bluuebunny/crossref_metadata_2025_split huggingface dataset:
A hierarchical analysis of population genetic structure in Rhizobium leguminosarum bv. trifolii
Authors: HAGEN M. J. , HAMRICK J. L. 
Published: November 2003

AbstractLittle is known about the population processes that shape the genetic diversity in natural populations of rhizobia. A sample of 912 Rhizobium leguminosarum biovar trifolii isolates were collected from naturalized red clover populations (Trifolium pratense) and analysed for 15 allozyme loci to determine the levels and distribution of genetic diversity. Hierarchical analyses compared different sampling levels, geographical separation, and temporal separation. Total genetic diversity across all isolates was H= 0.426, with 57.6% of the total diversity found among isolates obtained from individual red clover plants. Relatively low genetic differentiation among populations and high differentiation among plants within populations was observed; this suggests that gene flow and founder effect act differently at geographical and local scales. Significant differences were observed in (i) allele frequencies among populations and among plants within populations, and (ii) the frequency distribution of the most widespread and the most abundant strains. When multilocus linkage disequilibrium was calculated, significant levels of disequilibrium were observed in the total sample and in three of the eight populations.
Molecular scatology: the use of molecular genetic analysis to assign species, sex and individual identity to seal faeces
Authors: Reed J. Z. , Tollit D. J. , Thompson P. M. , Amos W. 
Published: November 2003

Seals and commercial fisheries are potential competitors for fish and cephalopods. Research into the diet of British seal species has been based on conventional dietary analyses, but these methods often do not allow assignment of species identity to scat samples. We present a protocol for obtaining DNA from seal scat (faecal) samples which can be used in polymerase chain reactions to amplify both nuclear and mitochondrial DNA. This can provide a method of identifying the species, sex and individual identity of the seal, from a particular scat sample. Combined with conventional dietary analyses these techniques will allow us to assess sources of variation in seal diet composition.Scat samples have been collected from intertidal haul‐out sites around the inner Moray Firth, north‐east Scotland. We have assessed methods to extract and purify faecal DNA, a combination of DNA from the individual seal, prey items, and gut bacteria, for use in PCR. Controls using faecal and blood samples from the same individual have enabled microsatellite primer sets from four pinniped species to be tested. Approximately 200 scat samples have been examined for species identity and individual matches. This study will provide essential information for the assessment of interactions between seals and commercial or recreational fisheries.
Conversion of an extracellular cytolysin into a phagosome‐specific lysin which supports the growth of an intracellular pathogen
Authors: Jones Siân , Preiter Karen , Portnoy Daniel A. 
Published: November 2003

Summary
Listeria monocytogenes is a facultative intracellular pathogen which secretes a pore‐forming cytolysin, listeriolysin O (LLO), necessary for intracellular growth. Clostridium perfringens is an extracellular pathogen which secretes a related cytolysin, perfrlngolysln O (PFO). When PFO is secreted by intracellular L. monocytogenes, it is toxic to the infected host cell. PFO‐mediated toxicity renders the infected host cell permeable to gentamicin and leads to the death of the intracellular bacteria. In this study, we selected for L. monocytogenes mutants in which PFO supported the intracellular growth of L. monocytogenes. Six independent mutants were isolated, each containing a single amino acid change within the PFO protein. Three classes of PFO mutations were identified, all capable of mediating lysis of the vacuole but without a toxic effect upon the infected host cell. The first class had a severe defect in haemolytic activity. The second class had a change in the pH optimum of PFO. The third class had nearly wild‐type levels of haemolytic activity, but had a decrease in protein half‐life in the host‐cell cytosol. Acquisition of single amino acid changes in PFO were sufficient to convert an extracellular cytolysin into a vacuole‐specific lysin which mediated growth of L. monocytogenes in cultured cells.
Protein folding in the cytoplasm of Escherichia coli: requirements for the DnaK‐DnaJ‐GrpE and GroEL‐GroES molecular chaperone machines
Authors: Thomas Jeffrey G. , Baneyx Francois 
Published: November 2003

SummaryWe have systematically investigated the influence of mutations in the σ32 heat‐shock transcription factor and the DnaK‐DnaJ‐GrpE and GroEL‐GroES molecular chaperone machines on the folding of preS2‐β‐galactosidase. This 120kDa fusion protein between the hepatitis B surface antigen preS2 sequence and β‐galactosidase was synthesized in a highly soluble and enzymatically active form in wild‐type Escherichia coli cells cultured at temperatures between 30°C and 42°C, but aggregated extensively in an rpoH165(Am) mutant. Proper folding was partially restored upon co‐overexpression of the dnaKJ operon, but not when the groE operon or dnaK alone were overproduced. The enzymatic activities in dnaK103, dnaJ259 and grpE280 mutants were 40–60% lower relative to a dnaK756 mutant or isogenic wild‐type cells at 30°C and 37°C. At 42°C, only 10–40% of the wild‐type activity was present in each of the early‐folding‐factor mutants. Although the synthesis levels of preS2‐β‐galactosidase were reduced in the dnaK103, dnaJ259 and grpE280 genetic backgrounds, aggregation was primarily responsible for the loss of activity when the cells were grown at 37°C or 42°C. By contrast, the groEL140, groES30 and groES619 mutations, which induced the aggregation of homodimeric ribulose bisphosphate carboxylase (Rubisco), did not affect the solubility of preS2‐β‐galactosidase at temperatures up to 42°C. Our results are discussed in terms of the current understanding of the E. coli protein‐folding cascade. The potential usefulness of heat‐shock protein mutants for the production of soluble proteins in an inclusion‐body form is addressed.
Multicopy fim B gene expression in Escherichia coli: binding to inverted repeats in vivo, effect on fimA gene transcription and DNA inversion
Authors: Dove Simon L. , Dorman Charles J. 
Published: November 2003

SummaryTranscription of fimA, the Escherichia coli gene encoding the type 1 fimbrial subunit protein, is driven by a promoter carried on a 314bp segment of invertible DNA. We have discovered that overexpression of fimB, one of the genes required for inversion of this DNA element, results in transcriptional repression of fimA. Furthermore, under these conditions inversion ceases to be dependent on the integration host factor (IHF) or the leucine‐responsive regulatory protein (LRP), cofactors hitherto considered to be essential for inversion. Inversion will even occur (albeit at a very low level) in the absence of both cofactors. The interaction of the fimB gene product with the invertible element was studied in vivo in the presence of single‐ and multicopy fimB genes. Dimethyl sulphoxide (DMS)‐mediated methylation of DNA at the 9 bp inverted repeats, which flank the invertible element, was found to vary in the presence and absence of functional fimB. The DMS reactivity profile at the left‐hand inverted repeat was similar with single or multicopy fimB. The corresponding profile at the right‐hand inverted repeat varied with fimB copy number. As this repeat lies between the fimA promoter and open reading frame, FimB binding here is likely to modulate fimA transcription and vice versa.
Topology of diphtheria toxin in lipid vesicle membranes: a proteolysis study
Authors: Quertenmont Pierre , Wattiez Ruddy , Falmagne Paul , Ruysschaert Jean‐Marie , Cabiaux Veronique 
Published: November 2003

Summary The diphtheria toxin (DT) membrane topology was investigated by proteolysis experiments. Diphtheria toxin was incubated with asolectin liposomes at pH 5 in order to promote its membrane insertion, and the protein domains located outside the lipid vesicles were digested with proteinase K (which is a non‐specific protease). The protected peptides were separated by electrophoresis and identified by microsequence analysis. Their orientation with respect to the lipid bilayer and their accessibility to the aqueous phase were determined by attenuated total reflection Fourier‐transform infrared spectroscopy (ATR‐FTIR). These data, combined with those provided by proteolytic cleavage with a specific protease (endoproteinase Glu‐C), led us to propose a topological model of the N‐terminal part of the diphtheria toxin B fragment inserted into the lipid membrane. In this model, two a‐helices adopt a transmembrane orientation, with their axes parallel to the lipid acyl chains, while a third o‐helix could adopt a transmembrane topology only in a small proportion of DT molecules.
Studies on prolysostaphin processing and characterization of the lysostaphin immunity factor (Lif) of Staphylococcus simulans biovar staphylolyticus
Authors: Thumm Günther , Götz Friedrich 
Published: November 2003

SummaryLysostaphin is an extracellular glycylglycine endopep‐tidase produced by Staphylococcus simulans biovar staphylolyticus ATCC1362 that lyses staphylococcal cells by hydrolysing the polyglycine interpeptide bridges of the peptidoglycan. Renewed analysis of the sequence of the lysostaphin gene (Iss), and the sequencing of the amino‐terminus of purified prolysostaphin and of mature lysostaphin revealed that lysostaphin is organized as a preproprotein of 493 amino acids (aa), with a signal peptide consisting of 36 aa, a propeptide of 211 aa from which 195 aa are organized in 15 tandem repeats of 13 aa length, and a mature protein of 246 aa. Prolysostaphin is processed in the culture supernatant of S. simulans biovar staphylolyticus by an extracellular cysteine protease. Although prolysostaphin was staphylolytically active, the mature lysostaphin was about 4.5‐fold more active. The controlled expression in Staphylococcus carnosus of Iss and Iss with deletions in the prepropeptide region indicated that the tandem repeats of the propeptide are not necessary for protein export or activation of Lss, but keep Lss in a less active state. Intracellular expressed pro‐ and mature lysostaphin exert staphy‐lolytic activity in cell‐free extracts, but do not affect growth of the corresponding clones. We characterized a lysostaphin immunity factor gene (lif) which is located in the opposite direction to Iss. The expression of lif in S. carnosus led to an increase in the serine/glycine ratio of the interpeptide bridges of peptidoglycan from 2 to 35%, suggesting that lysostaphin immunity depends on serine incorporation into the interpeptide bridge. If, in addition to lif, Iss is co‐expressed the serine/glycine ratio is further increased to 58%, suggesting that Lss selects for optimal serine incorporation. Lif shows similarity to FemA and FemB
DNA topology in hyperthermophilic archaea: reference states and their variation with growth phase, growth temperature, and temperature stresses
Authors: López‐García Purificación , Forterre Patrick 
Published: November 2003

SummaryIn order to address the dynamics of DNA topology in hyperthermophilic archaea, we analysed the topological state of several plasmids recently discovered in Thermococcales and Sulfolobales. All of these plasmids were from relaxed to highly positively super‐coiled in vitro, i.e. they exhibited a significant linking excess compared to the negatively supercoiled plasmids from mesophilic organisms (both Archaea and Bacteria). In the two archaeai orders, plasmid linking number (Lk) decreased as growth temperature was lowered from its optimal value, i.e. positively super‐coiled plasmids were relaxed whereas relaxed plasmids became negatively supercoiled. Growth temperatures above the optimum correlated with higher positive supercoiling in Sulfolobales (Lk increase) but with relaxation of positive supercoils in Thermococcus sp. GE31. The topological variation of plasmid DNA isolated from cells at different growth phases were found to be species specific in both archaeai orders. In contrast, the direction of topological variation under temperature stress was the same, i.e. a heat shock correlated with an increase in plasmid positive supercoiling, whilst a cold shock induced negative supercoiling. The kinetics of these effects were analysed in Sulfolobales. In both temperature upshift (from 80 to 85C) and downshift (from 80 to 65C), a transient sharp variation of Lk occurred first, and then DNA supercoiling progressively reached levels typical of steady‐state growth at the final temperature. These results indicate that DNA topology can change with physiological states and environmental modifications in hyperthermophilic archaea.
Roles of different phytochromes in Arabidopsis photomorphogenesis
Authors: WHITELAM G. C. , DEVLIN P. F. 
Published: November 2003

ABSTRACTThe red/far‐red light‐absorbing phytochromes play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. Higher plants possess multiple, discrete phytochromes, the apoproteins of which are the products of a family of divergent (PHY) genes. Arabidopsis thaliana has at least five PHY genes, encoding the apoproteins of phytochromes A‐E. Through the analysis of mutants that are deficient in phytochrome A or B and the corresponding double mutant, it is becoming clear that these phytochromes perform both discrete and overlapping roles throughout plant development. Through analysis of the phyA phyB double mutant, it has been possible to define several responses that are mediated by other members of the phytochrome family. This article reviews some of the recent progress in the study of phytochrome‐deficient mutants of the model plant Arabidopsis thaliana.
Phytochrome photoconversion
Authors: BRASLAVSKY S. E. , GÄRTNER W. , SCHAFFNER K. 
Published: November 2003

ABSTRACTThe spectral properties of native and modified phytochromes and the molecular events during phytochrome photoconversion, , are reviewed. Steady‐state and time‐resolved absorption spectra of native phytochrome A, as well as recombinant phytochromes (oat and potato phytochrome A and potato phytochrome B) reconstituted with phycocyanobilin and phytochromobilin as chromophores, are analysed. The vinyl double bond, present at position 18 in phytochromobilin and substituted by an ethyl group in phycocyanobilin, has a considerable influence on the photo‐transformation kinetics of phytochromes A and B, evidently due to a strong interaction of this region of the chromophore with the protein surrounding. The kinetics of the phototransformation of potato phytochrome B differs from that of oat phytochrome A (wild‐type and recombinant), indicating that the chromophore‐protein interaction in phytochrome B is different from that in phytochrome A. It remains to be seen whether this difference is due to the di‐ versus monocotyledon origin of the phytochromes. Optoacoustic spectroscopy, applied to native oat phytochrome A, afforded thermo‐dynamic, structural and kinetic parameters of the Pr→I700 and the I700→Pr phototransformations. Raman and infrared spectroscopic data for wild‐type phytochrome A suggest that the protonated chromophore in Pr undergoes torsions around two single bonds in addition to the Z→E isomerization of the 15,16 double bond, and that all transients, possibly with the exception of IbI, are protonated at the central pyrrole ring.
Photomorphogenic mutants of tomato
Authors: KENDRICK R. E. , KERCKHOFFS L. H. J. , VAN TUINEN A. , KOORNNEEF M. 
Published: November 2003

ABSTRACTPhotomorphogenesis of tomato (Lycopersicon esculentum Mill.) is being studied with the aid of mutants which are modified either in their photoreceptor composition or in their signal transduction chain(s). Phytochrome chromophore mutants, presumably deficient in all phytochromes, and mutants specifically deficient in phytochrome A (phy A) or B1 (phyB1) have been used to study the roles played by phytochromes in photomorphogenesis. In addition, other mutants, including transgenic lines overproducing phyA, exhibit exaggerated photomorphogenesis. Studies using these mutants are reviewed, with emphasis being placed on anthocyanin biosynthesis and plastid development as model systems for the dissection of the complex interactions between photoreceptors and to elucidate the nature of photoreceptor transduction chains. Recently, new mutants have been isolated by screening in a phyA, phyB1‐deficient background. The novel phenotypes selected are candidates for mutants in additional photoreceptors or their transduction chains.
The phytochrome photoreceptor in the green alga Mesotaenium caldariorum: implication for a conserved mechanism of phytochrome action
Authors: WU S.‐H. , LAGARIAS J. C. 
Published: November 2003

ABSTRACTChloroplast movement in the unicellular green alga Mesotaenium caldariorum is one of the earliest documented photomorphogenetic responses in plants. Photobiological studies have established that this response is under the control of phytochrome, whose rigid association with the plasma membrane and/or cytoskeleton enables the algal cells to orientate the chloroplast in response to the direction and intensity of light from the environment. While many of the key components of the algal phytochrome signalling pathway have been elucidated (i.e. Ca2+, calmodulin, actin and myosin), the primary biochemical mechanism of algal phytochrome action is unknown. To begin to address this important question, phytochrome and its corresponding genes have been isolated and characterized in this alga. These studies reveal that Mesotaenium cells contain a single type of phytochrome which is encoded by a small family of highly related genes. On the basis of its biochemical properties, primary structure and ability to interfere with the photoregulatory activity of phytochrome in transgenic plant seedlings, it appears likely that the primary mechanism of phytochrome action has been conserved throughout its evolution.
The cryptochrome family of photoreceptors
Authors: CASHMORE A. R. 
Published: November 2003

ABSTRACTCRY1, the primary photoreceptor responsible for blue light‐mediated inhibition of hypocotyl elongation in Arabidopsis thaliana, has been characterized. The properties of CRY1, and those of the related protein CRY2, and their relationship to the photolyase family of flavoproteins are discussed.
Sugar repression of photosynthesis: the role of carbohydrates in signalling nitrogen deficiency through source:sink imbalance
Authors: PAUL M. J. , DRISCOLL S. P. 
Published: November 2003

ABSTRACTThe aim of this work was to examine whether carbohydrates are involved in signalling N deficiency through source:sink imbalance. Photosynthetic metabolism in tobacco was studied over 8 d during the withdrawal of N from previously N‐sufficient plants in which the source:sink ratio was manipulated by shading leaves on some of the plants. In N‐sufficient plants over this time‐scale, there was a small decline in photosynthetic rate, Rubisco protein and amino acid content, with a larger decrease in carbohydrate content. Withdrawal of N from the growing medium induced a large decrease in the rate of photosynthesis (35% reduction after 8 d under the growing conditions, with a reduction also apparent at high and low measuring CO2), which was caused by a large decrease in the amount of Rubisco protein (62% after 8 d) and Rubisco activity. Higher amounts; of hexoses preceded the loss of photosynthetic activity and sucrose and starch accumulation. Reduction of the sourcersink ratio by shading prevented the loss of photosynthetic activity and the increase in hexoses and other carbohydrates. These data indicate that the reduction of photosynthesis that accompanies N deficiency in intact plants has the characteristics of sugar repression of photosynthesis observed in model systems, but that the accumulation of hexose prior to the decline in photosynthesis is small. The possibility that sugar repression of photosynthesis under physiological conditions depends more crucially on the C:N status of leaves than the carbohydrate status alone is discussed.
How is the relationship between the C4 cereal Sorghum bicolor and the C3 root hemi‐parasites Striga hermonthica and Striga asiatica affected by elevated CO2?
Authors: WATLING J. R. , PRESS M. C. 
Published: November 2003

ABSTRACTThe C4 cereal Sorghum bicolor was grown under either ambient (350 μmol mol−1) or elevated (700 μmol mol−1) [CO2] in either the presence or absence of the C3 obligate root hemi‐parasites Striga hermonthica or S. asiatica. Both uninfected and infected sorghum plants were taller and had greater biomass, photosynthetic rates, water‐use efficiencies and leaf areas under elevated compared with ambient [CO2]. There was no evidence of any downregula‐tion of photosynthesis in sorghum grown at elevated [CO2]. Biomass of infected sorghum was lower under both ambient and elevated [CO2], and although infected plants were larger under elevated [CO2] the relative impact of infection on host biomass was either the same (S. asiatica) or only slightly less (S. hermonthica) than under ambient [CO2]. In contrast, biomass of S. hermonthica and S. asiatica per host was lower under elevated than ambient [CO2], although rates of photosynthesis were higher at elevated [CO2] and parasite stomatal conductance was not responsive to [CO2]. Parasites emerged above‐ground and flowered earlier under ambient compared with elevated [CO2]. It appears that the mechanism(s) by which the parasites affect host growth is (are) relatively insensitive to increased atmospheric [CO2], although the parasites themselves were adversely affected by growth at elevated [CO2].
The impact of subcanopy light environment on the hydraulic vulnerability of Rhododendron maximum to freeze‐thaw cycles and drought
Authors: LIPP C. C. , NILSEN E.T. 
Published: November 2003

ABSTRACTThe vulnerability of xylem to embolism development in Rhododendron maximum L., an evergreen diffuse‐porous shrub, was investigated in relation to the frequency of winter freeze–thaw cycles in high and low light sites of the Eastern US. Though the frequency of freeze–thaw cycles during the winter was lower in North Carolina than in Virginia, the hydraulic conductivity of 3‐year‐old branches was reduced by up to 60% by winter embolism development in North Carolina compared to less than 30% in Virginia. Generally, small vessel diameters and volumes were associated with a significant resistance to embolism formation resulting from repeated freeze–thaws of xylem sap. In stems grown in high light sites (gaps), larger vessel volumes, and greater diameter growth of stems were associated with a significantly higher degree of freeze–thaw embolism development than in those grown in the low light sites. Thus, the growth patterns of R. maximum stems, under conditions of higher light availability, rendered them more susceptible to freeze–thaw‐induced embolisms. Vulnerability to drought‐induced embolism in stems was not affected by light environment. Rhododendron maximum was relatively sensitive to drought‐induced embolism because 50% loss of hydraulic conductivity occurred at a water potential of ‐2.2 MPa. The distribution and gas exchange of R. maximum are constrained by the dual effects of freeze‐thaw cycles and drought on vascular function.