bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of internal fields on gain and spontaneous emission in InGaN quantum wells
Authors: Hader J. , Moloney J. V. , Koch S. W.
Published: October 2006

Fully microscopic models are used to investigate the structural dependence of InGaN∕GaN quantum-well semiconductor-laser gain media. Due to the inherent piezoelectric fields, the amplitudes and spectral positions of gain and spontaneous emission strongly depend on the structural details. It is shown how quantitative experiment/theory comparisons can be used to determine the fields. As a general trend, it is found that the loss current due to spontaneous emission at threshold decreases with well width and indium composition.
Ultracompact silicon-on-insulator ridge-waveguide mirrors with high reflectance
Authors: Velha P. , Rodier J. C. , Lalanne P. , Hugonin J. P. , Peyrade D. , Picard E. , Charvolin T. , Hadji E.
Published: October 2006

Microcavities offering small modal volumes V≈0.6 (λ∕n)3 and consisting of two identical tapered Bragg mirrors etched into a monomode silicon-on-insulator ridge waveguide are studied for operation at telecommunications wavelengths. The authors have measured a Q factor of 8900, for a loaded cavity with a peak transmission at resonance in excess of 60%. The measured Q value quantitatively agrees with the calculation results and is 20 times larger than those previously reported for similar geometries without tapers.
The effect of fertiliser P on crop biomass production, partitioning, and quality in 'Challenger' sweet corn
Authors: Fletcher A. L. , Moot D. J. , Stone P.
Published: October 2006

Sweet corn kernel yield responds to phosphorous (P) supply, but whether the response is mediated through a general increase in crop biomass or increased partitioning to kernels is unclear. Furthermore, changes in ear quality (ear length, diameter, and unfilled tip length) may also result from changes in crop biomass or partitioning. This research quantifies the partitioning between vegetative and reproductive (including ear quality) components for field-grown sweet corn crops, with a range of total biomass yield resulting from different rates of P fertiliser.
To do this, ‘Challenger’ sweet corn was sown in 2 consecutive seasons (2001–02 and 2002–03) on a low-P site (Olsen P = 6.5 μg/g) at Lincoln, Canterbury, New Zealand. Five rates of P fertiliser were applied in each season. In 2001–02, 0, 50, 100, 150, or 200 kg P/ha was applied. These were followed by an additional 0, 0, 10, 20, and 40 kg P/ha in 2002–03. This gave a fertiliser range of 0–240 kg P/ha over 2 years. The resulting range in crop biomass (9.7–16.7 t DM/ha) was conservatively partitioned to vegetative (45%), rachis and husk leaf (32%), and kernel (23%) fractions, indicating that kernel yield responses were solely related to changes in crop biomass. The number of harvestable ears increased by 0.39 ears/m2 for every 1 t DM/ha increase in crop biomass. Similarly, ear quality was related to the kernel yield per primary ear. Specifically, the unfilled tip length decreased by 3.1 mm and individual kernel dry mass increased by 16 mg for every 10 g increase in kernel DM per ear. These results show that P fertiliser should be applied at optimum rates (in these experiments ≥100 kg P/ha) to maximise sweet corn crop biomass, which in turn will lead to maximum kernel yield and ear quality. The conservative partitioning of crop biomass suggests that other agronomic factors that increase total biomass production are likely to have a similar effect on crop yields.
Babel's tower revisited: a universal resource for cross-referencing across annotation databases
Authors: Drăghici Sorin , Sellamuthu Sivakumar , Khatri Purvesh
Published: October 2006

Motivation: Annotation databases are widely used as public repositories of biological knowledge. However, most of these resources have been developed by independent groups which used different designs and different identifiers for the same biological entities. As we show in this article, incoherent name spaces between various databases represent a serious impediment to using the existing annotations at their full potential. Navigating between various such name spaces by mapping IDs from one database to another is a very important issue which is not properly addressed at the moment.

Results: We have developed a web-based resource, Onto-Translate (OT), which effectively addresses this problem. OT is able to map onto each other different types of biological entities from the following annotation databases: Swiss-Prot, TrEMBL, NREF, PIR, Gene Ontology, KEGG, Entrez Gene, GenBank, GenPept, IMAGE, RefSeq, UniGene, OMIM, PDB, Eukaryotic Promoter Database, HUGO Gene Nomenclature Committee and NetAffx. Currently, OT is able to perform 462 types of mappings between 29 different types of IDs from 17 databases concerning 53 organisms. Among these, over 300 types of translations and 15 types of IDs are not currently supported by any other tool or resource. On average, OT is able to correctly map between 96 and 99% of the biological entities provided as input. In terms of speed, sets of ∼20 000 IDs can be translated in <30 s, in most cases.

Availability: OT is a part of Onto-Tools, which is freely available at

Contact:  sorin@wayne.edu
Adding sequence context to a Markov background model improves the identification of regulatory elements
Authors: Kim Nak-Kyeong , Tharakaraman Kannan , Spouge John L.
Published: October 2006

Motivation: Many computational methods for identifying regulatory elements use a likelihood ratio between motif and background models. Often, the methods use a background model of independent bases. At least two different Markov background models have been proposed with the aim of increasing the accuracy of predicting regulatory elements. Both Markov background models suffer theoretical drawbacks, so this article develops a third, context-dependent Markov background model from fundamental statistical principles.

Results: Datasets containing known regulatory elements in eukaryotes provided a basis for comparing the predictive accuracies of the different background models. Non-parametric statistical tests indicated that Markov models of order 3 constituted a statistically significant improvement over the background model of independent bases. Our model performed slightly better than the previous Markov background models. We also found that for discriminating between the predictive accuracies of competing background models, the correlation coefficient is a more sensitive measure than the performance coefficient.

Availability: Our C++ program is available at

Contact:  spouge@ncbi.nlm.nih.gov

Supplementary information: Supplementary data are available at Bioinformatics online.
MUSA: a parameter free algorithm for the identification of biologically significant motifs
Authors: Mendes Nuno D. , Casimiro Ana C. , Santos Pedro M. , Sá-Correia Isabel , Oliveira Arlindo L. , Freitas Ana T.
Published: October 2006

Motivation: The ability to identify complex motifs, i.e. non-contiguous nucleotide sequences, is a key feature of modern motif finders. Addressing this problem is extremely important, not only because these motifs can accurately model biological phenomena but because its extraction is highly dependent upon the appropriate selection of numerous search parameters. Currently available combinatorial algorithms have proved to be highly efficient in exhaustively enumerating motifs (including complex motifs), which fulfill certain extraction criteria. However, one major problem with these methods is the large number of parameters that need to be specified.

Results: We propose a new algorithm, MUSA (Motif finding using an UnSupervised Approach), that can be used either to autonomously find over-represented complex motifs or to estimate search parameters for modern motif finders. This method relies on a biclustering algorithm that operates on a matrix of co-occurrences of small motifs. The performance of this method is independent of the composite structure of the motifs being sought, making few assumptions about their characteristics. The MUSA algorithm was applied to two datasets involving the bacterium Pseudomonas putida KT2440. The first one was composed of 70 σ54-dependent promoter sequences and the second dataset included 54 promoter sequences of up-regulated genes in response to phenol, as suggested by quantitative proteomics. The results obtained indicate that this approach is very effective at identifying complex motifs of biological significance.

Availability: The MUSA algorithm is available upon request from the authors, and will be made available via a Web based interface.

Contact:  atf@inesc-id.pt

Supplementary information: An appendix is available at under ‘Papers on-line’.
Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays
Authors: Tembe Waibhav , Zavaljevski Nela , Bode Elizabeth , Chase Catherine , Geyer Jeanne , Wasieloski Leonard , Benson Gary , Reifman Jaques
Published: October 2006

Motivation: Advances in DNA microarray technology and computational methods have unlocked new opportunities to identify ‘DNA fingerprints’, i.e. oligonucleotide sequences that uniquely identify a specific genome. We present an integrated approach for the computational identification of DNA fingerprints for design of microarray-based pathogen diagnostic assays. We provide a quantifiable definition of a DNA fingerprint stated both from a computational as well as an experimental point of view, and the analytical proof that all in silico fingerprints satisfying the stated definition are found using our approach.

Results: The presented computational approach is implemented in an integrated high-performance computing (HPC) software tool for oligonucleotide fingerprint identification termed TOFI. We employed TOFI to identify in silico DNA fingerprints for several bacteria and plasmid sequences, which were then experimentally evaluated as potential probes for microarray-based diagnostic assays. Results and analysis of approximately 150 in silico DNA fingerprints for Yersinia pestis and 250 fingerprints for Francisella tularensis are presented.

Availability: The implemented algorithm is available upon request.

Contact:  jaques.reifman@us.army.mil.
Non‐invasive evaluation of hair interior morphology by X‐ray microscope
Authors: KIM Beom Joon , KWON Oh Sang , PARK Won Seok , YOUN Hwa Shik , CHOI Chong Won , KIM Kyu Han , EUN Hee Chul
Published: October 2006

Lots of trials have been performed to obtain better microscopic images of hair structure. Although scanning electron microscopy (SEM) and transmission electron microscopy (TEM) provide detailed images of hair, artificial processing may modify the original images during sample preparation. To overcome this limitation, we applied newly‐developed X‐ray microscopy with an 80–100 nm spatial resolution to produce a detailed view of the morphological change of hair interior. This X‐ray microscopy permits us to penetrate a hair shaft without any artificial change and also provides precise images of hair interior with fine resolution. We evaluated the interior morphological change of Japanese standard hair tress No. 8 by various treatments such as ultraviolet (UV) irradiation, heating, hair dyeing, decolorizing bleaching agents and permanent waving. Internal morphological images were relatively similar in both heated and UV‐irradiated hair. They revealed coarsening of cuticles and dehydration of cortex and medulla. When compared with TEM, X‐ray microscopy provides more intact images in the cuticle and may be a useful tool in observing fine cracks of hair cortex. Additionally, X‐ray images were intact and not influenced by any processing procedures. In observing the external and internal structure of hair, its resolution seems to be somewhat lesser than TEM and there are also several remaining weaknesses to be improved. Hopefully, forthcoming technology will solve these problems in the near future.
Case of acrodermatitis continua accompanied by psoriatic arthritis
Authors: JO Seong Jin , PARK Je Young , YOON Hyun Sun , YOUN Jai Il
Published: October 2006

Acrodermatitis continua of Hallopeau (ACH) is a rare chronic pustular eruption that predominantly involves the fingertips. The characterization of this disease has been confused. Some have considered it as a separate entity while others as a variant of pustular psoriasis. The presented patient simultaneously had ACH and joint lesions which were diagnosed as psoriatic arthritis. We believe that because ACH may be accompanied by psoriatic arthritis, as in this case, it could be evidence that it is a variant of psoriasis.
Urticarial vasculitis appearing in the progression of systemic sclerosis
Authors: KATO Yoko , AOKI Mikako , KAWANA Seiji
Published: October 2006

We report a case of urticarial vasculitis that appeared during the course of limited cutaneous systemic sclerosis. The urticarial lesions responded to systemic administration of prednisolone. After the appearance of urticarial vasculitis, the progression of scleroderma in distal sites of her elbow and knee joint became apparent. We consider this case to be consistent with limited cutaneous systemic sclerosis. The patient started treatment with prednisolone and her edema as well as scleroderma softened gradually. We analyzed, by immunohistochemistry, the number of tryptase‐positive mast cells of this case in the lesions of urticarial vasculitis as well as systemic sclerosis. The number of tryptase‐positive mast cells in the lesions of urticarial vasculitis as well as systemic sclerosis was significantly increased compared to normal skin (P < 0.05 and P < 0.005, respectively). We demonstrate that, in the present case, mast cells might be involved in both courses of urticarial vasculitis and systemic sclerosis as a common factor.
Necrobiotic xanthogranuloma of the nose without paraproteinemia
Authors: KUNIKATA Nagisa , KIKUCHI Katsuko , HASHIMOTO Akira , TAGAMI Hachiro
Published: October 2006

We report a 65‐year‐old Japanese woman who presented with a nodule on the nose near the left eye. Histological examination of the totally resected lesion revealed the typical features of necrobiotic xanthogranuloma (NXG). However, her laboratory investigation revealed no paraproteinemia. We believe that the present case represents a cutaneous variant of NXG without accompaniment of paraproteinemia or any systemic involvement.
The PKA‐CREB system encoded by the honeybee genome
Authors: Eisenhardt D. , Kühn C. , Leboulle G.
Published: October 2006

The cAMP‐dependent kinase (PKA) plays a crucial part in long‐term memory formation in the honeybee (Apis mellifera). One of the putative substrates of the PKA activity is the cAMP response element binding protein (CREB), a transcription factor in the bZIP protein family. We searched the honeybee genome to characterize genes from the CREB/CREM and the PKA families. We identified two genes that encode regulatory subunits and three genes encode catalytic subunits of PKA. Eight genes code for bZIP proteins, but only one gene was found that encodes a member of the CREB/CREM family. The phylogenetic relationship of these genes was analysed with their Drosophila and human counterparts.
Towards a molecular definition of worker sterility: differential gene expression and reproductive plasticity in honey bees
Authors: Thompson G. J. , Kucharski R. , Maleszka R. , Oldroyd B. P.
Published: October 2006

We show that differences in the reproductive development of honey bee workers are associated with locus‐specific changes to abundance of messenger RNA. Using a cross‐fostering field experiment to control for differences related to age and environment, we compared the gene expression profiles of functionally sterile workers (wild‐type) and those from a mutant strain in which workers are reproductively active (anarchist). Among the set of three genes that are significantly differentially expressed are two major royal jelly proteins that are up‐regulated in wild‐type heads. This discovery is consistent with sterile workers synthesizing royal jelly as food for developing brood. Likewise, the relative underexpression of these two royal jellies in anarchist workers is consistent with these workers’ characteristic avoidance of alloparental behaviour, in favour of selfish egg‐laying. Overall, there is a trend for the most differentially expressed genes to be up‐regulated in wild‐type workers. This pattern suggests that functional sterility in honey bee workers may generally involve the expression of a suite of genes that effectively ‘switch’ ovaries off, and that selfish reproduction in honey bee workers, though rare, is the default developmental pathway that results when ovary activation is not suppressed.
Rheological and Morphological Comparison of Thermal and Hydrostatic Pressure‐Induced Filamentous Myosin Gels
Authors: Iwasaki Tomohito , Washio Masahiro , Yamamoto Katsuhiro , Nakamura Kunio
Published: October 2006

The structure and rheological properties of heat‐ and pressure‐induced myosin filament gels were investigated. The apparent elasticity of heat‐induced gel peaked at 55 °C (4.35 ± 0.57 kPa), whereas that of pressure‐induced gel increased with elevating pressure, and the gel formed at 500 MPa had a value of 4.79 ± 0.25 kPa. All pressure‐ and heat‐induced gels showed similar internal structure, namely, the gels were composed of a fine‐strand network. The detailed structures of the strands induced by pressure‐ and heat‐treatment of myosin filaments were observed using an atomic force microscope. The structural differences among the strands were not observed, whereas the elasticity of the strands measured by atomic force microscope revealed differences among the strands formed with varying heating temperature and pressure. The elasticities of the heat‐induced strands were 1.19 ± 0.09 MPa, 10.24 ± 1.16 MPa, and 3.09 ± 0.25 MPa at 40 °C, 55 °C, and 70 °C, respectively. On the other hand, the elasticity of the pressure‐induced strand increased with elevating pressure. The elasticity values were 1.24 ± 0.09 MPa, 2.32 ± 0.17 MPa, and 9.80 ± 0.84 MPa at pressures of 150, 300, and 500 MPa, respectively. Because the changes in the elasticity of the whole gel corresponded to those of the strand, it is concluded that the rheological properties of the constituting strands determine that of myosin filamentous gel.
A Novel Technique for Ice Crystal Visualization in Frozen Solids Using X‐Ray Micro‐Computed Tomography
Authors: Mousavi Reza , Miri Taghi , Cox P.W. , Fryer Peter J.
Published: October 2006

A novel technique, using an X‐ray micro‐computed tomography system (X‐ray micro‐CT system) has been developed for visualization of the two‐ (2‐D) and three‐dimensional (3‐D) ice crystal structures formed during freezing. The system reconstructs all 3‐D images based on a set of 2‐D images obtained by multiple slicing of an X‐ray shadow image. This study demonstrates the capability of the technique to characterize the ice crystal microstructure of mycoprotein products after freezing. Results are presented for the 2‐D ice crystals formed within mycoprotein frozen at different rates. The method requires freeze‐drying of the sample to remove frozen water before scanning to indicate ice crystal and internal structure of the material at a depth of 1 cm. The dendrite spacing of ice crystals has been related to the freezing conditions of the material.
Effects of Calcium Ascorbate and Ionizing Radiation on the Survival of Listeria monocytogenes and Product Quality of Fresh‐cut ‘Gala’ Apples
Authors: Fan Xuetong , Sokorai Kimberly J. B. , Sommers Christopher H. , Niemira Brendan A. , Mattheis James P.
Published: October 2006

The interactive effects of calcium ascorbate (CaA) and ionizing radiation on viability of Listeria monocytogenes inoculated in solutions and on ‘Gala’ apple slices were investigated. The D10 values (radiation doses that inactivate 90% of bacterial population) for L. monocytogenes inoculated in water, 3.5%, and 7.0% CaA solutions were 0.32, 0.61, and 0.58 kGy, respectively. The D10 values of the pathogen on the surface of apple slices treated with water, 3.5%, and 7.0% CaA were 0.24, 0.32, and 0.32 kGy, respectively. To determine the impact of CaA and irradiation on quality of apple slices, apple slices treated with 0%, 3.5%, and 7.0% CaA were exposed to 1.6 kGy gamma radiation (a dose that produced a 5‐log reduction of L. monocytogenes) and stored under modified atmosphere at 4 °C for 14 d. CaA at levels of both 3.5% and 7.0% prevented the browning of the apple slices. The apple aroma intensity, however, decreased as the concentration of CaA increased. Irradiation at 1.6 kGy did not significantly affect color, soluble solid content, titratable acidity, or apple aroma intensity. The only negative effect of irradiation on apple slices appeared to be a loss of firmness. Our results suggest that CaA, used as an antibrowning agent, protected L. monocytogenes from radiation both in solution and on apple slices, but radiation at doses sufficient to inactivate 5‐log of the bacterium did not significantly influence product quality attributes except for the loss in firmness.
Survival Analysis Applied to Sensory Shelf Life of Yogurts–I: Argentine Formulations
Authors: Curia Ana , Aguerrido Martin , Langohr Klaus , HOUGH GUILLERMO
Published: October 2006

:Sensory shelf lives of Argentine commercial stirred yogurts of different compositions stored at 10 °C were studied. Variations were as follows: fat‐free and whole‐fat, and vanilla and strawberry flavors. Yogurts were tested between 0 and 84 d of storage by consumers who expressed their acceptance or rejection of each sample; yogurts also were measured overall, as well as their attribute acceptability, with a hedonic scale. Survival analysis statistics were used to estimate shelf lives. Considering 25% of consumers rejecting the product, shelf lives were between 28 and 41 d; thus, a unique shelf life for this product does not seem reasonable. 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. Overall, fat‐free yogurts had lower shelf lives than whole‐fat yogurts.
Consumer Acceptability of Muffins with Flaxseed (Linum usitatissimum)
Authors: Ramcharitar Anisa , Badrie Neela , Mattfeldt‐Beman Mildred , Matsuo Hisako , Ridley Charlotte
Published: October 2006

Flaxseed has recently gained attention as a functional food. The effect of adding flaxseed (7.3%, 11.6%, and 15.5%) to muffins on consumer acceptability was evaluated by a focus group, hedonic scoring, and food action rating scale (FACT). The majority of consumers (82.6%, P < 0.001) rated the control muffin (0 % flaxseed) higher than the flax muffin for appearance, color, flavor, texture, overall acceptability, and food acceptance. Flaxseed muffin (11.6%) was “neither liked nor disliked” to “liked slightly” in overall acceptability. This may have been accounted for by the observation that many persons aged 18 to 25 y did not think they needed to consume “health foods”. This “indifferent” and in some cases “negative” attitude toward the flax muffins, which they considered a “health food”, may have influenced the ratings the flax muffins received. Texture and flavor were strongly and positively correlated (P < 0.01) to overall acceptability. A flaxseed muffin provided at least 16% fiber of the daily recommended value.
Primary structure and subcellular localization of two fimbrial subunit‐like proteins involved in the biosynthesis of K99 fibrillae
Authors: Roosendaal E. , Jacobs A. A. C. , Rathman P. , Sondermeyer C. , Stegehuis F. , Oudega B. , de Graaf F. K.
Published: October 2006

Analysis of the nucleotide sequence of the distal part of the fan gene cluster encoding the proteins involved In the biosynthesis of the fibrillar adhesin, K99, revealed the presence of two structural genes, fanG and fanH. The amino acid sequence of the gene products (FanG and FanH) showed significant homology to the amino acid sequence of the fibrillar subunit protein (FanC). Introduction of a site‐specific frame‐shift mutation in lanG or fanH resulted in a simultaneous decrease in fibrillae production and adhesive capacity. Analysis of subcellular fractions showed that, in contrast to the K99 fibrillar subunit (FanC), both the FanH and the FanG protein were loosely associated with the outer membrane, possibly on the periplasmic side, but were not components of the fimbriae themselves.
Sequence of nifL from Klebsiella pneumoniae: mode of action and relationship to two families of regulatory proteins
Authors: Drummond1 M. H. , Wootton J. C.
Published: October 2006

We present the nucleotide sequence of K. pneumoniae nifL, which negatively regulates nif transcription in response to oxygen and fixed nitrogen. It shows partial sequence homology to the general nitrogen regulatory proteins NtrB of K. pneumoniae and Bradyrhizobium parasponiae. This homology is weaker than that shown between the NifA and NtrC activator components of the nif and general nitrogen control systems. The N‐terminal section of the NifL protein includes a structural duplication sharing sequence homology with part of NtrB, and a region containing a cysteine pair which might be implicated in redox control. Unlike NtrB, NifL appears to lack a DNA‐binding motif, consistent with evidence that NifL represses by interacting directiy with NifA. The C‐terminal section of NifL shows clear homology to NtrB and to a family of proteins involved in transcriptional control or chemotaxis, each of which probably interacts with a member of the family of regulatory proteins showing homology to NtrC.
Characterization of the toxicity and cytopathic specificity of a cloned Bacillus thuringiensis crystal protein using insect cell culture
Authors: Haider M. Z. , Ellar D. J.
Published: October 2006

An insecticidal protein gene from Bacillus thuringiensis var. aizawal was cloned in Escherichia coli. The cloned gene expressed at a high level and the synthesized protein appeared as an insoluble, phase‐bright inclusion in the cytoplasm. These inclusions were isolated by density gradient centrifugation, the isolated protein was activated in vitro by different proteloytic regimes and the toxicity of the resulting preparations was studied using insect cells grown in tissue culture. The inclusions consisted of a 130 kDa polypeptide which was processed to a protease‐resist‐ant 55 kDa protein by tryptic digestion. This preparation lysed lepidopteran (Choristoneura fumiferana) CFI ceils but not dipteran (Aedes albopictus) calls. When the crystal protein was activated by sequential treatment, first with trypsin and then with Aedes aegypti gut proteases, the resulting 53 kDa polypeptide was now toxic only to the dipteran cells and not to the lepidopteran cells. Thus the dual specificity of this var. aizawal toxin results from differential proteolytic processing of a single protoxin. The trypsin‐activated preparation was weakly active against Spodoptera frugiperda cells. Membrane binding studies of the trypsin‐activated toxin revealed a 68 kDa protein in the lepidopteran ceil membranes, which may be the receptor for this toxin.
Requirements for transcriptional activation in vitro of the nitrogen‐regulated gInA and nifLA promoters from Klebsiella pneumoniae: dependence on activator concentration
Authors: Austin S. , Henderson N. , Dixon R.
Published: October 2006

Three proteins involved in nitrogen regulation In Klebsiella pneumoniae, NTRA, NTRB and NTRC, have been purified. In a defined in vitro system all three NTR proteins are required for initiation of transcription at the ntr activatable glnA and nifLA promoters. However, in crude S‐30 extracts, transcription from the glnA promoter, but not the nifLA promoter, can be activated in the absence of NTRB. A higher concentration of NTRC is required for activation of nifLA transcription than for glnA transcription. Sequences located between ‐227 and ‐158 with respect to the nifL transcription start site are required for efficient activation of the nifLA promoter in vitro.
The frequency of expression of pyelonephritis‐associated pili is under regulatory control
Authors: Low D. , Robinson E. N. , McGee Z. A. , Falkow S.
Published: October 2006

The Bscherfchia coli urinary tract Isolate C1212 contains two pyelonephritis‐associated pili (pap) DNA sequences designated here as pap‐17 and pap‐21. Each of these pap sequences encodes antigenically‐distinct pilin monomers, pllin‐17 and pilin‐21, respectively. Most individual strain C1212 cells isolated from a single bacterial colony expressed pilin‐21. Only a small fraction (5%) of strain C1212 cells expressed pilin‐17. Most of the latter population simultaneously expressed pilin‐21, but a low percentage of cells expressed pill composed of pilin‐17 alone. In contrast, almost every E. coli K‐12 cell containing multicopy pap‐17 expressed pilin‐17 at the ceil surface. These results Indicated that the regulation of pilin‐17 expression observed for strain C1212 was lost when pap‐17 was in the multicopy state. Transfer of pap‐17 to a single copy vector resulted in a pilin‐17 expression frequency lower than strain C1212 (1%). Using E. coli K‐12 containing single copy pap‐17, we found that the frequency of piiin‐17 expression increased about 15‐foid when pap‐21 was present in multiple copies in trans. Subcloning of pap‐21 showed that a 2.2 kilobase‐pair DNA sequence adjacent to, but not including, the pilin‐21 structural gene was sufficient for activation of pilin‐17 expression.
Plasmid‐mediated sucrose metabolism in Escherichia coli K12: mapping of the scr genes of pUR400
Authors: Schmid K. , Ebner R. , Altenbuchner J. , Schmitt R. , Lengeler J. W.
Published: October 2006

The scr genes located on plasmid pUR400 and responsible for sAucrose (Scr) metabolism of Escherichia coli K12 and other enteric bacteria have been cloned on a 9.3 kb DNA fragment. The different genes were mapped by transposon insertion mutagenesis, by restriction endonuclease and deletion mapping, and the corresponding gene products were identified. Besides the known structural genes scrA, coding for an EnzymellScr (45 kD) of the phosphoenolypyruvate‐dependent phosphotransferase system (PTS), and scrB, coding for a sucrose 6‐phosphate hydrolase (invertase) (55 kD), two new structural genes were discovered. Gene scrK apparently codes for an intracellular and ATP‐dependent fructokinase (39 kD), while scry seems to code for a sucrose porin (58 kD) in the outer cell membrane. No genes for an Enzyme IIIScr of the PTS or for (a) glycosyltransferase(s) were detected. The four genes form an scr operon (gene order, scrK scrY scrA scrB, transcription from K to B), regulated by a repressor (gene scrR, 37 kD) and inducible by sucrose, fructose and fructose‐containing oligosaccharides
Divergent effects of a dnaK mutation on abnormal protein degradation in Escherichia coli
Authors: Keller J. A. , Simon L. D.
Published: October 2006

Escherichia coli bacteria produce at least one 70 kD stress protein, the product of the dnaK gene. We have compared the rates of degradation of different types of abnormal proteins in null Ion E. coli with a partial deletion of the dnaK gene with the rates observed in null Ion dnaK+ cells. We have found that both canavanyl proteins and puromycyl polypeptides are degraded more slowly in the null dnaK mutants than in the dnaK+ strain. However, a temperature‐sensitive mutant Lacl protein is degraded more rapidly in the null dnaK strain. The stability of this temperature‐sensitive Lad protein was also examined in detail under various other conditions.
Organization and regulation of the Corynebacterium glutamicum hom‐thrB and thrC loci
Authors: Follettie M. T. , Shin H. K. , Sinskey A. J.
Published: October 2006

The genes encoding the three terminal enzymes in the threonine biosynthetic pathway, homoserine dehydrogenasa (hom), homoserine kinase (thrB) and threonine synthase (thrC) have been isolated from Corynebacterium glutamicum. The C. glutamicum hom and thrB genes were subcloned on a 3.6 kb Sal l‐generated chromosomal fragment. The C. glutamicum thrC gene was shown not to be linked to the hom‐thrB locus. L‐methionine represses the cloned homoserine dehydrogenase and homoserine kinase similar to that of the chromosomally encoded hom and thrB gene products. Northern hybridization analysis demonstrates that this repression is mediated at the level of transcription and that hom‐thrB represents an operon in C. glutamicum.
The plasmid‐encoded Yop2b protein of Yersinia pseudotuberculosis is a virulence determinant regulated by calcium and temperature at the level of transcription
Authors: Bölin I. , Wolf‐Watz H.
Published: October 2006

The basic Yop2b protein, encoded by the virulence plasmid pIBI of Yersinia pseudotuberculosis, is produced under Ca2+‐deficient conditions. A mutant deleted for the entire yopH gene, which encodes the Yop2b protein, was found to be avirulent. Virulence could be restored by trans‐complementation. The DNA‐Sequence of yopH predicted a 50 737 D polypeptide lacking a typical signal peptide. Transcription of yopH is regulated by both temperature and Ca2+‐concentration. Mutations within the region of the virulence plasmid known to be involved in regulating gene expression in response to Ca2+ abolished transcription of yopH. Other temperature‐sensitive mutations in the Ca2+‐regulatory locus showed a high level of transcription regardless of Ca2+‐concentration. These responses were similar to those of the yopE gene. The promoter region of the yopE and yopH genes were compared and four conserved motifs identified.
Nucleotide sequencing and expression of the fadL gene involved in long‐chain fatty acid transport in Escherichia coli
Authors: Said B. , Ghosn C. R. , Vu L. , Nunn W. D.
Published: October 2006

The fadL gene of Escherichia coli codes for an outer membrane protein involved in long‐chain fatty acid transport. Its product was purified from outer membrane proteins. We determined the nucleotide sequence of a 2.8‐kb chromosomal DNA segment that contains the fadL gene. The fadL gene consists of a 1149‐nucEeottde coding region and contains a highly hydrophobic polypeptide of 383 amino acids with a calculated molecular weight of 42 380. We have used S1‐mapping analysis to identify the transcription initiation site. A region exhibiting extensive dyad symmetry and perfect homology to the catabolite activator protein binding site was detected.
Repression of the aroF promoter by the TyrR repressor in Escherichia coli K‐12: role of the ‘upstream’ operator site
Authors: Cobbett C. S.
Published: October 2006

Three sequences are required for complete repression of the aroF promoter by the TyrR repressor protein. Two of these operator sites lie adjacent to each other and overlap the −35 region of the aroF promoter while the third lies about 70 base pairs upstream of the promoter. An aroF‐cat (chloramphenicol acetyltransferase) gene fusion has been used to assay the effect of DNA insertions that alter the distance between the two promoter‐proximal and the third, distal, operator sites on the repression of the aroF promoter in vivo. The distal site contributes to the repression of the promoter up to a distance of about 400 base pairs and its effect is not dependent on its separation from the first and second sites by an integral number of turns of the DNA helix.
Nucleotide sequence of the mannitol (mtl) operon in Escherichia coli
Authors: Davis T. , Yamada M. , Elgort M. , Saier M. H.
Published: October 2006

The nucleotide sequence of the known portions of the mannitol operon in Escherichia coli (mtlOPAD) has been determined. Both the operator‐promoter region and the intercistronic region between the mtlA and mtID genes (encoding the mannitol‐specific Enzyme II of the phosphotransferase system and mannitol–1‐ phosphate dehydrogenase, respectively) show parallels with corresponding regions of the glucitol (gut) operon, but neither the mtlA nor the mtlD gene products show obvious homology with the corresponding gene products of the glucitol operon. Five potential cyclic AMP receptor protein binding sites were identified in the mtlOP region, all showing near identity with the consensus sequence. Four regions of dyad symmetry (four to seven bases in length), serving as potential repressor binding sites, overlap with the potential cyclic AMP receptor protein binding sites. Repetitive extragenic pallndromic (REP) sequences, forming stem‐loop structures in the intercistronic region between mtlA and mtlD and following the mtlD gene were identified. Probable terminator sequences were not found in any of these three regulatory regions. Mannitol–1‐phosphate dehydrogenase exhibits two overlapping, potential NAD+ binding sites near the W‐terminus of the protein. Computer techniques were used to analyse the mtlD gene and its product.
The role of activator binding sites in transcriptional control of the divergently transcribed nifF and nif LA promoters from Klebsiella pneumoniae
Authors: Minchin S. D. , Austin S. , Dixon R. A.
Published: October 2006

The regulatory region spanning the divergently transcribed nif F and nifLA promoters contains a NIFA‐specific upstream activator sequence (UAS) located around +59, and two NTRC binding sites centred at −142 and −163 with respect to the nifLA transcription start site. We have constructed mutations in each of these binding sites and examined their role in transcriptional activation of the divergently transcribed promoters. Analysis of a mutation at +60 confirms that the UAS is required for efficient NIFA‐mediated activation of nifF transcription. This sequence is also required for maximal activation of the nifLA promoter. Mutations at −169 and −148, within the two NTRC binding sites, reduce activation of the nifLA promoter by NTRC in vivo and lower the affinity of the activator for these sites in vitro. Phosphorylation of NTRC by NTRB is required for efficient binding of NTRC to these sites.
Alterations in the carboxy‐termianl half of cloacin destabilize the protein and prevent its export by Escherichia coli
Authors: van Putten A. J. , Stegehuis F. , van Bergen Henegouwen P. M. P. , De Graaf F. K. , Oudega B.
Published: October 2006

Several overlapping carboxy‐terminal and internal deletions were constructed in the cloacin structural gene. The expression, the binding of the cloacin DF13 immunity protein and the release into the culture medium of the mutant cloacin polypeptides were studied by immunoblotting and ELISAs. Minor alterations at the carboxy‐terminal end of the cloacin did not affect protein expression, stability or release to a large extent, but larger carboxy‐terminal deletions strongly destabilized the protein and no release was observed. The removal of a particular region within the carboxy‐terminal portion of cloacin strongly destabilize the polypeptide and made it a target for proteolytic degradation. Binding of immunity protein did not affect stability and release of the mutant polypeptides. By using immunoelectron microscopy, the polypeptides that were not exported were located in the cytoplasm of producing cells. Large aggregates of these mutant polypeptides were not observed in the cytoplasm: the polypeptides were present in a soluble form.
Analysis of the membrane‐binding domain of penicillin‐binding protein 5 of Escherichia coli
Authors: Jackson M. E. , Pratt J. M.
Published: October 2006

Internal deletions close to the C‐terminus of the Escherichia coli penicillin binding protein 5 (PBP5, DacA) have defined the C‐terminal 18 residues of the protein as essential for membrane binding. This C‐terminal sequence is capable of forming a strongly amphiphilic α‐helix. In this paper we show that the PBP5 amphiphilic helix is able to anchor the periplasmic TEM‐β‐lactamase to the inner membrane. In addition, we have demonstrated that mature PBP5 (lacking the N‐terminal signal sequence) possesses the ability to bind to the membrane from a soluble form of the protein, showing that translocation across the membrane is unnecessary for anchoring to be established.
Transcriptional analysis of the 16S rRNA gene of the rrnD gene set of Streptomyces coelicolor A3(2)
Authors: Baylis H. A. , Bibb M. J.
Published: October 2006

The nucleotide sequence of 2.5 kb of the Streptomyces coelicolor A3(2) rRNA gene set rrnD, extending from upstream of the 16S rRNA gene to the putative 5′ end of the 23S rRNA gene, has been determined (Baylis and Bibb, 1987; this paper). In addition to locating the 5′ end of the 16S rRNA gene, nuclease S1 mapping identified seven RNA 5′ end‐points upstream of the 16S rRNA gene; four of these were coincident with transcriptional initiation points for S. coelicolor A3(2) RNA poiymerase in vitro and were consequently regarded as in vivo transcription start points for promoters p1 to p4. One end‐point identified by nuclease S1 mapping localized a putative processing site analogous to those found upstream of 16S rRNA genes in other eubacteria. Sequence motifs similar to those discovered in low G+C Gram‐positive bacteria were found associated with two of the promoters and the processing site. A probable protein coding region was observed upstream of the promoter region.
Mapping and characterization of mutants of the Escherichia coli cell division gene, ftsA
Authors: Robinson A. C. , Begg K. J. , Donachie W. D.
Published: October 2006

Eight independent temperature‐sensitive mutants of the cell division protein FtsA have been studied. They fall into two classes in terms of their behaviour at 42°C and recovery at 30°C. The first class shows salt dependent temperature‐sensitivity and reversible in activation of FtsA protein at 42°C. The second shows irreversible inactivation which is not prevented by salt. Recovery of the ability to divide at 30°C is rapid in mutants of the first group, but is delayed for approximately a generation time in the second group. This suggests that irreversible inactivation of FtsA causes extensive damage to the division machinery. The amino acid substitutions show clustering to a limited domain of the protein, and one particular substitution is found in three of the mutants.
Nucleotide sequence of Acinetobacter baumannii aphA‐6 gene: evolutionary and functional implications of sequence homologies with nucleotide‐binding proteins, kinases and other aminoglycoside‐modifying enzymes
Authors: Martin P. , Jullien E. , Courvalin P.
Published: October 2006

A new kanamycin‐resistance gene, detected in Acinetobacter baumannii and designated aphA‐6, was sequenced. It specifiesa 30319 Dalton 3′‐aminoglycosidephospliotransferase (APH(3′)) that mediates resistance to kanamycin and structurally related aminogiycosides, including amikacin. Pairwise comparisons of the six types of APH(3′) so far detected inhuman pathogens (types I, II, IM and VI) and in aminoglycoside‐producing microorganisms (types IV and V), confirm that APH(3) enzymes have diverged from a common ancestor. Three highly retained motifs (1:V–HGD—N; 2: G–D‐GR/K‐G and 3: D–K/R‐Y/F—LDE) located in the C‐terminal part of the enzymes were defined. Screening of protein sequence databases for each of these motifs revealed that motifs 1and 2 are both found in nucleotide‐binding phosphotransferases associated with a variety of biological processes, namely adenylate kinase, viral oncogenic protein kinases, elongation factors, Na+/K+‐transporting ATPase, myosin and antibiotic‐modifying enzymes. Motif 2 probably corresponds to the MgATP binding site, while motifs 3 and 1 could be involved in the splitting of the phosphodiester bond and in the phosphate transfer, respectively. Moreover, an additional motif, almost invariably centrally located, was found in all aminoglycoside‐modifying enzymes. The occurrence of this motif, possibly a recombination site which would have allowed the association of units of separate functions, is compatible with a modular concept for the structure of aminoglycoside‐modifying enzymes.
The transmembrane topology of the sn‐glycerol‐3‐phosphate permease of Escherichia coli analysed by phoA and lacZ protein fusions
Authors: Gött P. , Boss W.
Published: October 2006

The Escherichia coli glpT gene encodes a transport protein that mediates uptake of sn‐glycerol‐3‐phosphate. This permease is a member of a class of bacterial organophosphate permeases which transport substrates by antiport with inorganic phosphate. The glpT gene product, probably an oligomer of a single polypeptide chain, is thought to span the cytoplasmic membrane several times, as predicted by the hydropathic profile. Protein fusions, in which varying lengths of the amino‐terminal end of the permease is attached to alkaline phosphatase (phoA) and to β‐galactosidase (lacZ) were constructed. On the assumption that phoA fusions only exhibit high enzymatic activity when fused to extra‐cytoplasmic regions of the target protein, whereas lacZ fusions will only be active when the β‐galactosidase portion is attached to cytoplasmic domains of the target protein, the activities of the fusions were used to test a two‐dimensional model for the permease. The model proposes that glpT contains 12 transmembrane segments divided by a larger cytoplasmic region. Despite some limitation caused by hot‐spot sites of transpositions, the TnphoA approach was consistent with the model. In contrast, we feel that the enzymatic activity of lacZ fusions is only a limited parameter for studying the topology of a complex membrane protein.
Identification and characterization of TnphoA mutants of Salmonella that are unable to pass through a polarized MDCK epithelial cell monolayer
Authors: Finlay B. B. , Starnbach M. N. , Francis C. L. , Stacker B. A. D. , Chatfield S. , Dougan G. , Falkow S.
Published: October 2006

Surface protein mutants of the invasive Salmonella species, S. choleraesuis, were generated using the transposon TnphoA. 626 alkaline phosphatase (PhoA+) fusion mutants were identified and screened for their ability to pass through (transcytose) polarized epithelial monolayers of Madin Darby canine kidney (MDCK) cells grown on membrane filters. Forty two mutants were unable to pass through this barrier. All of these transcytosis mutants were unable to adhere to or invade MDCK monolayers, yet these mutations were not in the genes encoding type 1 pili or mannose‐resistant haemagglutination (MRHA). These transcytosis mutants could be grouped into six classes. Class 1 mutants had altered lipopolysaccharide (LPS) O side‐chain structures while Class 2 mutants had defects in their LPS core. Mutants belonging to Classes 5 and 6 did not decrease the transepithelial electrical resistance of polarized MDCK cell mono‐layers, in contrast to the parental strain and the other mutants (Classes 1, 2, 3 and 4). Mutants belonging to Class 1 were less virulent in mice, while Class 2 (defective core) and Classes 4 and 5 (normal LPS) mutant strains were avirulent in mice. Mutants from Classes 3 and 6 were as virulent in mice as S. choleraesuis. These results suggest that the ability to pass through epithelial barriers may be an important virulence characteristic of Salmonella. These data indicate that bacterial adherence, internalization and monolayer transcytosis are closely linked events. It was also demonstrated that a mutant with decreased rates of intracellular replication still passed through the monolayer at rates similar to wild‐type S. choleraesuis.