bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular and cellular approaches for the detection of protein–protein interactions: latest techniques and current limitations
Authors: Lalonde Sylvie , Ehrhardt David W. , Loqué Dominique , Chen Jin , Rhee Seung Y. , Frommer Wolf B.
Published: February 2008

Homotypic and heterotypic protein interactions are crucial for all levels of cellular function, including architecture, regulation, metabolism, and signaling. Therefore, protein interaction maps represent essential components of post‐genomic toolkits needed for understanding biological processes at a systems level. Over the past decade, a wide variety of methods have been developed to detect, analyze, and quantify protein interactions, including surface plasmon resonance spectroscopy, NMR, yeast two‐hybrid screens, peptide tagging combined with mass spectrometry and fluorescence‐based technologies. Fluorescence techniques range from co‐localization of tags, which may be limited by the optical resolution of the microscope, to fluorescence resonance energy transfer‐based methods that have molecular resolution and can also report on the dynamics and localization of the interactions within a cell. Proteins interact via highly evolved complementary surfaces with affinities that can vary over many orders of magnitude. Some of the techniques described in this review, such as surface plasmon resonance, provide detailed information on physical properties of these interactions, while others, such as two‐hybrid techniques and mass spectrometry, are amenable to high‐throughput analysis using robotics. In addition to providing an overview of these methods, this review emphasizes techniques that can be applied to determine interactions involving membrane proteins, including the split ubiquitin system and fluorescence‐based technologies for characterizing hits obtained with high‐throughput approaches. Mass spectrometry‐based methods are covered by a review by Miernyk and Thelen (2008; this issue, pp. 597–609). In addition, we discuss the use of interaction data to construct interaction networks and as the basis for the exciting possibility of using to predict interaction surfaces.
Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus
Authors: Sanchez Diego H. , Lippold Felix , Redestig Henning , Hannah Matthew A. , Erban Alexander , Krämer Ute , Kopka Joachim , Udvardi Michael K.
Published: February 2008

The model legume Lotus japonicus was subjected to non‐lethal long‐term salinity and profiled at the ionomic, transcriptomic and metabolomic levels. Two experimental designs with various stress doses were tested: a gradual step acclimatization and an initial acclimatization approach. Ionomic profiling by inductively coupled plasma/atomic emission spectrometry (ICP‐AES) revealed salt stress‐induced reductions in potassium, phosphorus, sulphur, zinc and molybdenum. Microarray profiling using the Lotus Genechip® allowed the identification of 912 probesets that were differentially expressed under the acclimatization regimes. Gas chromatography/mass spectrometry‐based metabolite profiling identified 147 differentially accumulated soluble metabolites, indicating a change in metabolic phenotype upon salt acclimatization. Metabolic changes were characterized by a general increase in the steady‐state levels of many amino acids, sugars and polyols, with a concurrent decrease in most organic acids. Transcript and metabolite changes exhibited a stress dose‐dependent response within the range of NaCl concentrations used, although threshold and plateau behaviours were also observed. The combined observations suggest a successive and increasingly global requirement for the reprogramming of gene expression and metabolic pathways to maintain ionic and osmotic homeostasis. A simple qualitative model is proposed to explain the systems behaviour of plants during salt acclimatization.
FUSCA3 from barley unveils a common transcriptional regulation of seed‐specific genes between cereals and Arabidopsis
Authors: Moreno‐Risueno Miguel Ángel , González Noemi , Díaz Isabel , Parcy François , Carbonero Pilar , Vicente‐Carbajosa Jesús
Published: February 2008

Accumulation of storage compounds in the embryo and endosperm of developing seeds is a highly regulated process that allows seedling growth upon germination until photosynthetic capacity is acquired. A critical regulatory element in the promoters of seed storage protein (SSP) genes from dicotyledonous species is the RY box, a target of B3‐type transcription factors. However, the functionality of this motif in the transcriptional regulation of SSP genes from cereals has not been fully established. We report here the identification and molecular characterization of barley FUSCA3, a B3‐type transcription factor as yet uncharacterized in monocotyledonous plants. Our results show that both the barley and Arabidopsis FUS3 genes maintain a conserved functionality for the regulation of SSP genes and anthocyanin biosynthesis in these two distantly related phylogenetic groups. Complementation of the loss‐of‐function mutant fus3 in Arabidopsis by the barley HvFus3 gene resulted in restored transcription from the At2S3 gene promoter and normal accumulation of anthocyanins in the seed. In barley, HvFUS3 participates in transcriptional activation of the endosperm‐specific genes Hor2 and Itr1. HvFUS3, which specifically binds to RY boxes in EMSA experiments, trans‐activates Hor2 and Itr1 promoters containing intact RY boxes in transient expression assays in developing endosperms. Mutations in the RY boxes abolished the HvFUS3‐mediated trans‐activation. HvFus3 transcripts accumulate in the endosperm and in the embryo of developing seeds, peaking at mid maturation phase. Remarkably, HvFUS3 interacts with the Opaque2‐like bZIP factor BLZ2 in yeast, and this interaction is essential for full trans‐activation of the seed‐specific genes in planta.
The sucrose regulated transcription factor bZIP11 affects amino acid metabolism by regulating the expression of ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2
Authors: Hanson Johannes , Hanssen Micha , Wiese Anika , Hendriks Margriet M. W. B. , Smeekens Sjef
Published: February 2008

Translation of the transcription factor bZIP11 is repressed by sucrose in a process that involves a highly conserved peptide encoded by the 5′ leaders of bZIP11 and other plant basic region leucine zipper (bZip) genes. It is likely that a specific signaling pathway operating at physiological sucrose concentrations controls metabolism via a feedback mechanism. In this paper bZIP11 target processes are identified using transiently increased nuclear bZIP11 levels and genome‐wide expression analysis. bZIP11 affects the expression of hundreds of genes with proposed functions in biochemical pathways and signal transduction. The expression levels of approximately 80% of the genes tested are not affected by bZIP11 promoter‐mediated overexpression of bZIP11. This suggests that <20% of the identified genes appear to be physiologically relevant targets of bZIP11. ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2 are among the rapidly activated bZIP11 targets, whose induction is independent of protein translation. Transient expression experiments in Arabidopsis protoplasts show that the bZIP11‐dependent activation of the ASPARAGINE SYNTHETASE1 gene is dependent on a G‐box element present in the promoter. Increased bZIP11 expression leads to decreased proline and increased phenylalanine levels. A model is proposed in which sugar signals control amino acid levels via the bZIP11 transcription factor.
Quality control for plant metabolomics: reporting MSI‐compliant studies
Authors: Fiehn Oliver , Wohlgemuth Gert , Scholz Martin , Kind Tobias , Lee Do Yup , Lu Yun , Moon Stephanie , Nikolau Basil
Published: February 2008

The Metabolomics Standards Initiative (MSI) has recently released documents describing minimum parameters for reporting metabolomics experiments, in order to validate metabolomic studies and to facilitate data exchange. The reporting parameters encompassed by MSI include the biological study design, sample preparation, data acquisition, data processing, data analysis and interpretation relative to the biological hypotheses being evaluated. Herein we exemplify how such metadata can be reported by using a small case study – the metabolite profiling by GC‐TOF mass spectrometry of Arabidopsis thaliana leaves from a knockout allele of the gene At1g08510 in the Wassilewskija ecotype. Pitfalls in quality control are highlighted that can invalidate results even if MSI reporting standards are fulfilled, including reliable compound identification and integration of unknown metabolites. Standardized data processing methods are proposed for consistent data storage and dissemination via databases.
Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza
Authors: Roulin Anne , Piegu Benoît , Wing Rod A. , Panaud Olivier
Published: February 2008

Horizontal gene transfer, defined as the transmission of genetic material between reproductively isolated species, has been considered for a long time to be a rare phenomenon. Most well‐documented cases of horizontal gene transfer have been described in prokaryotes or in animals and they often involve transposable elements. The most abundant class of transposable elements in plant genomes are the long terminal repeat (LTR) retrotransposons. Because of their propensity to increase their copy number while active, LTR retrotransposons can have a significant impact on genomics changes during evolution. In a previous study, we showed that in the wild rice species Oryza australiensis, 60% of the genome is composed of only three families of LTR retrotransposons named RIRE1, Wallabi and Kangourou. In the present study, using both in silico and experimental approaches, we show that one of these three families, RIRE1, has been transferred horizontally between O. australiensis and seven other reproductively isolated Oryza species. This constitutes a new case of horizontal transfer in plants.
GASSHO1 and GASSHO2 encoding a putative leucine‐rich repeat transmembrane‐type receptor kinase are essential for the normal development of the epidermal surface in Arabidopsis embryos
Authors: Tsuwamoto Ryo , Fukuoka Hiroyuki , Takahata Yoshihito
Published: February 2008

Receptor‐like kinases (RLKs) containing leucine‐rich repeats (LRRs) act as both signal receptor and signal transducer in ligand‐mediated communication between cells. It is believed that many LRR‐RLKs are present in the Arabidopsis genome, but the functions of most are unknown. We recently identified Bnms4D‐82, an expressed sequence tag (EST) in Brassica napus that encodes an LRR‐RLK and is expressed at an early stage of its microspore embryogenesis. To elucidate the function of this gene we used GASSHO1 (GSO1) and GSO2, two Arabidopsis genes with a high degree of homology with Bnms4D‐82. The products of transcripts of GSO1 and GSO2 accumulate in parts of the embryo and in seedlings, but not in true leaves. Plants that lacked both GSO1 and GSO2 exhibited pleiotropy, including abnormal bending of embryos, ectopic adhesion between cotyledons, a highly permeable epidermal structure, and an abnormal pattern of distribution of stomata on cotyledons in embryos and seedlings. However, plants homozygous for either gso1‐1 or gso2‐1 had no visible abnormality. These results suggest that GASSHO genes are essential for the formation of a normal epidermal surface during embryogenesis.
CLINICAL STUDY: Adrenocorticotropic hormone and cortisol plasma levels directly correlate with childhood neglect and depression measures in addicted patients
Authors: Gerra Gilberto , Leonardi Claudio , Cortese Elena , Zaimovic Amir , Dell'Agnello Grazia , Manfredini Matteo , Somaini Lorenzo , Petracca Francesca , Caretti Vincenzo , Baroni Cristina , Donnini Claudio
Published: February 2008

Hypothalamic–pituitary–adrenal (HPA) axis dysfunction has been reported to be involved in vulnerability to alcohol and drug dependence in humans, possibly underlying both addictive behaviour and depression susceptibility. The aim of the present study was to investigate the possible interactions between childhood adverse experiences, depressive symptoms and HPA axis function in addicted patients, in comparison with healthy control. Eighty‐two abstinent heroin or cocaine dependent patients and 44 normal controls, matched for age and sex, completed the symptoms Check List‐90 (SCL‐90), measuring depressive symptoms, and the Childhood Experience of Care and Abuse Questionnaire. Blood samples were collected to determine adrenocorticotropic hormone (ACTH) and cortisol basal plasma levels at 8:00 and 8:30 a.m. Addicted individuals showed significantly higher neglect and depression scores and ACTH–cortisol plasma levels respect to control subjects. Depression scores at SCL‐90 in addicted patients positively correlated with plasma ACTH and cortisol values. In turn, plasma ACTH levels were directly associated with childhood neglect measures, reaching statistical significance with ‘mother‐neglect’ scores. Plasma cortisol levels were related to ‘father antipathy’ among cocaine addicts. These findings suggest the possibility that childhood experience of neglect and poor parent–child attachment may have a persistent effect on HPA axis function as an adult, partially contributing, together with genetic factors and other environmental conditions, to both depressive traits and substance abuse neurobiological vulnerability.
PRECLINICAL STUDY: Chronic deep brain stimulation in the rat nucleus accumbens and its effect on morphine reinforcement
Authors: Liu Hong‐Yu , Jin Jie , Tang Jing‐Shi , Sun Wei‐Xin , Jia Hong , Yang Xin‐Ping , Cui Jian‐Mei , Wang Chen‐Guang
Published: February 2008

In order to explore a novel method for the treatment of drug abuse, we evaluated the effect of chronic deep brain stimulation (DBS) of the rat nucleus accumbens (NAc) on morphine reinforcement, using a DBS apparatus and an implant method we developed. Thirty‐two adult rats weighing 240–260 g were divided into three groups, which included a DBS group (n = 10, administration of surgery, morphine and DBS), a sham DBS group (n = 12, administration of surgery and morphine) and a control group (n = 10, administration of physiological saline). The DBS electrode was stereotaxically implanted into the core of unilateral NAc and connected to an implantable pulse generator. Then, they were fixed to the rat skull. One week later, the rats in each group were intraperitoneally injected with morphine at an increasing dose (10–60 mg/kg) once daily. The rats in the DBS group were administered a 130‐Hz high‐frequency stimulation (HFS) once daily. A 900‐second conditioned place preference (CPP) paradigm was used for determining the effect of electrical stimulation on morphine reinforcement in rats. The data showed that 7–10 days later, the preference score of the DBS group was significantly lower than that of the sham DBS group. The results suggest that chronic HFS of the rat NAc can block CPP induced by morphine and attenuate morphine reinforcement.
CLINICAL STUDY: P3 components of the event‐related potential and marijuana dependence in Southwest California Indians
Authors: Ehlers Cindy L. , Gilder David A. , Phillips Evelyn
Published: February 2008

Native Americans have some of the highest rates of marijuana use and abuse, yet neurobiological measures associated with addiction to marijuana in this population remain unknown. The present investigation evaluated associations between the P350 and P450 components of the event‐related potential (ERP) elicited by affective stimuli, and marijuana dependence in a population of Southwest California (SWC) Indian adults. Three hundred and seventeen participants with a mean age of 30 years who were free of major Axis I and psychiatric diagnoses and antisocial personality disorder were categorized as: (1) no marijuana use disorders or other drug dependence diagnoses; (2) marijuana dependence and no other drug dependence diagnoses; and (3) marijuana dependence and other drug dependence diagnoses. ERPs were collected using a facial discrimination task that generated a late positive component with two peaks at approximately P350 and P450 milliseconds. Multivariate analyses of variance was used to detect associations between the two component peaks and the three participant groups taking into consideration age, gender and the presence of a lifetime diagnosis of alcohol dependence. Increases in the latency of both the P350 and P450 component peaks were found to be associated with the diagnosis of marijuana dependence and marijuana dependence co‐morbid with other drug dependence. Women appeared to be more impacted than men are. A diagnosis of marijuana dependence was not associated with any changes in late component amplitudes. Taken together these studies suggest that marijuana dependence may be associated with delays in the evaluation and identification of emotional stimuli in SWC Indians.
PRECLINICAL STUDY: A microdialysis study of extracellular levels of acamprosate and naltrexone in the rat brain following acute and repeated administration
Authors: Burattini Costanza , Mcgeehan Andrew J. , Griffin William C. , Gass Justin T. , Kinder Jennifer R. , Janak Patricia H. , Olive M. Foster
Published: February 2008

Acamprosate and naltrexone are widely used in the treatment of alcoholism. However, numerous studies in rodents have shown differential effects of these compounds on alcohol consumption and/or relapse‐like behavior following acute versus repeated administration. In order to determine if these differential behavioral effects could be attributable to changes in extracellular levels of these compounds, we used in vivo microdialysis to monitor extracellular levels of acamprosate and naltrexone in the rat medial prefrontal cortex following acute and repeated intraperitoneal administration. For acute treatment, animals received a single administration of acamprosate (100 or 300 mg/kg) or naltrexone (1 or 3 mg/kg). For repeated treatment, animals received once daily treatment with saline, acamprosate (300 mg/kg) or naltrexone (3 mg/kg) for 10 days before a subsequent challenge with the compound according to their respective pretreatment group. Dialysate levels of acamprosate and naltrexone were analyzed by liquid chromatography–tandem mass spectrometry and high performance liquid chromatography, respectively. Following acute administration, peak dialysate concentrations of each compound were dose‐dependent, observed within 1 hour of administration, and were found to be in the low micromolar range for acamprosate and in the low to mid‐nanomolar range for naltrexone. Pretreatment with acamprosate, but not naltrexone, for 10 days resulted in higher dialysate concentrations of the compound relative to saline‐pretreated controls. Thus, repeated administration of acamprosate, but not naltrexone, results in augmented extracellular levels of the compound in the brain relative to saline‐pretreated controls, which may explain the need for repeated administration of acamprosate in order to observe effects on alcohol consumption and/or relapse.
Original article: The economic costs of severe anaphylaxis in France: an inquiry carried out by the Allergy Vigilance Network
Authors: Flabbee J. , Petit N. , Jay N. , Guénard L. , Codreanu F. , Mazeyrat R. , Kanny G. , Moneret‐Vautrin D. A.
Published: February 2008

Background:  The prevalence of severe anaphylaxis, between 1 and 3 per 10 000, has increased sharply over recent years, with a rate of lethality of 1%. The economic burden is unknown.

Objective:  The aim of this study was to estimate the economic costs of anaphylaxis, including direct costs of treatment, hospitalization, preventive and long‐care measures, and the indirect cost: absenteeism.

Methods:  Analysis of 402 patients of anaphylaxis declared by 384 allergists was reported to the Allergy Vigilance Network. The global cost was estimated from the national data of hospital admissions: ICD‐10 coding available for 2003, 2004 and 2005.

Results:  Three work/classroom days were lost per patient. Diagnosis required oral challenge with hospitalization in 18% of cases. The estimated mean total cost was 1895€ for food‐ and drug‐related anaphylaxis (5610€ for the most severe), and 4053€ for Hymenoptera anaphylaxis. National statistics recorded 2575 patients in 2005; 22% more than in 2003. The estimated annual cost was 4 789 500 €. The possible reasons for this being an under‐estimate include: data coming only from hospitalized patients, poor identification by medical teams unfamiliar with ICD‐10 codes, peri‐operative anaphylaxis being insufficiently declared, rush‐immunotherapy and maintenance treatments for Hymenoptera anaphylaxis. Similarly, the extra cost of cow milk substitutes, as well as insurance costs where deaths are followed by litigation were not taken into account.

Conclusions:  The mean cost of anaphylaxis was 1895–5610€ in nonfatal patients. The prevalence was under‐estimated because of many biases, leading to under‐estimation of the national cost. Further studies would be necessary to evaluate the value of preventive strategies.
Short communication: Analysis of CD4+ T‐cell gene expression in allergic subjects using two different microarray platforms
Authors: Hansel N. N. , Cheadle C. , Diette G. B. , Wright J. , Thompson K. M. , Barnes K. C. , Georas S. N.
Published: February 2008

Background:  Allergic diseases are thought to involve dysregulated activation of T cells including CD4+ lymphocytes. T‐cell activation results in changes in gene expression, but the optimal method to study gene expression profiles in T cells, and how this changes over time, are not known.

Methods:  Circulating CD4+ T cells were obtained from subjects with atopic asthma, nonatopic asthma or nonallergic controls, and total mRNA was rapidly isolated. Atopy was defined as positive skin prick test to one of nine allergens. Gene expression was analyzed using hybridization and Affymetrix® oligonucleotide arrays (Hu133A and Hu133B chips, n = 84), or by reverse transcription‐polymerase chain reaction (RT‐PCR) with a pathway‐targeted array (Human Th1–Th2–Th3 RT2 ProfilerTM PCR Array, Superarray, n = 16).

Results:  Using Affymetrix arrays, it was difficult to discern a dominant allergy‐associated profile because of heterogeneity in gene expression profiles. In contrast, a Th2‐like signature was evident using RT‐PCR arrays with increased expression of expected genes (e.g. IL‐4, 5, 9, and 13, all P < 0.05) as well as unexpected gene transcripts (e.g. osteopontin). Gene expression profiles were relatively stable over time in circulating CD4+ T cells from two subjects using both platforms.

Conclusions:  Unstimulated CD4+ T cells isolated from allergic subjects express a characteristic profile of genes when analyzed using RT‐PCR based microarrays.
Original article: Effect of short‐term exposure to air pollution and pollen on medical emergency calls: a case‐crossover study in Spain
Authors: Carracedo‐Martinez E. , Sanchez C. , Taracido M. , Saez M. , Jato V. , Figueiras A.
Published: February 2008

Background:  A symmetric case‐crossover design was used to analyse the short‐term relationship between air pollution, pollen and emergency calls to medical services.

Methods:  This study covered patients who made medical emergency calls in the City of Vigo (Spain) during the period 1996–1999. Morbidity data were obtained from the records of the 061 Medical Emergency Control Center, in its capacity as the body officially coordinating all medical emergencies by telephone. Air pollution data were furnished by the Vigo Municipal Air Pollution Surveillance Grid. Pollen levels were provided by the staff of the Spanish Aerobiology Network in Vigo.

Results:  A rise of 10μg/m3 in ambient particulate levels led to the risk of medical emergency calls requesting attention increasing by: (i) 1.97% [95% confidence interval (95% CI): 1.83–2.11%] for circulatory causes on the same day; (ii) 1.95% (95% CI: 1.76–2.14%) for respiratory causes at 2 days and (iii) 1.34% (95% CI: 1.23–1.45%) for combined circulatory and respiratory causes on the same day. A number of pollens displayed a statistically significant relationship with emergency calls. No interaction was in evidence between pollens and air pollutants.

Conclusions:  While elevations in particulate air pollution increase medical emergency calls because of cardiac or respiratory causes or both combined, elevations in pollen levels increase medical emergency calls because of respiratory causes.
Original article: Assessing skin prick tests reliability in ECRHS‐I
Authors: Bousquet P.‐J. , Chatzi L. , Jarvis D. , Burney P.
Published: February 2008

Introduction:  Atopy, the clinical definition of an immunoglobulin E (IgE) high‐responder, can be documented either by the detection of IgE antibodies in serum or by a positive skin prick test. Epidemiological studies use different reaction sizes to define a skin test reaction as positive or negative. The aim of the study was to identify the best cut‐off level for skin prick tests.

Method:  Using the data collected during the European Community Respiratory Health Survey (ECHRS I) the association of serum allergen‐specific IgE and skin prick tests [Dermatophagoides pteronyssinus (Der p), cat, timothy grass and Cladosporium] were assessed.

Results:  The proportion of the 11 355 subjects (49.9% men), with positive skin tests ranged from 10.4% (cut‐off >5 mm) to 20.9% (cut‐off >0 mm) for Der p, 3.5–10.2% for cat, 9.3–16.6% for timothy grass and 0.2 and 2.3% for Cladosporium. For identifying subjects with detectable specific IgE (>0.35 kU/l) the most appropriate cut‐off appeared to be over 0 mm for Der p, cat and timothy grass (Youden Index over 0.81). However, the relationship between serum IgE and skin prick test for Cladosporium was weak (Youden index under 0.56).

Conclusion:  In epidemiological studies, a single method may be chosen to assess allergenic sensitivity. A cut‐off level of over 0 mm for skin prick tests was best at identifying those with allergen‐specific IgE.
Original article: Infections presenting for clinical care in early life and later risk of hay fever in two UK birth cohorts
Authors: Bremner S. A. , Carey I. M. , DeWilde S. , Richards N. , Maier W. C. , Hilton S. R. , Strachan D. P. , Cook D. G.
Published: February 2008

Background:  The ‘hygiene hypothesis’ proposes that infections in infancy protect against hay fever (HF). We investigated infections during infancy in relation to HF, including rarer ones not previously researched in this context, while examining the role of potential confounding variables.

Methods:  From birth cohorts derived within the General Practice Research Database (GPRD) and Doctors Independent Network (DIN) database of computerized patient records from UK general practice, we selected 3549 case–control pairs, matched for practice, age, sex and control follow‐up to case diagnosis. Conditional logistic regressions were fitted for each of 30 infections; behavioural problems (BP) acted as a control condition unrelated to HF. Odds ratios (OR), adjusted for consultation frequency were pooled across the databases using fixed effect models. We also adjusted for sibship size in GPRD and a socioeconomic marker in DIN.

Results:  Upper respiratory tract infections, diarrhoea and vomiting and acute otitis media in infancy were each related with a moderately increased risk of HF in both databases, as were BP. These associations were lost on adjustment for consultation frequency. Only bronchiolitis was significantly associated with a reduced pooled risk of HF after adjustment for consultations (OR = 0.8). Adjustment for sibship size in GPRD and a socioeconomic marker in DIN had little impact on the OR.

Conclusions:  Of 30 infectious illnesses investigated, none had strong or consistent associations with HF after adjustment for consultation frequency. Except for bronchiolitis, possibly a chance finding, none of the clinically apparent infections considered appear to have an important role in allergy prevention.
EU Forum: The CREATE Project: development of certified reference materials for allergenic products and validation of methods for their quantification
Authors: Van Ree R. , Chapman M. D. , Ferreira F. , Vieths S. , Bryan D. , Cromwell O. , Villalba M. , Durham S. R. , Becker W. M. , Aalbers M. , André C. , Barber D. , Bahima A. Cistero , Custovic A. , Didierlaurent A. , Dolman C. , Dorpema J. W. , Felice G. Di , Eberhardt F. , Caldas E. Fernandez , Rivas M. Fernandez , Fiebig H. , Focke M. , Fötisch K. , Gadermaier G. , Das R. G. , Mancebo E. Gonzalez , Himly M. , Kinaciyan T. , Knulst A. C. , Kroon A. M. , Lepp U. , Marco F. M. , Mari A. , Moingeon P. , Monsalve R. , Neubauer A. , Notten S. , Ooievaar‐de Heer P. , Pauli G. , Pini C. , Purohit A. , Quiralte J. , Rak S. , Raulf‐Heimsoth M. , Moncin M. M. San Miguel , Simpson B. , Tsay A. , Vailes L. , Wallner M. , Weber B.
Published: February 2008

Allergen extracts have been used for diagnosis and treatment of allergy for around 100 years. During the second half of 20th century, the notion increasingly gained foothold that accurate standardization of such extracts is of great importance for improvement of their quality. As a consequence, manufacturers have implemented extensive protocols for standardization and quality control. These protocols have overall IgE‐binding potencies as their focus. Unfortunately, each company is using their own in‐house reference materials and their own unique units to express potencies. This does not facilitate comparison of different products. During the last decades, most major allergens of relevant allergen sources have been identified and it has been established that effective immunotherapy requires certain minimum quantities of these allergens to be present in the administered maintenance dose. Therefore, the idea developed to introduce major allergens measurements into standardization protocols. Such protocols based on mass units of major allergen, quantify the active ingredients of the treatment and will at the same time allow comparison of competitor products. In 2001, an EU funded project, the CREATE project, was started to support introduction of major allergen based standardization. The aim of the project was to evaluate the use of recombinant allergens as reference materials and of ELISA assays for major allergen measurements. This paper gives an overview of the achievements of the CREATE project.
DNA typing by microbead arrays and PCR‐SSP: apparent false‐negative or ‐positive hybridization or amplification signals disclose new HLA‐B and ‐DRB1 alleles
Authors: Rahal M. , Kervaire B. , Villard J. , Tiercy J.‐M.
Published: February 2008

Human leukocyte antigen (HLA) typing by polymerase chain reaction–sequence‐specific oligonucleotide (PCR‐SSO) hybridization on solid phase (microbead assay) or polymerase chain reaction‐sequence‐specific primers (PCR‐SSP) requires interpretation softwares to detect all possible allele combinations. These programs propose allele calls by taking into account false‐positive or false‐negative signal(s). The laboratory has the option to validate typing results in the presence of strongly cross‐reacting or apparent false‐negative signals. Alternatively, these seemingly aberrant signals may disclose novel variants. We report here four new HLA‐B (B*5620 and B*5716) and HLA‐DRB1 alleles (DRB1*110107 and DRB1*1474) that were detected by apparent false‐negative or ‐positive hybridization or amplification patterns, and ultimately resolved by sequencing. To avoid allele misassignments, a comprehensive evaluation of acquired data as documented in a quality assurance system is therefore required to confirm unambiguous typing interpretation.
The functional R620W variant of the PTPN22 gene is associated with celiac disease
Authors: Santin I. , Castellanos‐Rubio A. , Aransay A. M. , Castaño L. , Vitoria J. C. , Bilbao J. R.
Published: February 2008

The functional (R620W) variant of human PTPN22 (protein tyrosine phosphatase non‐receptor 22) gene has been implicated in the risk to several autoimmune disorders, including type 1 diabetes, Graves’ disease, rheumatoid arthritis and systemic lupus erythematosus. In an association study of this single nucleotide polymorphism with celiac disease (CD), comparison of 262 young diagnosis patients and 214 adult controls from Spain showed a higher frequency of the minor allele in the CD group (9.7% vs 5.6% in controls; P = 0.018), suggestive of an increased genetic risk to the disease (odds ratio = 1.82; 95% confidence interval 1.1–3.0). These results support the role of PTPN22 as a general autoimmunity locus involved in tolerance induction in the thymus.
Modifying effect of HLA haplotypes located trans to DQB1*02‐DRB1*03 in celiac patients of Southern Europe
Authors: Hernández‐Charro B. , Donat E. , Miner I. , Aranburu E. , Sánchez‐Valverde F. , Ramos‐Arroyo M. A
Published: February 2008

The DQ2 heterodimer, encoded by the human leukocyte antigen (HLA)‐DQA1*05‐DQB1*02 alleles, is the major genetic susceptibility factor for celiac disease (CD). However, the risk associated to HLA alleles varies among populations. While DRB1*03 is almost the only CD susceptibility allele in Northern Europe with a homozygote frequency of around 30%, CD in south European countries is also associated with the DRB1*07, and DRB1*03 homozygotes patients are rare. Some authors have suggested that DQB1*02‐DRB1*03/DQB1*02‐DRB1*03 and DQB1*02‐DRB1*03/DQB1*02‐DRB1*07 may confer different risk susceptibility to CD. This hypothesis, however, has not been demonstrated in a recent family‐based study carried out in Finland, suggesting that the proposed differences in risk may be secondary to stratification burdens of case–control studies. To assess this issue, we have investigated the effect of different haplotypes carried trans to DQB1*02‐DRB1*03 as additional factors for CD in Spain, using two statistical approaches, a case–control study and a family‐based study. We found that DQB1*02‐DRB1*03/DQB1*02‐DRB1*03 and DQB1*02‐DRB1*03/DQB1*02‐DRB1*07 were the only combinations that showed a strong and independent association to CD. We did not observe any difference in susceptibility risk conferred by DQB1*02‐DRB1*03 and DQB1*02‐DRB1*07 when carried trans to DQB1*02‐DRB1*03, suggesting that variation in HLA haplotype frequencies among populations may not represent real differences in risk to CD development. We also confirmed a gene dosage effect of the DQB1*02‐DRB1*03 haplotype estimating that DQB1*02 homozygotes are at fivefold increased risk for CD compared with DQB1*02 heterozygotes. This risk is conferred by the second copy of the DQB1*02 allele and it seems to be independent of the DQA1.
Neutrophil but not eosinophil inflammation is related to the severity of a first acute epidemic bronchiolitis in young infants
Authors: Marguet Christophe , Bocquel Nathalie , Benichou Jacques , Basuyau Jean Pierre , Hellot Marie France , Couderc Laure , Mallet Eric , Macé Bertrand
Published: February 2008

Acute bronchiolitis is the main cause of emergency visits and hospitalizations in infants. Recent data suggest that neutrophil‐ and eosinophil‐mediated inflammations were part of bronchiolitis pathophysiology. Apart from the defined risk factors, few was known on the underlying pathophysiology, which might point out the differences observed in the severity of the disease. The aim of this study was to assess whether the clinical severity of acute epidemic bronchiolitis in young infants might be related to a specific underlying inflammatory process. Total and differential cell counts, IL‐8, eotaxin, eosinophil cationic protein (ECP) and albumin levels were assessed at the time of admission in bronchial secretions from 37 infants (median age 17 wk) with acute bronchiolitis. Outcome severity variables were: hypoxemia, Silverman score, tachypnea, feeding alteration, and duration of hospitalization. Neutrophils predominated, and eosinophils were present in 54% of the infants. IL‐8 levels strongly correlated with ECP and albumin levels. Albumin levels were correlated with ECP and eotaxin levels. IL‐8 levels were higher in infants with hypoxemia and inversely related with SaO2 levels. IL‐8 and albumin levels significantly rose with respiratory rate, and Silverman score. IL‐8, albumin and ECP levels were significantly higher in infants hospitalized ≥7 days. Furthermore, IL‐8 levels were correlated with the duration of hospitalization. Neither cell counts nor eotaxin levels were related to the severity criteria studied. This study suggests that IL‐8‐associated airway inflammation significantly contributed to the severity of acute epidemic bronchiolitis.
Ribavirin for respiratory syncytial virus bronchiolitis reduced the risk of asthma and allergen sensitization
Authors: Chen Chien‐Han , Lin Yu‐Tsan , Yang Yao‐Hsu , Wang Li‐Chieh , Lee Jyh‐Hong , Kao Chuan‐Liang , Chiang Bor‐Luen
Published: February 2008

Respiratory syncytial virus (RSV) bronchiolitis in early life is a risk factor for later development of asthma and atopy. Ribavirin is the only effective drug currently available against acute RSV bronchiolitis. However, the long‐term effects of ribavirin remain unclear. We investigated a cohort of children hospitalized with RSV bronchiolitis from when they were under 2 yr old until they reached a mean age of 6.2 yr. In total, we enrolled 175 children in this study. Both the group treated with ribavirin and the group not treated with ribavirin included high‐risk young children with congenital heart disease or chronic lung disease. Their respective age‐matched controls, that we labeled groups A and B, both without ribavirin treatment, consisted of previously healthy subjects. Wheezing was either verified by physicians or estimated by a questionnaire. Allergen sensitization was judged by serum allergen‐specific IgE levels. The cumulative incidence of physician‐diagnosed asthma or recurrent wheezing in the ribavirin group (15%) was significantly lower than its incidence in the non‐ribavirin‐treated group (34%, p = 0.049), and in the control A group (43%, p = 0.005). Allergen sensitization was also least frequent in the ribavirin group. Ribavirin therapy was an independent factor in reducing the risk of developing asthma, asthma/recurrent wheezing, and sensitization to D. pteronyssinus/D. farinae. The long‐term value of ribavirin for acute RSV bronchiolitis and its underlying mechanisms deserves further research.
Nutritional problems related to food allergy in childhood
Authors: Noimark Lee , Cox Helen E.
Published: February 2008

Food allergy is becoming an increasing problem worldwide with an estimated 6–8% of children affected at some point in their childhood. The perceived prevalence of food allergy is even higher with an estimated 20% of children adhering to some form of elimination diet. Against this background, accurate diagnosis is essential to prevent the imposition of unnecessarily restrictive diets on young children. Raising clinical awareness amongst health professionals as to the clinical characteristics, epidemiology, investigation, and management of food allergic disorders is key to tackling this growing problem. In this article, three separate cases of children with poor nutrition and secondary morbidity are presented, highlighting the varying scenarios in which these conditions can be encountered. In the first child, the features clinically displayed were hypocalcemic seizures and rickets due to prolonged breast feeding, poor weaning, and inadequate dietary supplementation. The second case reveals the dangers of complementary diagnostic allergy testing leading to poor nutrition as a consequence of an unsupervised elimination diet. The last report describes a child with multiple food allergies, failure to thrive, and protein losing enteropathy to highlight the diversity of nutritional problems faced by allergists and to underline the importance of specialist dietetic input in the management of a child with food allergy.
Bronchiolitis obliterans organizing pneumonia associated with Pneumocystis jiroveci infection in orthotopic liver transplantation
Authors: Almaslmani M. , Derbala M.F. , Albozom I. , Khattab M. , Chacko K. , Alani A.
Published: February 2008

Abstract: We report a patient who presented 6 months after orthotopic liver transplantation (OLT) with fever, dyspnea, and pulmonary infiltrates with biopsy‐confirmed Pneumocystis jiroveci infection associated with a process of bronchiolitis obliterans organizing pneumonia (BOOP). We present this second case of BOOP associated with P. carinii pneumonia after OLT to highlight the risk of such disease combination in all transplant patients as well as discuss the protective effect of post‐transplant prednisolone with trimethoprim‐sulfamethoxazole prophylaxis and the possible duration of prophylaxis.
Effects of Salt Stress on Some Physiological and Photosynthetic Parameters at Three Different Temperatures in Six Soya Bean (Glycine max L. Merr.) Cultivars
Authors: Çiçek N. , Çakırlar H.
Published: February 2008

The effect of NaCl (−0.1, −0.4 and −0.7 MPa) on some physiological parameters in six 23‐day‐old soya bean cultivars (Glycine max L. Merr. namely A 3935, CX‐415, Mitchell, Nazlıcan, SA 88 and Türksoy) at 25, 30 and 35 °C was investigated. Salt stress treatments caused a decline in the K+/Na+ ratio, plant height, fresh and dry biomass of the shoot and an increase in the relative leakage ratio and the contents of proline and Na+ at all temperatures. Effects of salt stress and temperature on Chl content, Chl a/b ratio (antenna size) and qN (heat dissipation in the antenna) varied greatly between cultivars and treatments; however, in all cases approximately the same qP value was observed. It indicates that the plants were able to maintain the balance between excitation pressure and electron transport activity. Pigment content and the quantum efficiency of photosystem II exhibited significant differences that depended on the cultivar, the salt concentration and temperature. The cultivars were relatively insensitive to salt stress at 30 °C however they were very sensitive both at 25 and 35 °C. Of the cultivars tested CX‐415 and SA 88 were the best performers at 25 °C compared with SA 88 and Türksoy at 35 °C.
Analysis of Water Supply of Plants Under Saline Soil Conditions and Conclusions for Research on Crop Salt Tolerance
Authors: Schleiff U.
Published: February 2008

Abstract In the dry areas of the world there is an increasing pressure to apply low quality brackish waters for plant irrigation (agriculture, horticulture, landscape greening). Consequently there is a demand to improve salt tolerance of conventional crops and to develop adequate irrigation techniques too. The efforts in the past decades to approach the understanding of salt stress mechanism by focusing on biochemical and physiological research were disappointing with respect to progress for crop growth and yields under saline soil conditions. However, it is generally agreed by all disciplines involved in research for crop salt tolerance that under saline soils conditions the reduced water supply of crops is the most critical growth factor. The paper presents some model calculations and field investigations that demonstrate the effect of root water uptake on the salinity of the root surrounding soil fraction (rhizospheric soil). It is shown that root hair length and rhizospheric soil volumes are factors most relevant for understanding crop salt tolerance, when growing in soils. It is postulated that short root hairs contribute to a lower salt tolerance (onions), whereas long root hairs enhance water uptake from saline soils and crop salt tolerance (rape). As interactions between roots and soil contribute to the salt tolerance of crops under field conditions, it is doubtful that selection for salt tolerant varieties and breeding for salt tolerance under conditions of water and flow culture experiments is very efficient. Breeding for more salt‐tolerant crops and brackish irrigation techniques should consider root morphology and soil/root contact zone.
Interveinal Yellowing Caused by Tomato infectious chlorosis virus in Lettuce and Escarole in Southern Italy
Authors: Parrella G.
Published: February 2008

In 2005 and 2006, a severe disease of lettuce and escarole, characterized by interveinal yellowing of the leaves, was observed in the Calabria region (Southern Italy). Samples collected were positive in RT‐PCR assay when specific primers for Crinivirus were used. The identity of the virus was determined by using Tomato infectious chlorosis virus (TICV)‐specific primers and probe. An amplicon of the same size (501 bp) as that from TICV‐infected tomato controls, corresponding to the partial Hsp70 viral gene, was obtained from 36 of 40 lettuce samples and from 19 of 24 escarole samples tested in 2005. The sequences obtained had 99–100% nucleotide sequence identity with other TICV sequences. In an extensive survey carried out in 2006 with TICV‐specific probe, 92% of symptomatic lettuce and 89% of escarole samples were infected with TICV. Adults of Trialeurodes vaporariorum, harvested from symptomatic lettuce and escarole plants, transmitted the virus to healthy plants of the same species. This is the first evidence of a disease caused by TICV in lettuce in Italy and the first record of TICV infection in escarole.
Successful treatment of disseminated Geotrichum capitatum infection with a combination of caspofungin and voriconazole in an immunocompromised patient
Authors: Etienne A. , Datry A. , Gaspar N. , Morel V. , Delabesse E. , Lmimouni B. , Vernant J. P. , Dhédin N.
Published: February 2008

Disseminated Geotrichum capitatum infection is uncommon, and has been reported exclusively in immunocompromised patients. The prognosis is poor with a mortality rate of approximately 50–75%. We report a case of disseminated G. capitatum infection in a severely neutropenic patient who was receiving chemotherapy for acute myeloblastic leukaemia. G. capitatum was isolated from blood cultures, skin lesions, bronchoalveolar lavage fluid, throat swabs and stools. The infection was successfully cured with a combination of voriconazole and caspofungin.
Antimicrobial activity of a protein purified from the latex of Hevea brasiliensis on oral microorganisms
Authors: Kanokwiroon Kanyanatt , Teanpaisan Rawee , Wititsuwannakul Dhirayos , Hooper Alan B. , Wititsuwannakul Rapepun
Published: February 2008

This study aimed at screen for antimicrobial activity present in the non‐rubber constituents of rubber latex of Hevea brasiliensis against various microbial strains. An antimicrobial protein, hevein was extracted from the bottom fraction after centrifugation and purified by acetone fractionation and anion exchange chromatography on a DEAE‐Sepharose Fast Flow column. This procedure was more efficient and rapid than the previously described procedures. The antimicrobial activity was investigated and revealed that hevein, a small (4.7 kDa) cysteine‐rich protein, had strong antimicrobial activity, especially against Candida spp. including Candida albicans, Candida tropicalis and Candida krusei. The MIC80 value for hevein was as low as 12 μg ml−1 with C. tropicalis ATCC 750. Higher MIC80 values were obtained for C. albicans ATCC 10231 (95 μg ml−1) and C. krusei ATCC 6258 (190 μg ml−1). To confirm the antifungal activity, hevein also inhibited the growth of those fungi in a disk diffusion assay and its inhibition was enhanced when a Hevea latex protease inhibitor was also included. Hevein at a concentration of 30 μg ml−1 also caused a Ca2+‐dependent aggregation of C. tropicalis yeast cells. These data indicate that hevein can inhibit the growth of certain potential oral fungal pathogens.