bluuebunny/crossref_metadata_2025 huggingface dataset:
Distribution and growth of benthic macroinvertebrates among different patch types of the littoral zones of two arctic lakes
Authors: BEATY STEVEN R. , FORTINO KENNETH , HERSHEY ANNE E.
Published: October 2006

1. To evaluate the effect of habitat patch heterogeneity on abundance and growth of macroinvertebrates in arctic lakes, macroinvertebrate abundance, individual biomass, and potential food resources were studied in three patch types in two arctic lakes on the Alaskan North Slope near the Toolik Lake Field Station. An experiment was conducted to determine which sediment patch type supported higher growth rates for Chironomus sp., a commonly occurring macroinvertebrate.

2. Potential organic matter (OM) resources were significantly higher in both rock and macrophyte patches than in open‐mud patches. Total macroinvertebrate densities in both lakes were highest in rock patches, intermediate in macrophytes and lowest in open‐mud. The open‐mud patches also had lower species richness compared with other patch types. Additionally, individual biomass for one clam species and two chironomid species was significantly greater in rock patches than in open‐mud.

3. In a laboratory experiment, Chironomus showed two to three times greater mass increase in sediments from macrophyte and rock patches than from open‐mud patches. Rock and macrophyte experimental sediments had at least 1.5 × the percentage OM as open‐mud sediments.

4. Chlorophyll a appeared to be the best predictor for invertebrate abundances across all patch types measured, whereas OM content appeared to be the variable most closely associated with Chironomus growth.

5. Our results combined with previous studies show that the relationships between macroinvertebrate community structure, individual growth, and habitat heterogeneity are complex, reflecting the interaction of multiple resources, and biotic interactions, such as the presence or absence of a selective vertebrate predator (lake trout, Salvelinus namaycush).
Immune pathways and defence mechanisms in honey bees Apis mellifera
Authors: Evans J. D. , Aronstein K. , Chen Y. P. , Hetru C. , Imler J.‐L. , Jiang H. , Kanost M. , Thompson G. J. , Zou Z. , Hultmark D.
Published: October 2006

Social insects are able to mount both group‐level and individual defences against pathogens. Here we focus on individual defences, by presenting a genome‐wide analysis of immunity in a social insect, the honey bee Apis mellifera. We present honey bee models for each of four signalling pathways associated with immunity, identifying plausible orthologues for nearly all predicted pathway members. When compared to the sequenced Drosophila and Anopheles genomes, honey bees possess roughly one‐third as many genes in 17 gene families implicated in insect immunity. We suggest that an implied reduction in immune flexibility in bees reflects either the strength of social barriers to disease, or a tendency for bees to be attacked by a limited set of highly coevolved pathogens.
Caste development and reproduction: a genome‐wide analysis of hallmarks of insect eusociality
Authors: Cristino A. S. , Nunes F. M. F. , Lobo C. H. , Bitondi M. M. G. , Simões Z. L. P. , Da Fontoura Costa L. , Lattorff H. M. G. , Moritz R. F. A. , Evans J. D. , Hartfelder K.
Published: October 2006

The honey bee queen and worker castes are a model system for developmental plasticity. We used established expressed sequence tag information for a Gene Ontology based annotation of genes that are differentially expressed during caste development. Metabolic regulation emerged as a major theme, with a caste‐specific difference in the expression of oxidoreductases vs. hydrolases. Motif searches in upstream regions revealed group‐specific motifs, providing an entry point to cis‐regulatory network studies on caste genes. For genes putatively involved in reproduction, meiosis‐associated factors came out as highly conserved, whereas some determinants of embryonic axes either do not have clear orthologs (bag of marbles, gurken, torso), or appear to be lacking (trunk) in the bee genome. Our results are the outcome of a first genome‐based initiative to provide an annotated framework for trends in gene regulation during female caste differentiation (representing developmental plasticity) and reproduction.
Kinetics of Thiamin Degradation in Solutions under Ambient Storage Conditions
Authors: Pachapurkar Darshan , Bell Leonard N.
Published: October 2006

Thiamin is being incorporated into a variety of nutritionally enhanced beverages. Although thiamin degradation during thermal processing has been extensively studied, minimal data exist regarding its stability in solution during ambient storage. This study collected kinetic data for thiamin degradation in solutions as a function of pH, buffer type, and buffer concentration at 25 °C. Thiamin was incorporated into sodium phosphate and citrate buffer solutions, each prepared at 0.02 and 0.1 M and pH 4, 5, 6, and 7. Experimental solutions were stored in an incubator at 25 °C. Thiamin concentrations were analyzed at 9 time points over a 42‐wk period. Thiamin degradation data were modeled using pseudo‐1st‐order kinetics. Thiamin stability generally decreased as pH and buffer concentration increased in both phosphate and citrate buffers. In 0.1 M phosphate buffer, the time for a 10% loss of thiamin decreased from 79 wk at pH 4 to 3 wk at pH 7. At pH 6 and 7, thiamin stability was greater in citrate buffer than in phosphate buffer. However, at pH 4 and 5, thiamin stability was greater in phosphate buffer than citrate buffer. To optimize thiamin stability in low pH beverages, phosphate buffer would be more appropriate to use than citrate buffer, whereas citrate buffer should be used for better thiamin stability in high pH beverages.
Protein Oxidation in Frankfurters with Increasing Levels of Added Rosemary Essential Oil: Effect on Color and Texture Deterioration
Authors: Estévez Mario , Ventanas Sonia , Cava Ramón
Published: October 2006

The development of protein oxidation as assessed by the total carbonyl content and its influence on color and texture deterioration during the refrigerated storage (+4 °C/60 d) of frankfurters, were studied. The effect of the addition of a rosemary essential oil at different levels (150, 300, and 600 ppm) on the protein oxidative stability of the frankfurters was also evaluated. Frankfurters with no added essential oil were used as controls. The amount of carbonyls from protein oxidation significantly increased during refrigerated storage, and this increase was significantly higher in control frankfurters than in those treated with 300 and 600 ppm. Rosemary essential oil at levels of 300 and 600 ppm successfully protected the heme molecule from degradation and significantly inhibited the increase of nonheme iron (NHI) in refrigerated stored frankfurters. Color changes were directly related to oxidation processes because frankfurters with added antioxidants (300 and 600 ppm) suffered less color modifications than the controls. The addition of rosemary essential oil enhanced texture characteristics of frankfurters by reducing hardness, adhesiveness, gumminess, chewiness, and controlling the lost of elasticity during refrigeration. Statistically significant correlations were calculated between protein oxidation and instrumentally measured parameters, suggesting that the alteration of protein functionality caused by oxidation likely affected color and texture characteristics of frankfurters.
Effect of Gamma‐Irradiated Red Pepper Powder on the Chemical and Volatile Characteristics of Kakdugi, a Korean Traditional Fermented Radish Kimchi
Authors: Lee Jeung Hee , Lee Ki‐Teak , Kim Mee Ree
Published: October 2006

The chemical and volatile characteristics of kakdugi batches prepared with irradiated red pepper powders were determined during fermentation for 7 wk at 5 °C. Acidities of kakdugies with irradiated red pepper powder (3, 5, and 7 kGy) were lower than that of kakdugi with nonirradiated control at 3 wk of fermentation, which indicated that the irradiated red pepper powder might delay the initial fermentation. Pungency and red color caused by capsanoids and capsanthin, respectively, were not altered by irradiated red pepper powder, whereas the fermentation decreased the capsanoid content. The headspace volatile compounds extracted by solid‐phase microextraction, except 2‐tricanone, were not significantly different in fresh made kakdugies with red pepper powder irradiated at dosed of 0, 3, 5, and 7 kGy; however, as fermentation progressed, the composition of volatiles was changed. A FOX 3000 electronic nose separated the odor of kakdugies with red pepper powder irradiated at 0, 3, 5, and 7 kGy into 4 different groups, and the odor patterns developed differently during fermentation.
Protein Structural Changes During Preparation and Storage of Surimi
Authors: Moosavi‐Nasab Marzieh , Alli Inteaz , Ismail Ashraf A. , Ngadi Michael O.
Published: October 2006

The changes in protein structure associated with the preparation and frozen storage of surimi were investigated. Raw surimi was prepared by repeatedly washing Alaska pollock flesh with chilled water. The product was either slowly frozen or underwent rapid freezing using liquid air; in either case it was then subjected to frozen storage at ‐20 °C for 24 mo. Fourier transform infrared/attenuated total reflectance (FTIR/ATR) spectroscopy showed that during preparation of surimi, the a‐helix content increased with increased number of washing cycles. Differential scanning calorimetry (DSC) revealed a shift in the thermal transition of actin to a higher temperature during surimi preparation. Electrophoresis, FTIR/ATR spectroscopy, and DSC results revealed a loss of myofibrillar proteins from surimi after 3 washing cycles, suggesting that 3 washing cycles were adequate to prepare surimi. Sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) showed relatively minor changes in protein subunit structure with some loss of the myosin light chains (MLC); myosin heavy chain (MHC), actin, and tropomyosin were found to be relatively stable. Native‐PAGE showed no major changes in surimi after 24 mo storage at ‐20 °C. FTIR/ ATR spectroscopy indicated a significant decrease in a‐helix relative to p‐sheet structure in surimi after 2 y of storage at ‐20 °C. The loss of α‐helical content was more significant in slowly frozen surimi compared with rapid‐frozen surimi samples. DSC results revealed a shift in the thermal transition of actin to lower temperatures during frozen storage of surimi.
Impact of Ionizing Radiation and Thermal Treatments on Furan Levels in Fruit Juice
Authors: Fan Xuetong
Published: October 2006

The formation of furan in freshly prepared apple and orange juices as affected by ionizing radiation and thermal treatments was studied using a newly developed solid‐phase microextraction method coupled with gas chromatography‐mass spectrometry (GC‐MS). Results show that furan levels increased linearly as radiation dose increased from 0 to 5 kGy. Irradiation induced more furan in apple juice than in orange juice. During post‐irradiation storage at 4 °C, furan levels increased in both apple and orange juices, particularly in the 1st 3 d. On the other hand, irradiation degraded deuterated furan (d4‐furan) spiked in water and fruit juices. The rate of degradation as a function of radiation dose was the highest in water and the lowest in orange juice. Submerging the juice samples in boiling water for 5 min induced higher amounts of furan in orange juice than in apple juice, but autoclaving (121 °C, 25 min) resulted in more furan formation in apple juice than in orange juice. Results reported here suggest that both ionizing radiation and thermal treatments induce furan formation in fruit juices.
Effects of Brining Conditions on Weight Gain in Herring (Clupea harengus) Fillets
Authors: Birkeland Sveinung , Sivertsvik Morten , NIELSEN Henrik H. , Skåra Torstein
Published: October 2006

Salted herring is an important product category in many European countries. Reduced need for salt as a preserving agent and the increased emphasis on less salt in the human diet has changed the basis for the traditional processing of these products. This has led to significant changes in the processing conditions and in the characteristics of the salted products. In this perspective, the effects of different brine concentrations (10.0%, 16.5%, and 25.5%), brining temperatures (3.5 °C and 17.5 °C), the presence of skin or not on the fillets, and brining time (1, 2, 3, 4, and 7 d) were investigated on the weight gain (%) and final salt content (%) of herring (Clupea harengus). A significant (P < 0.001) higher weight gain of the fillets were observed at the lowest brining temperature (3.5 °C) compared with at the higher temperature (17.5 °C), independently of brine concentration and brining time. Increased brine concentration and skinning of the fillets caused the weight gain to significantly decrease (P < 0.001) and increase (P < 0.001), respectively. After 1 d of brining, the weight gain was in the range of 10% to 12% for both brining temperatures, and at the lowest temperature, the weight gain increased significantly (P < 0.001) as a function of brining time. At the higher temperature, no further significant increase in weight was observed from 1 to 7 d of brining. It is concluded that the weight gain in herring fillets brined according to the present commercial practice is significantly affected by temperature, brine concentration, brining time, and the presence or not of skin on the fillets and that the weight gain may be of high magnitude.
Listeria monocytogenes Inhibition by Whey Protein Films and Coatings Incorporating the Lactoperoxidase System
Authors: Min Seacheol , Harris Linda J. , Krochta John M.
Published: October 2006

Antimicrobial effects of whey protein isolate (WPI) films and coatings incorporating the lactoperoxidase system (LPOS) against Listeria monocytogenes were studied by turbidity, plate counting, disc‐covering, and disc‐surface‐spreading tests using various growth media. Survival of L. monocytogenes applied to smoked salmon before or after the coating was monitored immediately after application and during storage at 4 °C and 10 °C for up to 35 d. Tensile properties (elastic modulus [EM], tensile strength [TS], elongation [E]), oxygen permeability (OP), and color (Hunter L, a, b) of WPI films, with and without LPOS, were also compared. LPOS inhibited L. monocytogenes in broth and on agar media. WPI films incorporating 29 mg of LPOS per gram of film (dry basis) inhibited 4.2 log colony‐forming units (CFU)/cm2 of L. monocytogenes inoculated on agar media. WPI coatings prepared with LPOS at 0.7% (w/w) in a coating solution (40 mg LPOS/g coating [dry basis]) initially reduced >3 and 1 log CFU/g of L. monocytogenes and total aerobic microorganisms in smoked salmon, respectively. The WPI coatings incorporating LPOS prevented the growth of L. monocytogenes in smoked salmon at 4 °C and 10 °C for 35 d and 14 d, respectively. The tensile properties, oxygen permeability, and color of WPI films were not significantly changed by incorporation of LPOS (P >0.05).
Development of Shelf‐stable Intermediate‐moisture Meat Products Using Active Edible ChitosanCoating and Irradiation
Authors: Rao M. Shobita , Chander Ramesh , Sharma Arun
Published: October 2006

Shelf‐stable intermediate‐moisture (IM) meat products were developed using a combination of hurdles such as reduced aw, active edible coating of chitosan, and irradiation. Chitosan prepared from chitin had a viscosity of 16 c P, molecular weight of 17.54 kDa, and a degree of deacetylation (DD) of 74%. The nitrogen content of the chitosan was estimated to be 7.56%. The antioxidant activity of chitosan increased upon irradiation without significantly affecting its antimicrobial property. The effect of irradiated chitosan coating in terms of its antimicrobial and antioxidant properties in IM meat products immediately after irradiation and during storage was assessed. The aw of meat products such as mutton sheek kababs and streaky bacon was first reduced to 0.85 ± 0.02. The products were then coated with chitosan and irradiated (4 kGy). No viable bacteria or fungi were detected in chitosan‐coated, irradiated products. In contrast, IM meat products that were not subjected to gamma radiation showed visible fungal growth within 2 wk. The chitosan‐coated products showed lower thiobarbituric acid‐reactive substances (TBARS) than the noncoated samples for up to 4 wk of storage at ambient temperature. The studies thus clearly indicated the potential use of chitosan coating for the preparation of safe and stable meat products.
Serving Temperature Effects on Milk Flavor, Milk Aftertaste, and Volatile Compound Quantification in Nonfat and Whole Milk
Authors: Francis Logan L. , Chambers Delores H. , Kong Son Hee , Milliken George A. , Jeon Ike J. , Schmidt Karen A.
Published: October 2006

Many people seem to prefer to drink cold milk. Research describing the flavor and aftertaste of milk and their correlation with chemical composition has not been reported previously. The study objectives were to describe milk flavor and aftertaste with a descriptive sensory panel and to quantify the headspace compounds of nonfat and whole milks as a function of serving temperature, and then to determine if correlations exist between the data sets. Headspace compounds of milk samples served at 4 °C and 15 °C were quantified by using solid‐phase microextraction (SPME) gas chromatography, flame ion detection (GC‐FID). Descriptive panel results indicated that serving temperature did not affect milk flavor. Nonfat milk was rated as having more sour aromatics, bitter, cooked, and fat character and as being slightly more chalky and flat, but less sweet than whole milk. Characterization of milk aftertaste at 15 s after swallowing indicated that nonfat milk had very slight sour and cooked attributes. Characterization of milk aftertaste at 90 s after swallowing indicated that nonfat milk had very slight cooked attributes and was less sweet than whole milk. Nonfat milk had a greater concentration of hexanal and lesser concentrations of benzaldehyde, ethyl caproate, heptanal, 2‐heptanone, and nonanal than whole milk did. Significant correlations were found between fat derived compounds and fat influenced descriptors. These data provide evidence that fat content/composition contributes to the “flavor” and aftertaste attributes of milk more than serving temperature does.
Chemical Markers for Tracking the Sensory Contribution of Production Stages in Muscat Wine Distillates
Authors: Lillo Marcial Peña Y , Agosin Eduardo , Belancic Andrea , Latrille Eric
Published: October 2006

The main sensory contribution of each post‐fermentation production stage of muscat wine distillates can be tracked by following the concentration of just 1 corresponding chemical marker. Matching sample clusters of sensory and chemical data by using principal components analysis (PCA) revealed potential chemical markers. The data used in this study correspond to 12 sensory attributes that showed significant differences among products (P < 0.05) and concentrations of 23 volatile compounds of 14 distillate fractions and 15 finished Piscos. Artificial fruit attribute, characteristic of the head fraction (FR1) can be tracked with esters. Linalool, main odor attribute of the 1st part of the heart (FR2) can be tracked with linalool molecule. The 2nd part of the heart (FR3) can be tracked with octanoic acid, decanoic acid, furfural and ethyl lactate, accounting for tails attribute. In blended and aged finished products, chemical markers accounting for the effects of distillate fractions were similar but not identical to the markers from samples obtained from the purely distilled samples. Chemical markers for FR1 are ethyl hexanoate, ethyl octanoate, ethyl decanoate. Differentiation between FR1 and FR2 is less evident than in the purely distilled samples due to the linalool and artificial fruit attribute correlation. Chemical markers for FR2, therefore, include linalool and esters ethyl hexanoate, ethyl octanoate, and ethyl decanoate. The blending of the 2nd part of the heart (FR3) can be tracked with 2‐phenylethanol, ethyl lactate, and decanoic acid. Oak aging was tracked with eugenol and whisky lactones, while 5‐hydroxy‐methyl‐2‐furfural accounted for added caramel.
Survival Analysis Applied to Sensory Shelf Life of Yogurts–II: Spanish Formulations
Authors: Salvador Ana , Fiszman Susana M. , Curia Ana , Hough Guillermo
Published: October 2006

Sensory shelf lives of commercial Spanish yogurts stored at 10 °C were studied. Yogurts were strawberry flavored and differed in fat content (free and whole‐fat) and consistency (stirred and set‐style). Yogurts were tested between 0 and 90 d of storage by consumers who expressed acceptance or rejection of each sample and measured overall and attribute acceptability on a 9‐point hedonic scale. Survival analysis statistics were used to estimate sensory shelf lives. Considering 25% of consumers rejecting the product, shelf lives varied from 38 to 69 d, depending on the composition, so if useful life were to be established using sensory criteria, a single shelf life for yogurt would not appear to be very appropriate. A log‐linear model and a direct quantile comparison formula were introduced to analyze the effect of formulation on rejection time distributions and shelf life values, respectively. Fat‐free yogurts had shorter shelf lives than whole‐fat yogurts. Acceptability of yogurts measured on a 9‐point hedonic scale varied less than percentage rejection over the storage times.
The Protease‐Resistant Fraction of Smoked, Dried Bonito Lowers Serum Cholesterol in Ovariectomized Rats Fed Cholesterol‐Free Diets
Authors: Matsumoto Junichi , Erami Kazuo , Ogawa Hiroshi , Doi Mikiharu , Kishida Taro , Ebihara Kiyoshi
Published: October 2006

The hypocholesterolemic effects of smoke‐dried bonito undigested fractions remaining after microbial proteases treatment (SDBR), SDBR undigested fractions remaining after pepsin treatment (P‐SDBR), SDBR undigested fractions remaining after alcalase treatment (A‐SDBR), and defatted A‐SDBR (A‐SDBR/DF) were studied in 6‐month‐old, ovariectomized rats. Casein was used as the control. Smoke‐dried bonito, Katsuobushi, is a traditional Japanese food. SDBR, P‐SDBR, and A‐SDBR contain mainly 2 components: bonito oil and protease‐undigested proteins. In comparison with casein, SDBR, P‐SDBR, and A‐SDBR decreased plasma cholesterol concentration and increased fecal bile acid excretion and fecal output, whereas A‐SDBR/DF increased fecal bile acid excretion and fecal output, but did not decrease plasma cholesterol concentration. In addition, SDBR, P‐SDBR, and A‐SDBR, when compared with casein, decreased plasma triglyceride (TG) concentration and increased hepatic total lipid concentration, free cholesterol, and TG concentrations and CYP7A1 mRNA levels. Yet, these effects were not observed in rats fed A‐SDBR/DF. These results suggest that the hypocholesterolemic effect of SDBR, P‐SDBR, and A‐SDBR is mediated by an increase in bile acid excretion through a combination of promoted secretion of bile acids by bonito oil and binding of bile acids to resistant proteins. The hypotriglyceridemic effect may be mediated by reduced hepatic TG synthesis and secretion due to the intake of bonito oil.
Cutting Shape and Storage Temperature Affect Overall Quality of Fresh‐cut Papaya cv. ‘Maradol’
Authors: Rivera‐López Javier , Vázquez‐Ortiz Francisco A. , Ayala‐Zavala J. Fernando , Sotelo‐Mundo Rogerio R. , González‐Aguilar Gustavo A.
Published: October 2006

: The effect of cutting shape (cubes or slices) and storage temperature (5 °C, 10 °C, and 20 °C) on overall quality of fresh‐cut papaya were investigated. CO2 production, color, firmness, total soluble solids (TSS), weight loss, overall quality, ascorbic acid, β‐carotene, and antioxidant capacity were evaluated as a function of shelf life. CO2 production was high on day 0 for cubes and slices with an average of 150 and 100 mL/ kg/h, respectively. Storage temperature did not affect color changes; however, lower temperatures prevented loss of firmness. Fresh‐cut papaya stored at 20 °C showed the lowest TSS value and the highest weight losses. Shelf life based on visual quality ended before significant losses of total ascorbic acid, b‐carotene, and antioxidant capacity occurred. In general, quality parameters were not affected by shape. However, slices stored at 10 °C and 5 °C had a shelf life of 1 d and 2 d longer than cubes, respectively.
Micro Review Bending the rules: the 2μ plasmid of yeast
Authors: Murray J.A.H.
Published: October 2006

The replication of euckaryotic DNA is normally initiated at each origin only once per ceil cycle. Yet, In spite of this restriction, the 2μ plasmid of yeast has evolved an elegant mechanism which can allow it to rapidly amplify its copy number without initiating multiple rounds of replication. It achieves this by exploiting a plasmid‐en coded site‐specific recombination system in a way that is apparently unique to this plasmid. The 2μ plasmid has also evolved a mechanism that allows effective partition of itself between mother and daughter cells. Together these processes ensure the persistence of the 2μ plasmid within a population, even though retention of the plasmid Is of no advantage to the host cell and causes a slightly slower growth rate. The success of this survival strategy is illustrated by the near ubiquity of the 2μ. plasmid in both wild‐type and laboratory strains of yeast.
Translation of galE and coordination of galactose operon expression in Escherichia coli: effects of insertions and deletions in the non‐translated leader sequence
Authors: Bingham A. H. A. , Busby S. J. W.
Published: October 2006

Using gene‐manipulation techniques, we made a set of short insertions and deletions in the Escherichia coli galactose operon between the transcription start site and the Shine‐Dalgarno sequence of the first gene of the operon, galE. Translation initiation is severely reduced when the distance between the 5′ end of the message and the Shine‐Daigarno sequence drops below 15 bases.

Transcription of the gal operon can start at two distinct sites, S1 and S2, separated by 5 bp, situated 16 and 21 bp upstream of the galE Shine‐Dalgarno sequence, respectively. When transcription starts at S2, gal operon expression is discoordinate as the galE gene is better translated than promoter‐distal genes. Here we report that gal operon expression is discoordinate even when message starting at S2 is shortened. This shortened. that the better translation of galE from transcripts starting at S2 is not simply due to the fact that they are longer than transcripts starting at S1.
Evolutionary relationships in the genus Bordetella
Authors: Arico B. , Gross R. , Smida J. , Rappuoli R.
Published: October 2006

The nucleotide sequence of the pertussis toxin operon of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica, has shown that the last two species contain many common mutations and are likely to derive from a common ancestor (Arico and Rappuoli, 1987). To elucidate further the evolutionary relationships between the Bordetella species, we have cloned and sequenced the promoter region and the gene coding for the S1 subunit of pertussis toxin from additional B. pertussis strains, such as the type strain BP 18323 and two recent clinical isolates, namely strain BP 13456 from Sweden and strain BP SA1 from Italy. While the strains BP SA1 and BP 13456 are shown to differ from the published B. pertussis sequences by only one base pair, the type strain BP 18323 contains a total of 11 base‐pair substitutions. Remarkably, 9 of the 11 substitutions found in BP 18323 are also common to B. parapertussis and B. bronchiseptica, strongly suggesting that this strain derives from the same ancestor as B. parapertussis and B. bronchiseptica.

Computer analysis of the sequence data allows the construction of an evolutionary ‘tree’ showing that the B. pertussis strains are very homogeneous and significantly distant from B. parapertussis and B. bronchiseptica. Therefore the proposed conversion from B. parapertussis to B. pertussis appears highly improbable.
Molecular characterization of the resolvase gene, res, carried by a multicopy plasmid from Clostridium perfringens: common evolutionary origin for prokaryotic site‐specific recombinases
Authors: Garnier T. , Saurin W. , Cole S. T.
Published: October 2006

Clostridium perfringens strain CPN50 harbours a 10.2 kb plasmid known as plP404 which, in addition to a set of UV‐inducible genes involved in bacteriocin production, carries res, a gene probably encoding a site‐specific recombinase. The RES protein is highly homologous to the resolvases of transposons from both Gram‐negative and Gram‐positive bacteria as well as enzymes involved in site‐specific DNA inversion. A likely role for the RES protein would be to stabilize plP404 by reducing the number of plasmid multimers resulting from homologous recombination. A putative resolution site for RES action was found overlapping the res promoter. Phylogenetic analysis of the primary structures of ten site‐specific recombinases suggested a common descent and showed the RES protein to be closest to the resolvase encoded by Tn917 from Strepfococcus faecalis.
The calmodulin‐sensitive adenylate cyclase of Bordetella pertussis: cloning and expression in Escherichia col
Authors: Glaser P. , Ladant D. , Sezer O. , Pichot F. , Ullmann A. , Danchin A.
Published: October 2006

The adenylate cyclase toxin of the prokaryote Bordetella pertussis is stimulated by the eukaryotic regulatory protein, calmodulin. A general strategy, using the adenylate‐cyclase‐calmodulin interaction as a tool, has permitted cloning and expression of the toxin in Escherichia coli in the absence of any B. pertussis trans‐activating factor. We show that the protein is synthesized in a large precursor form composed of 1706 amino acids. The calmodulin‐stimulated catalytic activity resides in the amino‐terminal 450 amino acids of the adenylate cyclase. The enzyme expressed in E. coli is recognized in Western blots by antibodies directed against purified B. pertussis adenylate cyclase, and its activity is inhibited by these antibodies.
The three‐dimensional structures of S‐layers of two novel Eubacterium species isolated from inflammatory human processes
Authors: Sjögren A. , Wang D. N. , Hovmöller S. , Haapasalo M. , Ranta H. , Kerosuo E. , Jousimies‐Somer H. , Lounatmaa K.
Published: October 2006

The three‐dimensional structures of the crystalline surface layers of two species of Eubacteria have been determined by electron microscopy and computerized image processing. The S‐layer of Eubacterium sp. ES4C has tetragonal symmetry, with a unit cell spacing of 10.6 nm and a thickness of 9.5 nm, while that of Eubacterium sp. AHN 990 has hexagonal symmetry a = b = 15.7 nm and a thickness of 13 nm. The resolutions in the reconstructions were 2.5 nm and 1.8 nm, respectively. The reconstruction of the S‐layer of strain ES4C reveals a distinct domain structure: a major tetramer, arms connecting adjacent unit cells, and a minor tetramer. The S‐layer of strain AHN 990, on the other hand, has a rather complex arrangement, centred around the six‐fold axis.
The virulence protein Yop5 of Yersinia pseudotuberculosis is regulated at transcriptional level by plasmid‐plB1 ‐encoded trans‐acting elements controlled by temperature and calcium
Authors: Forsberg A. , Wolf‐Watz H.
Published: October 2006

The DNA sequence of the structural gene (yopE) of one of the Yersinia pseudotuberculosis virulence plas‐mid‐plB1‐encoded proteins, Yop5, is presented. The deduced protein showed a molecular weight of 22971 Daltons. A specific mutant, having a kanamycin‐resistance fragment inserted within the yopE gene was no longer virulent for mice. The expression of the Yop5 protein is regulated at the level of transcription by temperature as well as by the Ca2+ ‐concentration of the medium. A significant increase in the level of transcription was not detected until 45 min after a temperature shift from 26°C to 37°C in the absence of calcium; addition of Ca2+ inhibited the expression. The yopE promoter is under positive, as well as negative, plB1‐encoded control. The positive function is solely regulated by temperature, while the regulation of the negative function involves at least five different plasmid‐encoded gene loci; one of these genes encodes the V‐antigen.
Differential specificity of two insecticidal toxins from Bacillus thuringiensis var. aizawai
Authors: Knowles B. H. , Ellar D. J.
Published: October 2006

Bacillus thuringlensis var. aizawai HD–249 produces more than one protein of 130–135 kD in its insecticidal crystal δ‐endotoxin. We describe an indirect method of assessing the relative contribution to toxicity of two of these protoxins using monospecific antibodies directed against their active proteolytic products. Our results show that one toxin is active against Spodoptera frugiperda but not Choristoneura fumiferana cells in vitro, while the other lyses C. fumiferana but not S. frugiperda cells. There is no indication of synergism between these toxins in vitro.
The expression of Pseudomonas aeruginosa PAK pilin gene mutants in Escherichia coli
Authors: Pasloske B. L. , Carpenter M. R. , Frost L. S. , Finlay B. B. , Paranchych† W.
Published: October 2006

Previous work has demonstrated the expression of the cloned pilin gene of Pseudomonas aeruginosa PAK within Escherichia coli and has pinpointed this protein's localization exclusively to the cytoplasmic membrane (Finlay et al., 1986). To define regions of the pilin subunit necessary for its stability and transport within E. coli, we constructed six mutants of the pilin gene and studied their expression and localization using a T7 promoter system. Two of the mutants have either a 4‐ or 8‐amino‐acid deletion at the N‐terminus and both were stably expressed and transported primarily to the cytoplasmic membrane of E. coli. The other four mutants are C‐terminal truncations having between 36 and 56 amino acids of the C‐terminal region of the unprocessed pilin. Studies with these truncated mutants revealed that only the first 36 residues of the unprocessed pilin subunit were required for insertion into the E. coli membrane.
Cloning, characterization and regulation of an α‐amylase gene from Streptomyces limosus
Authors: Virolle M.‐J. , Bibb M. J.
Published: October 2006

An α‐amylase gene (aml) of Streptomyces limosus ATCC 19778 was cloned in Streptomyces lividans 66. S1 mapping experiments identified an aml transcript 1.8 kb in length and the extracellular enzyme was estimated to be 59 kD in size, suggesting that aml was transcribed as a monocistronic mRNA species. Expression of the gene was induced by maltose (or maltodextrins) in S. Iimosus and when aml was cloned in S. lividans or Streptomyces coelicolor A3(2). In S. Iimosus, mannitol repressed aml expression while glucose had little or no effect; in S. lividans and S. coelicolor the relative effects of the two sugars were reversed. Both induction and carbon‐source repression of aml expression appeared to occur at the level of transcriptional initiation. Glucose repression in S. coelicolor was dependent upon a functional glucose kinase gene.
Recombination among Protein II genes of Neisseria gonorrhoeae generates new coding sequences and increases structural variability in the Protein II family
Authors: Connell T. D. , Black W. J. , Kawula T. H. , Barritt D. S. , Dempsey J. A. , Kverneland K. , Stephenson A. , Schepart B. S. , Murphy G. L. , Cannon J. G.
Published: October 2006

Expression of Neisseria gonorrhoeae Protein II (P.II) is subject to phase variation and antigenic variation. The P.II proteins made by one strain possess both unique and conserved antigenic determinants. To study the mechanism of antigenic variation, we cloned several P.II genes, using as probes a panel of monoclonal antibodies (MAbs) specific for unique determinants. The DNA sequences of three P.II genes showed that they shared a conserved framework, with two short hypervariable (HV) regions being responsible for most of the differences among them. We demonstrated that unique epitopes recognized by the MAbs were at least partially encoded by one of the HV regions. Moreover, we found that reassortment of the two HV regions among P.II genes occurs, generating increased structural and antigenic variability in the P.II protein family.
Proteins from the prokaryotic nucleoid: primary and quaternary structure of the 15‐kD Escherichia coli DNA binding protein H‐NS
Authors: Falconl M. , Gualtierl M. T. , La Teana A. , Losso M. A. , Pon C. L.
Published: October 2006

The primary sequence of H‐NS (136 amino acid residues, Mr = 15402), an abundant Escherichia coli DNA‐binding protein, has been elucidated and its quaternary structure has been investigated by protein‐protein cross‐linking reactions. It was found that H‐NS exists predominantly as a dimer, even at very low concentrations, but may form tetramers at higher concentrations and that the protein‐protein interaction responsible for the dimerization is chiefly hydrophobic.
Expression of a biologically active diphtheria toxin fragment B in Escherichia coli
Authors: Cabiaux V. , Phalipon A. , Wattiez R. , Falmagne P. , Ruysschaert J. M. , Kaczorek M.
Published: October 2006

The toxB gene of Corynebacterium diphtheriae bacteriophage β encoding the B fragment of diphtheria toxin was cloned into an inducible expression vector. When expressed In Escherichia coli, fragment B was not proteolysed and was indistinguishable, by immunological criteria, from wild‐type C. diphthsriae derived fragment B. Soluble fragment B was partially purified from the cytoplasm by saline precipitation steps and was shown to compete with the wild‐type diphtheria toxin for binding to receptors of sensitive eukaryotic cells. A complete diphtheria toxin was reconstituted by formation of the disulphide bridge between purified fragment A and recombinant fragment B, which migrates at the expected Mr on Western blots and which was able to block protein synthesis by ADP‐ribosylation of elongation factor–2, thereby indicating that the recombinant fragment B had retained its biological activity.
Catabolite control of the elevation of PGK mRNA levels by heat shock in Saccharomyces cerevisiae
Authors: Piper P. W. , Curran B. , Davies M. W. , Hirst K. , Lockheart A. , Seward K.
Published: October 2006

Heat shock enhances the very high level of transcription of the phosphoglycerate kinase (PGK) gene in fermentative cultures of Saccharomyces cerevisiae. This response of PGK mRNA levels was not found on gluconeogenic carbon sources, and could be switched on or off subject to availability of fermentable carbon source. The addition of glucose to yeast growing on glycerol resulted in acquisition, within 30–60 min, of the ability to elevate PGK mRNA levels after heat shock. In addition, in aerobic cultures growing on glucose the exhaustion of the medium glucose coincided with a loss of the heat‐shock effect on PGK mRNA and a switch‐over to slower growth by aerobic respiration. Levels of hsp26 mRNA were analysed during these experiments.

Contrasting with this requirement for fermentable catabolite for manifestation of a heat‐shock response of PGK mRNA levels, the PGK enzyme was not synthesized at a greater level in heat‐shocked fermentative than in gluconeogenic cultures. PGK is one of only a few proteins made efficiently after mild heat shock of yeast. Thus, heat‐stress‐induced elevation of PGK mRNA levels does not appreciably increase PGK synthesis during exposure to high temperatures and so its role may be to assist cells repressed in mitochondrial function during recovery following a heat shock.
virA and virG are the Ti‐plasmid functions required for chemotaxis of Agrobacterium tumefaciens towards acetosyringone
Authors: Shaw C. H. , Ashby A. M. , Brown A. , Royal C. , Loake G. J. , Shaw C. M.
Published: October 2006

Octopine and nopaline Ti‐plasmids confer upon Agrobacterium tumefaciens C58C1 the ability to respond chemotactically to the vir‐inducing phenolic wound exudate, acetosyringone. A. tumefaciens C58C1 containing Ti‐plasmids with Tn5 insertions in virB, C., D or E exhibited marked chemotaxis towards acetosyringone. However, Ti‐plasmids with mutations in virA or VirG were unable to confer the responsive phenotype. Of the cosmid clones pVK219 (virAB) pVK221 (virBGC) pVK225 (virGCDE) and pVK257 (virABGC) mobilized to cured A. tumefaciens C58C1, only pVK257 bestowed acetosyringone chemotaxis. virA and virG are thus required for chemotaxis of A. tumefaciens towards acetosyringone. This suggests a multifunctional role for virA and virG: at low concentrations of acetosyringone they mediate chemotaxis and at higher concentrations they effect vir‐induction.
Nucleotide sequence and transcriptional analysis of the aerCaerA region of Aeromonas sobria encoding aerolysin and its regulatory region
Authors: Husslein V. , Huhle B. , Jarchau T. , Lurz R. , Goebel W. , Chakraborty T.
Published: October 2006

The nucleotide sequence of a 2510 base pair chromosomal fragment containing the aerolysin gene aerA, and its regulatory region aerC, from a clinical isolate of Aeromonas sobria was determined. The aerolysin gene coded for a 54.5 kD polypeptide and had a G + C content of 59%, indicating that it is endogenous to the genus Aeromonas. In contrast, the aerC region was characterized by its high A + T content (61%) and the presence of a core motif, aATAAAa, repeated eight times within 300 base pairs. A 12 base pair repeat, 5′ AATAAAACCGGG3′, present within this region occurred as a direct repeat 544 base pairs away, within the coding region of aerolysin. RNA polymerase binding studies and S1 mapping allowed the detection of two divergent non‐overlapping promoters within aerC. Despite having identical transcriptional start sites in both A. sobria and Escherichia coli, the amount of aerolysin transcript produced in E. coli is 30–40 times less than that found in A. sobria. The signal peptide of preproaerolysin was shown by deletion to be essential for export of the toxin to the external medium. The mature toxin is a hydrophilic protein with no hydrophobic stretches long enough to cross a membrane. A search for similarities to the primary sequence of aerolysin revealed that the toxin may share a functional similarity to haemolysin (hly A) of E. coli.
Overexpression, solubilization and refolding of a genetically engineered derivative of the penicillin‐binding protein 3 of Escherichia coli K12
Authors: Belder J. Bartholomé‐De , Nguyen‐Disteche M. , Houba‐Herin N. , Ghuysen J. M. , Maruyama I. N. , Hara H. , Hirota Y. , Inouye M.
Published: October 2006

Replacement of the amino‐terminal 40‐amino‐acid region of the 588‐ammo‐acid precursor of the membrane‐bound penicillin‐binding protein 3 (P6P3) by the decapeptide MKGKEFQAWI was carried out by altering the amino‐coding end of the ftsl gene. Insertion of the modified gene into a runaway‐replication plasmid under the control of a fused Ipp promoter and lac promoter/operator, resulted in the overexpression by Escherichia coli of the modified PBP3 (designated PBP3**) in the cytoplasm. About 80% of the accumulated PBP3** underwent sequestration in the form of insoluble protein granules that were isolated by cell breakage or cell lysis. After selective removal of contaminants by an EDTA‐lysozyme/DNase (de‐oxyribonuclease)/Nonidet extraction, treatment of the granules with guanidinium chloride followed by dialysis against buffer containing 0.5 M NaCI yielded a refolded, water‐soluble PBP3**, which, upon chromatography on Superose 12, exhibited the expected 60000 molecular mass. The refolded PBP3** bound benzytpenicillin in a 1 to 1 molar ratio, was highly sensitive to aztreonam and showed the same degree of thermostability, in terms of penicillin‐binding capacity, as the parent, membrane‐bound PBP3, suggesting that protein refolding occurred with formation of the correct intramolecular interactions. Two to three mg of refolded PBP** can be obtained from 1 litre of culture of the overproducing strain.
The protein encoded by gvpC is a minor component of gas vesicles isolated from the cyanobacteria Anabaena flos‐aquae and Microcyctis sp.
Authors: Hayes P. K. , Lazarus C. M. , Bees A. , Walker J. E. , Walsby A. E.
Published: October 2006

The proteins present in gas vesicles of the cyanobacteria Anabaena flos‐aquae and Microcystis sp. Were separated by SDS‐polyacrylamide gel electrophoresis. Each contained a protein of Mr 22 K whose N‐terminal amino acid sequences showed homology with that of the Calothrix sp. PCC 7601 gvpC gene product. The gvpC gene from A. flos‐aquae was cloned and sequenced. The derived amino acid sequence for the gene product indicated a protein, GVPc, of 193 residues and Mr 21985 containing five highly conserved 33 amino acid repeats. The sequence was identical at the N‐terminus to that of the Mr 22K protein present in gas vesicles and showed correspondence to seven tryptic peptides isolated from gas vesicles. This establishes that GVPc forms a second protein component of the gas vesicle, in addition to the main constituent, the 70 residue GVPa. Quantitative amino acid analysis of entire gas vesicles reveals that GVPc accounts for only 2.9% of the protein molecules and 8.2% of the mass present: this is insufficient to form the conical end caps of the gas vesicles. It is suggested that GVPc provides the hydrophilic outer surface of the gas vesicle wall; the 33 amino acid repeats may interact with the periodic structure provided by GVPa.
Molecular cloning, identification and ranscriptional analysis of genes involved in acetate utilization in Neurospora crassa
Authors: Thomas C. M. , Connerton I. F. , Fincham J. R. S.
Published: October 2006

Four Neurospora crassa genomic clones have been selected as hybridizing much more strongly to labeled mRNA isolated from acetate‐grown mycelium than to mRNA from sucrose‐grown mycelium. Hybridization of restriction fragments with acetate‐specific mRNA or cDNA has been used to delimit the transcribed region(s) of each clone. The transcription of all four clones is strongly induced by transfer of growing mycelium from sucrose to acetate as sole carbon source. In wild‐type mycelium, mRNAs corresponding to the four clones reach maximum levels after four hours of induction. They accumulate more rapidly and reach higher levels in an acetate non‐utilizing mutant, acu‐7, which has been found to overproduce enzymes of the glyoxylate cycle and to have a partial block in the TCA cycle. Molecular transformation of a Neurosporaacu‐5 mutant and of an Aspergillus nidulans acuE mutant by DNA of clone 2 and clone 1, respectively, strongly suggests that clone 2 codes for acetyl‐coenzyme A synthetase and that clone 1 codes for malate synthase. The transcribed segments of clones 1 and 2each hybridize to corresponding clones from Aspergillusnidulans (R. A. Sandeman and M. J. Hynes, personal communication).
Studies of UV‐inducible promoters from Clostridium perfringens in vivo and in vitro
Authors: Gamier T. , Cole S. T.
Published: October 2006

Expression of a 4kb segment of the bacteriocinogenic plasmid, plP404, from Clostridium perfringens inducible by UV‐irradiation. DNA sequence analysis revealed that this region contains three genes: uviA, uviB and bcn encoding the bacteriocin BCN5. Biochemical studies with mRNAs showed that expression was controlled at the transcriptional level and that the genes were organized in two independent transcriptional units, uviAB and ben both directed by tandem promoters inducible by UV light. The bcn gene is transcribed from three promoters (P1, P2, P3) while transcription of uviAB is directed by two promoters (P4, P5). With the exception of P4, which bears some resemblance to the consensus eubacterial promoter sequence, none of these promoters was recognized invitro by the major forms of RNA polymerase from C. perfringens, Bacillus subtilis or Escherichia coli, Promoters P1, P3 and P5, which show striking homology with each other, contain unusual sequences in the ‘−35’ and ‘−10’ regions known to be recognized by RNA polymerase and this might indicate positive control.