoir suggests that the production of Daphnia accounts for less than 2% of gross primary production. However, the pattern of population growth of Daphnia in Eglwys Nynydd almost certainly reflects a food limited system. In summer, blue‐green algae may be abundant but serve as a poor food source: throughout the blue‐green bloom egg production remains low, at times remaining below 0‐5 eggs/adult.
Improved methods for the measurement of dissolved and particulate organic carbon in fresh water and their application to chalk streams
Authors: BAKER C. D. , BARTLETT P. D. , FARR I. S. , WILLIAMS G. I.
Published: May 2006

The development and use of an improved automatic system for the accurate measurement of dissolved organic carbon (D.O.C.) in fresh waters is described. The method, which covers the range 0‐25 mgl−1 D.O.C., is based on the oxidation of organic carbon to carbon dioxide by U.V. radiation. The carbon dioxide produced is measured by a non dispersive infra‐red gas analyser (I.R.G.A.). The I.R.G.A. is also used in the semi‐automatic measurement of particulate organic carbon (P.O.C.) by a combustion method which allows very low concentrations to be measured using samples of 200 ml or less.

Results of surveys of two river systems indicate that D.O.C. concentrations of less than 2.0 mg l−1 are typical in unpolluted chalk streams. D.O.C. concentrations of streams draining acid heathland were found to be significantly higher (3‐5.5 mg l−1).

D.O.C. concentration was found to increase rapidly during a spate, in a river draining areas of mixed underlying geology. The throughput of D.O.C. during the twenty‐five to fifty spates which occur annually in the river could amount to 20‐30% of the annual flux of D.O.C.

P.O.C. concentration in chalk spring waters (0.03–0.04 mg l−1) were found to be higher than expected from preliminary estimates using membrane filtration techniques.

The relevance of the measurement of D.O.C. and P.O.C. flux to estimates of the energy budgets of stream ecosystems is discussed and published methods for the automatic measurement of D.O.C. are reviewed.
The ecology of populations of dace, Leudscus leuciscus (L.), from two tributaries of the River Wye, Herefordshire, England
Authors: HELAWELL J. M.
Published: May 2006

Samples of dace were taken from the Afon Llynfi and the River Lugg each month for 13 consecutive months. Male dace grew faster than females and rates were comparable with those described for several other populations. Variations in year‐class strengths were observed and these differed between the populations although 1959 was strongly represented in both. The sex ratio varied throughout life and disturbances in the expected ratio were attributed to the attainment of sexual maturity at the end of the fourth year of life (3+). Observation of the seasonal gonad cycles indicated that spawning occurred in March or April. Fecundity was estimated at about forty eggs per gram of total weight.

A seasonal cycle of feeding activity was established with highest food consumption during summer. There was evidence of a fast during the spawning period. No correlation between temperature and feeding activity could be established. Dace were omnivorous, but aquatic insects and algae were the main components of the diet. Seasonal variations generally followed availability. The importance of aerial insects declined with age. Many differences in feeding habits were detected between the populations.
RURAL SUBSISTENCE, MIGRATION, AND URBANIZATION: THE PRODUCTION, DESTRUCTION, AND REPRODUCTION OF CHEAP LABOUR IN THE WORLD MARKET ECONOMY*
Authors: Stuckey Barbara , Fay Margaret A.
Published: May 2006

Nicholas Forsyte, cocking his rectangular eyebrows, wore a smile. He had succeeded during the day in bringing to fruition a scheme for the employment of a tribe from Upper India in the gold‐mines of Ceylon. A pet plan, carried at last in the teeth of great difficulties — he was justly pleased. It would double the output of his mines, and, as he had often forcibly argued, all experience tended to show that a man must die; and whether he dies of a miserable old age in his own country or prematurely of damp in the bottom of a foreign mine, was surely of little consequence, provided that by a change in his mode of life he benefited the British Empire.

John Galsworthy, A Man of Property, 1906
SCARCITY AND AGRICULTURAL LAND RENT IN LIGHT OF THE CAPITAL CONTROVERSY: THREE VIEWS*
Authors: BARNES TREVOR J.
Published: May 2006

ABSTRACTS

This paper examines the different theories of agricultural land rent proposed by the neoclassical, Marxist, and neo‐Ricardian schools of economic thought. In so doing the paper undertakes two tasks: first, to explore the different definitions of scarcity that emerge from each school; and secondly to check the consistency between the view of scarcity and the analytical theory of rent that each school proposes. It is concluded that for each of the schools there is an inconsistency between their respective view of scarcity and the corresponding theory of rent, although the reasons for that inconsistency vary. It is further argued that although this inconsistency cannot be resolved for the case of neoclassical economics, there is some prospect of resolution for Marxist and neo‐Ricardian theories.
FLEXIBLE SPECIALISATION AND SMALL FIRMS IN ITALY: MYTHS AND REALITIES
Authors: AMIN ASH
Published: May 2006

Abstracts

This paper offers a critical evaluation of the ‘Flexible Specialisation’ model which asserts that a new and dominant model of industrial organisation based upon craft principles is emerging, or can be nurtured in places where it does not yet exist. Drawing upon recent evidence from Italy, the country whose economic resurgence around small firms has become a cornerstone for the flexible specialisation thesis, the paper argues that there is little cause for the thesis's optimism for small flexible firms and their emancipatory role for the working class.
IN OTHER WOR(L)DS: FRAGMENTED AND INTEGRATED OBSERVATIONS ON GENDERED LANGUAGES, GENDERED SPACES AND LOCAL TRANSFORMATION
Authors: PRED ALLAN
Published: May 2006

The build up of individual and collective linguistic repertoires is inseparable from situated practices and power relations. Place‐to‐place variations in gendered consciousness, the consciousness of gender, and female subordination cannot be pried apart from place‐to‐place variations in the language out of which gender is constituted and to which gendered practices and unequal gender relations contribute. In the course of local transformation, whereby local traditions and practices are eased out or crushed by exogenous powers, women as well as men are apt to become involved in the contestation of meanings and other forms of linguistic struggle.
“LOCAL” DEVELOPMENT IN SOUTHERN EUROPE: TOWARDS A NEW MYTHOLOGY
Authors: HADJIMICHALIS COSTIS , PAPAMICHOS NICOS
Published: May 2006

Abstracts

From the mid‐1970s onwards, many southern European regions experienced a pattern of decentralized development and growth. This pattern has been largely explained by theories of “local” or “endogenous” development which became the new catch‐phrases during a period of great financial difficulties. Despite logical improvements and the use of some radical rhetoric, local development approaches based on rationalization of existing cases (especially in Third Italian regions) suffer both in their theory and practice from the same inherent limitations of two decades ago. The paper argues for an alternative interpretation of local development characteristics in Portugal, Spain, Italy and Greece, discussing the political implications of proposed policies.
SOCIAL AND SPATIAL PATTERNS UNDER FORDISM AND FLEXIBLE ACCUMULATION
Authors: OBERHAUSER ANN M.
Published: May 2006

Current debate surrounding Fordism and flexible accumulation centers on explaining their transition and the implications for capital and labor. This article disagrees with the argument that technology and capital competition are the basis for transition and focuses instead on the labor process. Using a case study of the French automobile industry since the Second World War, the analysis examines the transition in production and the link between spatial organization and the labor process. Contradictions in the current phase of capitalist production are apparent in the divergent trends towards international dispersal and regional integration of automobile production, and the deepening social divisions of labor.
STATE, CLASS AND INTERNATIONAL CAPITAL 2: THE DEVELOPMENT OF THE BRASILIAN STEEL INDUSTRY
Authors: FOOT S.P.H. , WEBBER MICHAEL
Published: May 2006

This paper examines the forces underlying the development and form of the Brasilian steel industry since the 1930s. Foreign direct investment has been limited by Brasilian nationalist policies and by higher costs of steel production, but large scale, integrated plants could not be built by private capital due to insufficient resources. Thus the Brasilian steel industry combines large scale state owned plants (financed by foreign capital) and smaller scale privately owned plants. The operations of the plants are coordinated to reduce market uncertainty, permit the steel sector to advocate its own expansion plans, and delimit the spheres of public and private capital while excluding foreign commodity and productive capital. Even so, in the 1980s the steel industry in Brasil has faced a crisis of declining local demand, prompting a rapid expansion of exports.
RURAL AND REGIONAL RESTRUCTURING OF APARTHEID: IDEOLOGY, DEVELOPMENT POLICY AND THE COMPETITION FOR SPACE
Authors: PICKLES JOHN , WEINER DANIEL
Published: May 2006

If we are serious about socialist reconstruction, we have to pay as much attention to the countryside as we do the industrial centres, and in this respect I am afraid we are not even at the beginning of the beginning.

(Rosa Luxemburg 1986: 233)
THE CRISIS OF THE MOVEMENTS: THE ENABLING STATE AS QUISLING
Authors: TAYLOR PETER J.
Published: May 2006

The basic argument of this paper is that the anti‐systemic movements political successes over the last century have turned out to be medium‐term cul de sacs at the expense of the real longue duree purposes of the movements. The discovery of the enabling state by radicals towards the end of the nineteenth century has resulted in a Quisling in the anti‐systemic ranks. This argument brings to the fore the anarchist critique which never accepted the enabling state as a legitimate part of the radical political repertoire. Nevertheless this essay is not a plea for a return to anarchist roots but rather attempts to reinsert anarchism, and feminism, into a single framework of anti‐systemic movements alongside socialism and nationalism. As the state is being shown to be disenabling rather than enabling across the various zones of the world‐economy it is argued that anarchist ideas deserve some priority as we revise radical political strategies.
GAME THEORIES? SPATIAL DIVISIONS OF LABOUR AND RATIONAL CHOICE MARXISM
Authors: SUNLEY PETER
Published: May 2006

Criticisms of Spatial Divisions of Labour have argued that the model ultimately dissolves into empirical particularities so that its theoretical tenets and context have been neglected. This paper attempts to draw out these premises by comparing Spatial Divisions of Labour with rational choice Marxism. Rational choice Marxism has aimed to provide microfoundations for structural categories by analysing the strategic interactions of individual actors. The approach has been criticised for relying on a rational, utilitarian and individualistic theory of action and, therefore, for assuming the constitution of agents to be given. The spatial divisions of labour approach also involves a move towards the microscale and emphasises the importance of strategic relations. In this case, the specified actors are collective entities. Once again, the aims and interests of the actors appear to be predetermined so that the significance of their interactions is limited. In conclusion it is argued that studies of uneven development should pay greater attention to the historical constitution of agents within their institutional contexts.
LOCAL POLITICAL PRACTICE IN RESPONSE TO A MANUFACTURING PLANT CLOSURE: HOW GEOGRAPHY COMPLICATES CLASS ANALYSIS
Authors: HEROD ANDREW
Published: May 2006

This paper analyzes the responses to two separate closures of a large glass manufacturing plant in Clarksburg, West Virginia, to examine how geography has been integral to the conduct of local political practice in this community. When the plant, by far the local area's largest manufacturing employer, first closed in 1979 the state and local government put together a considerable package of incentives to attract a purchaser for the facility. However, although glass production continued, the plant was again closed in 1987 after a corporate takeover. In response to this second closure the characteristically pro‐business Governor of West Virginia initiated an almost $650 million lawsuit against the plant's new owners. The plant's union leaders on the other hand collaborated with city government officials and local business interests to constrain community opposition to the closure. The paper argues that this paradoxical situation, of actors taking up positions contrary to those which an ageographical class analysis would have predicted, was the result precisely of their locality dependence in the face of mobile capital.
SOME CRITICAL QUESTIONS FOR ANTI‐ESSENTIALISM
Authors: Peet Richard
Published: May 2006

A so‐called “going beyond” Marxism will be at worst only a return to pre‐Marxism; at best, only the rediscovery of a thought already contained in the philosophy which one believes he has gone beyond. As for “revisionism,” this is either a truism or an absurdity. There is no need to readapt a living philosophy to the course of the world; it adapts itself by means of thousands of new efforts, thousands of particular pursuits, for the philosophy is one with the movement of society.

—J.‐P. Sartre, Search for a Method (1968: 7)