bluuebunny/crossref_metadata_2025_split huggingface dataset:
The AGUAAA motif in cspA1/A2 mRNA is important for adaptation of Yersinia enterocolitica to grow at low temperature
Authors: Neuhaus Klaus , Anastasov Natasa , Kaberdin Vladimir , Francis Kevin P. , Miller Virginia L. , Scherer Siegfried 
Published: November 2003

SummaryAcclimatization of the psychrotolerant Yersinia enterocolitica after a cold shock from 30°C to 10°C causes transcription of the major cold shock protein (CSP) bicistronic gene cspA1/A2 to increase by up to 300‐fold. Northern blot analysis of cspA1/A2 using four probes that hybridize specifically to different regions of CSP mRNA revealed the appearance of a number of cspA1/A2 transcripts that are smaller than the original transcript and transiently visible at the end of the acclimation period. Primer extension and RNA protection experiments demonstrated that these smaller mRNAs have 5′ ends located in the same core sequence (5′‐AGUAAA‐3′) at five different places within the mRNA, indicating preferential cleavage of the CSP mRNA transcripts. A similar result was obtained for cspB of Escherichia coli, containing two such core sequences. Furthermore, this motif is present in the major CSP genes of a variety of Gram‐negative and Gram‐positive bacteria. We have therefore termed this sequence cold shock cut box (CSC‐box). After inserting a CSC‐box into a plasmid‐bound lacZ gene in Y. enterocolitica, the mRNA of this construct was cleaved within the CSC‐box, and a change in this CSC‐box from AGUAAA to AGUCCC dramatically reduced cleavage of the mutated lacZ gene. Mutating all CSC‐boxes in Y. enterocolitica of a plasmid bound cspA1/A2 dramatically increases the lag time after a cold shock before re‐growth occurs. Based on these results, we suggest that the role of the CSC‐box is related to downregulation of cspA mRNA after acclimation to low temperature.
Modulation of Pseudomonas aeruginosa gene expression by host microflora through interspecies communication
Authors: Duan Kangmin , Dammel Carol , Stein Jeffrey , Rabin Harvey , Surette Michael G. 
Published: November 2003

SummaryThe change in gene expression patterns in response to host environments is a prerequisite for bacterial infection. Bacterial diseases often occur as an outcome of the complex interactions between pathogens and the host. The indigenous, usually non‐pathogenic microflora is a ubiquitous constituent of the host. In order to understand the interactions between pathogens and the resident microflora and how they affect the gene expression patterns of the pathogens and contribute to bacterial diseases, the interactions between pathogenic Pseudomonas aeruginosa and avirulent oropharyngeal flora (OF) strains isolated from sputum samples of cystic fibrosis (CF) patients were investigated. Animal experiments using a rat lung infection model indicate that the presence of OF bacteria enhanced lung damage caused by P. aeruginosa. Genome‐wide transcriptional analysis with a lux reporter‐based promoter library demonstrated that ≈ 4% of genes in the genome responded to the presence of OF strains using an in vitro system. Characterization of a subset of the regulated genes indicates that they fall into seven functional classes, and large portions of the upregulated genes are genes important for P. aeruginosa pathogenesis. Autoinducer‐2 (AI‐2)‐mediated quorum sensing, a proposed interspecies signalling system, accounted for some, but not all, of the gene regulation. A substantial amount of  AI‐2  was  detected  directly  in  sputum  samples from CF patients and in cultures of most non‐pseudomonad bacteria isolated from the sputa. Transcriptional profiling of a set of defined P. aeruginosa virulence factor promoters revealed that OF and exogenous AI‐2 could upregulate overlapping subsets of these genes. These results suggest important contributions of the host microflora to P. aeruginosa infection by modulating gene expression via interspecies communications.
Heterologous expression of a mammalian protein tyrosine phosphatase gene in Leishmania: effect on differentiation
Authors: Nascimento Mirna , Abourjeily Nay , Ghosh Anirban , Zhang Wen Wei , Matlashewski Greg 
Published: November 2003

Summary Leishmania is a protozoan pathogen which is transmitted to humans through the bite of an infected sandfly. This infection results in a spectrum of diseases throughout the developing world, collectively known as leishmaniasis. During its life cycle, Leishmania differentiates from the promastigote stage in the sandfly vector into the amastigote stage in the mammalian host where it multiplies exclusively in macrophage phagolysosomes. Although differentiation of Leishmania is essential for its survival and pathogenesis in the mammalian host, this process is poorly understood. In higher eukaryotic cells, protein tyrosine phosphorylation plays a central role in cell proliferation, differentiation and overall function. We have therefore investigated the role of protein tyrosine phosphorylation in Leishmania differentiation by undertaking complementary approaches to mediate protein tyrosine dephosphorylation in vivo. In the present study, L. donovani were engineered to express a mammalian protein tyrosine phosphatase, or were treated with inhibitors of protein tyrosine kinases, and the resulting phenotype was examined. Both approaches resulted in a partial differentiation from promastigotes to amastigotes including the expression of the amastigote specific A2 protein, morphological change and increased virulence. These data provide support for the involvement of tyrosine phosphorylation in the differentiation of Leishmania.
Regulation of Arabidopsis SHY2/IAA3 protein turnover
Authors: Tian Qing , Nagpal Punita , Reed Jason W. 
Published: November 2003

SummaryAuxin/indole acetic acid (Aux/IAA) proteins regulate transcriptional responses to the plant hormone auxin. Gain‐of‐function mutations in the Arabidopsis SHORT HYPOCOTYL 2 (SHY2/IAA3) gene encoding an Aux/IAA protein increase steady‐state levels of SHY2/IAA3 protein and decrease auxin responses, indicating that SHY2/IAA3 negatively regulates auxin signaling. These shy2 mutations also cause ectopic light responses, suggesting that SHY2/IAA3 may promote light signaling. Auxin regulates turnover of the related Auxin‐resistant (AXR)2/IAA7 and AXR3/IAA17 proteins by increasing their interaction with the Skp1‐Cdc53/cullin‐F‐box (SCFTIR1) E3 ubiquitin ligase complex. To investigate whether SHY2/IAA3 is regulated similarly, we have used a turnover assay to reveal that axr1 and transport inhibitor resistant (tir)1 mutations affecting SCFTIR1 decrease SHY2/IAA3 turnover. In pull‐down assays, SHY2/IAA3 protein interacted with TIR1, the F‐box component of SCFTIR1 and with the photoreceptor phytochrome B. Auxin stimulated SHY2/IAA3 interaction with TIR1, whereas the shy2‐2 gain‐of‐function mutation decreased this interaction. Light did not affect the interaction, suggesting that light regulates some other aspect of Aux/IAA gene or protein function. The chemical juglone (5‐hydroxy‐1,4‐naphthoquinone) inhibited the interaction, suggesting that peptidyl‐prolyl isomerization may mediate auxin‐induced SHY2/IAA3 protein turnover.
Mutational analysis of forkhead transcriptional factor 2 (FOXL2) in Korean patients with blepharophimosis–ptosis–epicanthus inversus syndrome
Authors: Cha SC , Jang YS , Lee JH , Kim HK , Kim SC , Kim S , Baek S‐H , Jung WS , Kim J‐R 
Published: November 2003

We screened for mutations in the forkhead transcription factor gene, FOXL2, in Korean patients with sporadic or familial blepharophimosis–ptosis–epicanthus inversus syndrome (BPES) by polymerase chain reaction‐single‐stranded conformation polymorphism (PCR‐SSCP) and direct sequencing. Five of nine BPES families and three of seven sporadic cases were detected to have FOXL2 mutations. We identified four types of FOXL2 mutations, two of which are novel. A new 14 bp deletion (939–952del14) causing a frameshift from G235W and the extension of the predicted protein to 527 amino acids was detected in a BPES family patient. In addition, a novel 845C > A transversion, resulting in a nonsense mutation (S203X), was found in a sporadic case of BPES. The previously reported in‐frame 30 bp duplication(909–938dup30) was the most common mutation and was found in eight patients of four BPES families and one sporadic case. A known 17 bp duplication (1080–1096dup17) was observed in a sporadic BPES case. We were unable to find a causal mutation in four BPES families and four sporadic cases. These results suggest that in a fraction of BPES patients, the genetic defect might be associated with a mutation in the non‐coding region of the FOXL2 gene or in other genes.
IMPACT OF LEAD TRANSPORT ON CHILDREN'S BLOOD AND ENVIRONMENTAL LEAD LEVELS
Authors: Mak Donna B. , Plant Aileen J. , Bulsara Max , Body Peter 
Published: November 2003

ABSTRACTIntroduction: A lead monitoring project was established in 1996 to monitor the environmental and health effects of lead being transported through a remote town in tarpaulin‐covered trucks.Methods: Dust samples from sites on the transport route were collected at 3–6 monthly intervals between 1996 and 1999. Annual blood lead testing clinics, offering voluntary testing to children, were conducted from 1997 to 1999.Results: Of the 55 dust samples analysed, only nine contained particles of lead concentrate and these were present at very low levels. During the project 167 children were tested. The geometic mean of blood lead levels in 1997, 1998 and 1999 were 4.5 μg/dL, 5.0 μg/dL and 5.1 μg/dL, respectively (all within the normal range). Residence on the transport route was not associated with higher lead levels (P > 0.05).Conclusions: Lead transport was not associated with any detectable environmental contamination or increase in children's blood lead levels.
Experimental therapeutics of Parkinson's disease
Authors: Henderson Jasmine M 
Published: November 2003

Summary1. The loss of central dopamine, which characterises Parkinson's disease, led to the main pharmacological strategy for treatment, namely levodopa, a dopamine‐replacement therapy. Several years after treatment, the majority of patients experience dose‐limiting side‐effects and loss of symptom control. There is a resurgence of interest in neurosurgery for treating the Parkinson's disease, particularly in new techniques targeting the subthalamic nucleus (STN), which is overactive in Parkinson's disease and contributes to symptom development.2. We performed unilateral subthalamotomy (lesioning the subthalamic nucleus via the toxin N‐methyl‐d‐aspartate) in marmosets and rats with experimentally induced parkinsonism (induced using the toxin 6‐hydroxydopamine). A range of similar behaviours common to both rodents and primates were evaluated before and after each type of surgery. Post‐mortem histology was used to confirm the lesions. We also provide details of a case with Parkinson's disease who underwent high‐frequency bilateral stimulation of the STN and in whom we analysed the STN post‐mortem.3. Unilateral subthalamotomy improved akinesia in parkinsonian primates. However, both monkeys and rodents showed postural abnormalities. The patient who underwent bilateral high‐frequency stimulation showed improvement of akinesia and other disease symptoms and no postural abnormalities. Post‐mortem analysis did not demonstrate substantial damage of the STN as a result of the electrodes.4. Although unilateral subthalamotomy improves some aspects of parkinsonism, it causes postural abnormalities in animal models of Parkinson's disease. Because bilateral high‐frequency STN stimulation improves disease symptoms, is reversible and is not reported to induce postural side‐effects, it may be a better surgical therapy for Parkinson's disease than lesioning the STN.
Science and physicianly practice: Are they compatible?
Authors: Seale J Paul 
Published: November 2003

Summary1. Science, in the present paper, is defined as the systematic study of humans, based on deduction and inferences from reproducible observation and measurement. Physicianly practice is the art of healing through accurate diagnosis and treatment.2. The science that is conducted by clinical pharmacologists involves both clinical studies, which is working with patients or normal volunteers, and a variety of in vitro techniques.3. Studies of patients with exercise‐induced asthma (EIA) suggest that inhaled β‐adrenoceptor agonists may afford protection against EIA by inhibiting mast cell mediator release. In vitro experiments with human lung tissue demonstrate dose‐dependent inhibition of histamine and leukotriene release by fenoterol, a β‐adrenoceptor agonist.4. Studies in normal volunteers following the inhalation of corticosteroids (fluticasone and budesonide), which are used for the treatment of asthma, detected the presence of the administered drugs in the plasma. The potency ratio of fluticasone : budesonide for inhibition of the hypothalamic–pituitary–adrenal (HPA) axis in these normal volunteers was similar to the potency ratio determined in animal models of inflammation.5. Studies in vitro showed that fluticasone and budesonide have effects on alkaline phosphatase release from human osteoblasts, with a potency ratio of similar rank order to that observed in vivo on the HPA axis.6. These studies have shown that in vivo and in vitro techniques can be used in a complementary fashion to address questions of clinical relevance.
Mouse isolated perfused heart: Characteristics and cautions
Authors: Sutherland Fiona J , Shattock Michael J , Baker Kathryn E , Hearse David J 
Published: November 2003

Summary1. Owing to the considerable potential for manipulating the murine genome and, as a consequence, the increasing availability of genetically modified models of cardiovascular diseases, the mouse is fast becoming a cornerstone of animal research. However, progress in the use of various murine preparations is hampered by the lack of facilities and skills for the adequate physiological assessment of genetically modified mice.2. We have attempted to address this problem by refining and characterizing a mouse isolated heart preparation that was originally developed for use with larger hearts.3. We used the isolated buffer‐perfused Langendorff preparation (perfused at constant flow or constant pressure) to characterize: (i) the frequency–response characteristics; (ii) heart isolation conditions; (iii) perfusion chamber conditions; (iv) temperature–function relationships; (v) stability over extended periods of perfusion; (vi) perfusate calcium–function relationships; (vii) pressure–volume relationships; (viii) pressure–rate relationships; and (ix) flow–function relationships.
Activin and TR3 orphan receptor: Two ‘atheroprotective’ genes as evidenced in dedicated mouse models
Authors: Engelse Marten A , Arkenbout E Karin , Pannekoek Hans , De Vries Carlie JM 
Published: November 2003

Summary1. Atherosclerosis is a multifactorial, inflammatory disease of the arterial vessel wall that is promoted by various well‐defined risk factors. Although numerous genes, expressed in different vascular and inflammatory cells, have been implicated in this disease, it is widely appreciated that most of the genes and gene products vital for initiation and progression of atherosclerosis are unknown.2. We follow two strategies in an attempt to make up for the void of essential knowledge. First, we study candidate genes that have not been implied in human atherosclerosis before, notably the differentiation factor activin A.3. Second, we performed a genome‐wide search by differential display reverse transcription–polymerase chain reaction. This study indicated potential involvement of the TR3 orphan receptor transcription factor in smooth muscle cell (SMC) (patho)physiology.4. To reveal functional involvement of these proteins in SMC during atherosclerosis, we performed experiments with mouse models, adjusted either to the characteristics of a secreted protein or to that of an intracellular transcription factor.5. The secreted protein activin A was studied in mice infected systemically with recombinant adenoviral vehicles, resulting in predominant hepatic expression and subsequent high protein levels in the circulation.6. To study the role of TR3 in atherosclerosis, we generated transgenic mice in which promoter sequences were applied that direct expression of the transgenes to SMC of the arterial tree.7. Two approaches were taken to induce the formation of SMC‐rich lesions: (i) activation of femoral artery SMC by placement of a loosly fitting cuff; and (ii) ligation of the carotid artery.8. The aim of the present review is to illustrate the different approaches that can be taken to assess the potential relevance of genes in atherosclerosis in carefully selected mouse models.9. Based on the results described, we propose that both activin A and TR3 prevent excessive SMC proliferation.
A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function
Authors: Krishnan V.G. , Westhead D.R. 
Published: November 2003

Abstract
Motivation: The large volume of single nucleotide polymorphism data now available motivates the development of methods for distinguishing neutral changes from those which have real biological effects. Here, two different machine-learning methods, decision trees and support vector machines (SVMs), are applied for the first time to this problem. In common with most other methods, only non-synonymous changes in protein coding regions of the genome are considered.
Results: In detailed cross-validation analysis, both learning methods are shown to compete well with existing methods, and to out-perform them in some key tests. SVMs show better generalization performance, but decision trees have the advantage of generating interpretable rules with robust estimates of prediction confidence. It is shown that the inclusion of protein structure information produces more accurate methods, in agreement with other recent studies, and the effect of using predicted rather than actual structure is evaluated.
Availability: Software is available on request from the authors.
Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction
Authors: Doytchinova I.A. , Flower D.R. 
Published: November 2003

Abstract
Motivation: The immunogenicity of peptides depends on their ability to bind to MHC molecules. MHC binding affinity prediction methods can save significant amounts of experimental work. The class II MHC binding site is open at both ends, making epitope prediction difficult because of the multiple binding ability of long peptides.
Results: An iterative self-consistent partial least squares (PLS)-based additive method was applied to a set of 66 peptides no longer than 16 amino acids, binding to DRB1*0401. A regression equation containing the quantitative contributions of the amino acids at each of the nine positions was generated. Its predictability was tested using two external test sets which gave rpred = 0.593 and rpred = 0.655, respectively. Furthermore, it was benchmarked using 25 known T-cell epitopes restricted by DRB1*0401 and we compared our results with four other online predictive methods. The additive method showed the best result finding 24 of the 25 T-cell epitopes.
Availability: Peptides used in the study are available from http://www.jenner.ac.uk/JenPep. The PLS method is available commercially in the SYBYL molecular modelling software package. The final model for affinity prediction of peptides binding to DRB1*0401 molecule is available at http://www.jenner.ac.uk/MHCPred. Models developed for DRB1*0101 and DRB1*0701 also are available in MHCPred.
A Novel Neuroimmune Mechanism in Cannabinoid-mediated Attenuation of Nerve Growth Factor–induced Hyperalgesia
Authors: Farquhar-Smith W. Paul , Rice Andrew S. C. 
Published: November 2003

Background
Nerve growth factor (NGF) is central to processes involved in an inflammatory hyperalgesia. Administration of exogenous NGF induces a hyperalgesia that is dependent on local neutrophil influx. The effects of administration of the cannabinoid anandamide and the cannabimimetic palmitoylethanolamide on an NGF-induced hyperalgesia and neutrophil accumulation were examined in this study.

Methods
Baseline hind limb withdrawal latencies to a noxious heat stimulus were recorded before intraplantar administration of NGF (1 microg in 0.05 ml) to the hind paw of 75 male Wistar rats. Anandamide or palmitoylethanolamide (a substance that has cannabinoid-like actions but little affinity for cannabinoid receptors) at doses of 10 and 25 mg/kg were given (intraperitoneally) immediately after NGF. CB1 (SR141716A) and CB2 (SR144528) receptor antagonists were coadministered with the higher dose of cannabinoids. Withdrawal latencies were expressed as difference from baseline. Seventy rats received intraplantar NGF and intraperitoneal treatments. Neutrophil accumulation in the injected paw was assessed using a myeloperoxidase assay.

Results
Administration of NGF reduced latencies consistent with hyperalgesia. Anandamide and palmitoylethanolamide significantly reduced this hyperalgesia. The action of anandamide was CB1 receptor-mediated. SR144528 abrogated the action of palmitoylethanolamide. NGF also provoked neutrophil accumulation in the injected paw, denoted by an increase in myeloperoxidase. Palmitoylethanolamide significantly reduced neutrophil accumulation by an SR144528-sensitive action, whereas anandamide was without effect.

Conclusions
NGF induced a thermal hyperalgesia that was attenuated by anandamide and palmitoylethanolamide. Only palmitoylethanolamide reduced neutrophil influx. Thus, cannabinoids show a neuronal CB1 receptor-mediated antihyperalgesic action and a separate inhibition of a proinflammatory neuroimmune process. Such a mechanism suggests a therapeutic site of analgesic action separable from central side effects.
Social Struggles in Present Day Argentina
Authors: Carerra Nicolás Iñigo , Cotarelo María Celia 
Published: November 2003

Since the mid 1970s, Argentine society has gone through a period characterised as counterrevolutionary. The conservative social forces, led by the financial oligarchy, seized power and government by means of the coup d’état of 1976, and imposed an economic and social policy towards the working class, based on wage cuts and a lengthening of the working day. When the military governments were replaced by civilian ones, physical coercion was replaced by economic coercion, through market laws with unemployment and wage cuts reaching unprecedented levels. Although the popular forces were weakened by the unfavourable development of social struggles since the mid–1970s, during the 1990s government policies were confronted by the people through different forms of struggle.This article presents the results of research on the different forms of social struggle carried out by the working class and other popular classes since the end of the 1980s until today. It aims to conceptualise the forms of rebellion (foot riot, riot, strikes and roadblocks), to determine the different moments of social struggle and the likely trends of its development.
A QCM Study on Adsorption of Macrocyclic Sugar-Cluster to Variously-Functionalized Monolayers
Authors: Ariga Katsuhiko , Isoyama Kouta , Hayashida Osamu , Aoyama Yasuhiro , Okahata Yoshio 
Published: November 2003

Abstract
Adsorption of the aqueous sugar-cluster molecule 1 to variously-functionalized monolayer was evaluated using a quartz crystal microbalance (QCM). The molecule 1 favorably adsorbed to the anionic (acidic) and OH-condensed lipid monolayers.