bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic and Transcriptional Characterization of the Meningococcal PhoPQ System, a Magnesium-Sensing Two-Component Regulatory System That Controls Genes Involved in Remodeling the Meningococcal Cell Surface
Authors: Newcombe J. , Jeynes J. C. , Mendoza E. , Hinds J. , Marsden G. L. , Stabler R. A. , Marti M. , McFadden J. J. 
Published: July 2005

ABSTRACT

We previously identified and characterized a two-component regulatory system in the meningococcus with homology to the
phoP-phoQ
system in salmonella and showed that allele replacement of the NMB0595 regulator gene led to loss of virulence, sensitivity to antimicrobial peptides, perturbed protein expression, and magnesium-sensitive growth. On the basis of these findings we proposed that the system should be designated the meningococcal PhoPQ system. Here we further characterized the NMB0595 mutant and demonstrated that it had increased membrane permeability and was unable to form colonies on solid media with low magnesium concentrations, features that are consistent with disruption of PhoPQ-mediated modifications to the lipooligosaccharide structure. We examined the transcriptional profiles of wild-type and NMB0595 mutant strains and found that magnesium-regulated changes in gene expression are completely abrogated in the mutant, indicating that, similar to the salmonella PhoPQ system, the meningococcal PhoPQ system is regulated by magnesium. Transcriptional profiling of the mutant indicated that, also similar to the salmonella PhoPQ system, the meningococcal system is involved in control of virulence and remodeling of the bacterial cell surface in response to the host environment. The results are consistent with the hypothesis that the PhoP homologue plays a role in the meningococcus similar to the role played by PhoP in salmonella. Elucidating the role that the PhoPQ system and PhoPQ-regulated genes play in the response of the meningococcus to the host environment may provide new insights into the pathogenic process.
The Genome ofSulfolobus acidocaldarius, a Model Organism of theCrenarchaeota
Authors: Chen Lanming , Brügger Kim , Skovgaard Marie , Redder Peter , She Qunxin , Torarinsson Elfar , Greve Bo , Awayez Mariana , Zibat Arne , Klenk Hans-Peter , Garrett Roger A. 
Published: July 2005

ABSTRACTSulfolobus acidocaldariusis an aerobic thermoacidophilic crenarchaeon which grows optimally at 80°C and pH 2 in terrestrial solfataric springs. Here, we describe the genome sequence of strain DSM639, which has been used for many seminal studies on archaeal and crenarchaeal biology. The circular genome carries 2,225,959 bp (37% G+C) with 2,292 predicted protein-encoding genes. Many of the smaller genes were identified for the first time on the basis of comparison of threeSulfolobusgenome sequences. Of the protein-coding genes, 305 are exclusive toS. acidocaldariusand 866 are specific to theSulfolobusgenus. Moreover, 82 genes for untranslated RNAs were identified and annotated. Owing to the probable absence of active autonomous and nonautonomous mobile elements, the genome stability and organization ofS. acidocaldariusdiffer radically from those ofSulfolobus solfataricusandSulfolobus tokodaii. TheS. acidocaldariusgenome contains an integrated, and probably encaptured, pARN-type conjugative plasmid which may facilitate intercellular chromosomal gene exchange inS. acidocaldarius. Moreover, it contains genes for a characteristic restriction modification system, a UV damage excision repair system, thermopsin, and an aromatic ring dioxygenase, all of which are absent from genomes of otherSulfolobusspecies. However, it lacks genes for some of their sugar transporters, consistent with it growing on a more limited range of carbon sources. These results, together with the many newly identified protein-coding genes forSulfolobus, are incorporated into a publicSulfolobusdatabase which can be accessed athttp://dac.molbio.ku.dk/dbs/Sulfolobus.
Localization of Translocation Complex Components in
Bacillus subtilis:
Enrichment of the Signal Recognition Particle Receptor at Early Sporulation Septa
Authors: Rubio Aileen , Jiang Xin , Pogliano Kit 
Published: July 2005

ABSTRACT

We here demonstrate that in
Bacillus subtilis
, the signal recognition particle receptor, FtsY, transiently localizes to early sporulation septa, whereas three SecYEG translocase-associated membrane proteins (SecDF, SpoIIIJ, and YqjG) are uniformly distributed. These results suggest FtsY delivers secreted proteins to SecYEG at the septum, consistent with initial septal localization of forespore membrane proteins.
Characterization of the Multiple Transferable Resistance Repressor, MtrR, fromNeisseria gonorrhoeae
Authors: Hoffmann Katherine M. , Williams Daniel , Shafer William M. , Brennan Richard G. 
Published: July 2005

ABSTRACTMtrR represses expression of theNeisseria gonorrhoeae mtrCDEmultidrug efflux transporter genes. MtrR displays salt-dependent DNA binding, a stoichiometry of two dimers per DNA site, and, for a protein that was expected to be essentially all helical, a high percentage of random coil and possibly β-sheet structure.
The F
1
F
o
-ATP Synthase of
Mycobacterium smegmatis
Is Essential for Growth
Authors: Tran Sieu L. , Cook Gregory M. 
Published: July 2005

ABSTRACT

The F
1
F
o
-ATP synthase plays an important role in a number of vital cellular processes in plants, animals, and microorganisms. In this study, we constructed a Δ
atpD
mutant of
Mycobacterium smegmatis
and demonstrated that
atpD
encoding the β subunit of the F
1
F
o
-ATP synthase is an essential gene in
M. smegmatis
during growth on nonfermentable and fermentable carbon sources.
Adenylyl Cyclase Activity of Cya1 from the Cyanobacterium
Synechocystis
sp. Strain PCC 6803 Is Inhibited by Bicarbonate
Authors: Masuda Shinji , Ono Taka-aki 
Published: July 2005

ABSTRACT

Bicarbonate stimulates the activities of several class III adenylyl cyclases studied to date. However, we show here that bicarbonate decreased
V
max
and substrate affinity in Cya1, a major adenylyl cyclase in the cyanobacterium
Synechocystis
sp. strain PCC 6803. This indicates that manifestation of the bicarbonate responsiveness is specifically modulated in Cya1.
Photoresponsive Flagellum-Independent Motility of the Purple Phototrophic Bacterium
Rhodobacter capsulatus
Authors: Shelswell Kristopher J. , Taylor Terumi A. , Beatty J. Thomas 
Published: July 2005

ABSTRACT

We report the discovery of photoresponsive, flagellum-independent motility of the α-proteobacterium
Rhodobacter capsulatus
, a nonsulfur purple phototrophic bacterium. This motility takes place in the 1.5% agar-glass interface of petri plates but not in soft agar, and cells move toward a light source. The appearances of motility assay plates inoculated with wild-type or flagellum-deficient mutants indicate differential contributions from flagellar and flagellum-independent mechanisms. Electron microscopy confirmed the absence of flagella in flagellar mutants and revealed the presence of pilus-like structures at one pole of wild-type and mutant cells. We suggest that
R. capsulatus
utilizes a flagellum-independent, photoresponsive mechanism that resembles twitching motility to move in a line away from the point of inoculation toward a light source.
Mutator Effects in
Escherichia coli
Caused by the Expression of Specific Foreign Genes
Authors: Gabrovsky Vanessa , Yamamoto Mitsuko Lynn , Miller Jeffrey H. 
Published: July 2005

ABSTRACT

Certain genes from
Lactococcus lactis
and
Pseudomonas aeruginosa
, including the
nfxB
gene, generate a mutator phenotype in
Escherichia coli
. The results of this study, together with those of a previous study, support conservation of regulatory sequences in
E. coli
and
P. aeruginosa
and suggest that some efflux pumps prevent mutagenicity by exporting mutagenic products of metabolism.
Chemotactic Responses to Metals and Anaerobic Electron Acceptors in
Shewanella oneidensis
MR-1
Authors: Bencharit Sira , Ward Mandy J. 
Published: July 2005

ABSTRACT

Although a previous study indicated that the dissimilatory metal-reducing bacterium
Shewanella oneidensis
MR-1 lacks chemotactic responses to metals that can be used as anaerobic electron acceptors, new results show that this bacterium responds to both Mn(III) and Fe(III). Cells were also shown to respond to another unusual electron acceptor, the humic acid analog anthraquinone-2,6-disulfonate. These results indicate that
S. oneidensis
is capable of moving towards a number of unusual anaerobic electron acceptors, including some that would normally be insoluble in the environment. Additionally,
S. oneidensis
was shown to migrate in gradients of several divalent cations under anaerobic conditions. Although responses to the reduced forms of redox-active metals, such as Mn(II) and Fe(II), might indicate that
S. oneidensis
uses gradients of these metals to locate the insoluble electron acceptors Mn(III/IV) and Fe(III) for dissimilatory purposes, responses to non-redox-active metals, such as Zn(II), suggest that movement towards divalent cations might serve other, potentially assimilatory, purposes.
Effect of
sdiA
on Biosensors of
N
-Acylhomoserine Lactones
Authors: Lindsay Amber , Ahmer Brian M. M. 
Published: July 2005

ABSTRACT

Many gram-negative bacteria synthesize
N
-acylhomoserine lactones (AHLs) and then use transcription factors of the LuxR family to sense and respond to AHL accumulation in the environment; this phenomenon is termed quorum sensing. Bacteria produce a variety of AHLs, and numerous bacterial reporter strains, or biosensors, that can detect subsets of these molecules have been constructed. Many of these are based on
Escherichia coli
because this species does not produce AHLs. However, both
Escherichia
and
Salmonella
spp. contain a LuxR homolog named SdiA that can detect exogenous AHL synthesized by other microbial species. In this study we have determined that
sdiA
of
E. coli
and
Salmonella
spp. can activate an RhlR-based biosensor plasmid in response to AHLs other than what the biosensor was designed to detect. SdiA does not activate LuxR-, LasR-, or AhyR-based biosensor plasmids, although the presence of
sdiA
in
E. coli
does interfere with the function of the AhyR-based biosensor. Because
sdiA
interferes with the function of two of the four reporters, we have constructed a set of
E. coli
biosensor strains that lack
sdiA
. The set includes control reporters that allow the
luxR
dependence of responses to be determined.
A Study of High-Gain Servo Controller with Complex Zeros for Optical Disk Drives
Authors: Urakawa Yoshiyuki , Watanabe Tetsu 
Published: July 2005

As optical disk drives are increasingly used in various applications, their servo systems must be made more robust. Various control technologies have been studied, [rf1,rf2] but they require larger circuits and longer computational times. In this paper, a high-gain servo controller with complex zeros, which is the same order controller as the conventional controller, is proposed. The complex zeros allow higher gain without the loss of phase margin. We implemented the high-gain servo controller in a digital servo system. The discrete model of the digital servo system had 3 sampling time delays, and it caused an enhancement of disturbances at high frequencies. We suppressed the enhancement, using the pole assignment method directly in the discrete model. The experimental data had small rotational errors and good performance for torque disturbance.
Hybrid Equalized Partial Response Path-Feedback Maximum Likelihood for 35.4 GB Blu-ray Disc ROM
Authors: Higashino Satoru , Kajiwara Yoshiyuki , Kobayashi Shoei 
Published: July 2005

The decoding method with larger margin has been required according to the recent high density optical recordings. Since the optical reproduced signal has a strict cutoff of modulation transfer function (MTF), the high linear density equalization will cause the equalization error. In such a case, adaptive Viterbi [rf1,rf2,rf3] has been investigated as a decoding method which compensates tangential inter-symbol interference (ISI) and the scanty high frequency components. This fundamental theory is based on path feedback Viterbi detection. [rf4] We have developed hybrid equalized partial response path-feedback maximum likelihood (HEPR-PFML) which compensates the scanty frequency components more efficiently than conventional adaptive Viterbi. By using this system, the decoding performance is not only improved, but phase locked loop (PLL) will be stable because of the clear timing error information. We will show the experimental results for the higher density 35.4 GB Blu-ray Disc ROM (BD-ROM) than standard linear densities.
Supervised Learning in a Recurrent Network of Rate-Model Neurons Exhibiting Frequency Adaptation
Authors: Fortier Pierre A. , Guigon Emmanuel , Burnod Yves 
Published: July 2005

For gradient descent learning to yield connectivity consistent with real biological networks, the simulated neurons would have to include more realistic intrinsic properties such as frequency adaptation. However, gradient descent learning cannot be used straightforwardly with adapting rate-model neurons because the derivative of the activation function depends on the activation history. The objectives of this study were to (1) develop a simple computational approach to reproduce mathematical gradient descent and (2) use this computational approach to provide supervised learning in a network formed of rate-model neurons that exhibit frequency adaptation. The results of mathematical gradient descent were used as a reference in evaluating the performance of the computational approach. For this comparison, standard (nonadapting) rate-model neurons were used for both approaches. The only difference was the gradient calculation: the mathematical approach used the derivative at a point in weight space, while the computational approach used the slope for a step change in weight space. Theoretically, the results of the computational approach should match those of the mathematical approach, as the step size is reduced but floating-point accuracy formed a lower limit to usable step sizes. A systematic search for an optimal step size yielded a computational approach that faithfully reproduced the results of mathematical gradient descent. The computational approach was then used for supervised learning of both connection weights and intrinsic properties of rate-model neurons to convert a tonic input into a phasic-tonic output pattern. Learning produced biologically realistic connectivity that essentially used a monosynaptic connection from the tonic input neuron to an output neuron with strong frequency adaptation as compared to a complex network when using nonadapting neurons. Thus, more biologically realistic connectivity was achieved by implementing rate-model neurons with more realistic intrinsic properties. Our computational approach could be applied to learning of other neuron properties.
Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases
Authors: Reimers Mark , Weinstein John N 
Published: July 2005

Abstract
Background
Quality-control is an important issue in the analysis of gene expression microarrays. One type of problem is regional bias, in which one region of a chip shows artifactually high or low intensities (or ratios in a two-channel array) relative to the majority of the chip. Current practice in quality assessment for microarrays does not address regional biases.

Results
We present methods implemented in R for visualizing regional biases and other spatial artifacts on spotted microarrays and Affymetrix chips. We also propose a statistical index to quantify regional bias and investigate its typical distribution on spotted and Affymetrix arrays.
We demonstrate that notable regional biases occur on both Affymetrix and spotted arrays and that they can make a significant difference in the case of spotted microarray results. Although strong biases are also seen at the level of individual probes on Affymetrix chips, the gene expression measures are less affected, especially when the RMA method is used to summarize intensities for the probe sets. A web application program for visualization and quantitation of regional bias is provided at http://www.discover.nci.nih.gov/affytools.

Conclusion
Researchers should visualize and measure the regional biases and should estimate their impact on gene expression measurements obtained. Here, we (i) introduce pictorial visualizations of the spatial biases; (ii) present for Affymetrix chips a useful resolution of the biases into two components, one related to background, the other to intensity scale factor; (iii) introduce a single parameter to reflect the global bias present across an array. We also examine the pattern distribution of such biases and conclude that algorithms based on smoothing are unlikely to compensate adequately for them.
A new short-term toxicity assay using Aspergillus awamori with recombinant aequorin gene
Authors: Kozlova Olga , Zwinderman Mark , Christofi Nick 
Published: July 2005

Abstract

Background
Most currently available short-term toxicity assays are based on bacterial cells. Therefore there is a need for novel eukaryotic microbial bioassays that will be relevant to higher eukaryotes such as animals and plants. Ca2+ is a universal intracellular signalling molecule found in all organisms from prokaryotes to highly specialized animal cells. In fungi calcium has been demonstrated to be involved in control of many important processes. The recombinant aequorin gene from the jellyfish Aequorea victoria responsible for the expression of the Ca2+-sensitive aequorin photoprotein has been cloned in the filamentous fungus Aspergillus awamori. This has allowed real life monitoring of [Ca2+]c changes in living fungal cells. When subjected to different physico-chemical stimuli fungal cells respond by transiently changing the concentration of free Ca2+ in the cytosol ([Ca2+]c) and the pattern of these changes (Ca2+ signature) is specific to each particular stimulus. Therefore it was interesting to investigate whether different environmental toxicants would be able to affect the pattern of [Ca2+]c changes in a reproducible and dose dependant manner.

Results
Toxicity bioassay has been developed to monitor changes [Ca2+]c of the recombinant fungus in the presence of toxicants representing heavy metals – Cr6+ and Zn2+ and a phenolic polar narcotic -3,5-DCP. The fungus responds to toxicants by a decrease in the amplitude of [Ca2+]c response to 5 mM external CaCl2 and an increase in Ca2+ final resting levels and recovery time.

Conclusion
A novel toxicity bioassay utilizing eukaryotic cells has been developed based on filamentous fungi transformed with the recombinant aequorin gene. A range of parameters characterising changes in [Ca2+]c has been identified, e.g. Amplitude, Length of Transient, Final Resting Level and Recovery Time. These parameters can be used to determine the toxicity of a range of chemicals to eukaryotic cells in a 96-well microtitre plate method.
A Review of Referrals of New Patients to the Paediatric Department of a Teaching Hospital during a Six-Month Period in 2004
Authors: Salam Samer , Badri Sondos Al , Lee George TR 
Published: July 2005

Aims The aims of this review were to assess the reasons why patients were referred to a specialist dental paediatric unit and the quality of the referral letters received. Material and Method All patients referred to the paediatric consultation clinic at the Liverpool University Dental Hospital from January 2004 to July 2004 were included in the review. The reasons for their referral, as stated by the referring practitioners, were compared with the clinical findings from initial assessments in the consultation clinic and the quality of referral letters was assessed. Results Ninety-nine out of a total of 102 referrals were from general dental practitioners. Sixty were girls and 42 boys. Their mean age was 9.5 years. The commonest reason (25 patients) was for treatment under general anaesthesia. In 90 (88.2%) cases the main reason for referral stated in the letters was consistent with the findings of the clinical assessment in the consultant clinic. All 102 letters included the patient's name, address, date of birth and telephone number and 89 (87.3%) were dated. However, only 25 (24.5%) included any mention of medical history and fewer than 30% included details of any treatment provided by the referring practitioner. Conclusions The vast majority of patients were referred for good reasons. The quality of the referral letters was generally poor. The use of a structured referral pro forma could improve the quality of the referral.
Dentists with Special Interests (DwSIs): Further Developments
Authors: Eaton Kenneth A 
Published: July 2005

The Faculty of General Dental Practice (UK) (the Faculty) has been intimately involved in the plans to introduce dentists with special interests (DwSIs) into the National Health Service (NHS).1 It was therefore appropriate that the Faculty combined with the Faculty of Dental Surgery (FDS) of The Royal College of Surgeons of England to host a national event on Thursday, 21st April 2005 on the topic. The aims of this study day were to provide: • An update on the development work to implement a scheme for DwSIs. • Details of the clinical competency frameworks developed as guidance for practitioners and Primary Care Trusts (PCTs) in each of the four clinical areas designated as the first in which DwSIs will work. The event was sold out with an audience of over 260 drawn from all areas of dentistry, and included clinicians from both primary and secondary care and administrators from PCTs and other NHS bodies.
A Survey of General Dental Practitioners on the Mersey Postgraduate Register regarding the National Institute for Clinical Excellence (NICE) Guidelines for the Removal of Wisdom Teeth
Authors: Rogers Simon N , Reginald Anusha , Lowe Derek , Grieveson Brian 
Published: July 2005

Aim To ascertain the awareness of and response to the National Institute for Clinical Excellence (NICE) guidelines among general dental practitioners (GDPs) in the Mersey region. Methods A pre-piloted postal questionnaire was sent to all GDPs (522) on the Mersey postgraduate register. Day case statistics for third molar surgery at the local hospital were reviewed. Results Three hundred and eighty-seven (74%) of the GDPs responded and virtually all reported seeing patients with problems arising from third molars in the previous month. Thirteen per cent claimed that they were either unaware or unsure of the NICE guidelines and 34% reported that they did not have a copy. Seventy-eight per cent reported that they either definitely or probably agreed with the NICE guidelines, 56% that the guidelines had definitely or probably changed their management of third molar problems, 64% that they considered that the guidelines had definitely or probably reduced numbers of extractions/surgical removals, and 56% that they definitely or probably referred fewer patients with third molar problems. However, 89% said they had either frequently or occasionally encountered problems when they left a wisdom tooth on review (untreated). Eighty-four respondents provided free text comments on the NICE guidelines; half were favourable and half were critical. The local hospital's day case statistics indicated that there had been a fall in the annual number of patients undergoing third molar surgery from 494 in 1998 to 287 in 2002. Conclusions It was concluded that the majority of respondents were aware of the guidelines and were using them. However, it was unclear whether or not the guidelines had, in themselves, led to a reduction in the number of referrals of patients with third molar problems, or that the reduction had already started, before the guidelines were published, and might have continued even if the guidelines had not been published.