bluuebunny/crossref_metadata_2025 huggingface dataset:
Biochemical and Genomic Characterization of Terpene Synthases inMagnolia grandiflora
Authors: Lee Sungbeom , Chappell Joseph
Published: May 2008

Magnolia grandiflora (Southern Magnolia) is a primitive evergreen tree that has attracted attention because of its horticultural distinctiveness, the wealth of natural products associated with it, and its evolutionary position as a basal angiosperm. Three cDNAs corresponding to terpene synthase (TPS) genes expressed in young leaves were isolated, and the corresponding enzymes were functionally characterized in vitro. Recombinant Mg25 converted farnesyl diphosphate (C15) predominantly to β-cubebene, while Mg17 converted geranyl diphosphate (C5) to α-terpineol. Efforts to functionally characterize Mg11 were unsuccessful. Transcript levels for all three genes were prominent in young leaf tissue and significantly elevated for Mg25 and Mg11 messenger RNAs in stamens. A putative amino-terminal signal peptide of Mg17 targeted the reporter green fluorescent protein to both chloroplasts and mitochondria when transiently expressed in epidermal cells of Nicotiana tabacum leaves. Phylogenetic analyses indicated that Mg25 and Mg11 belonged to the angiosperm sesquiterpene synthase subclass TPS-a, while Mg17 aligned more closely to the angiosperm monoterpene synthase subclass TPS-b. Unexpectedly, the intron-exon organizations for the three Magnolia TPS genes were different from one another and from other well-characterized TPS gene sets. The Mg17 gene consists of six introns arranged in a manner similar to many other angiosperm sesquiterpene synthases, but Mg11 contains only four introns, and Mg25 has only a single intron located near the 5′ terminus of the gene. Our results suggest that the structural diversity observed in the Magnolia TPS genes could have occurred either by a rapid loss of introns from a common ancestor TPS gene or by a gain of introns into an intron-deficient progenote TPS gene.
The AP2/ERF Domain Transcription Factor ORA59 Integrates Jasmonic Acid and Ethylene Signals in Plant Defense
Authors: Pré Martial , Atallah Mirna , Champion Antony , De Vos Martin , Pieterse Corné M. J. , Memelink Johan
Published: May 2008

Plant defense against pathogens depends on the action of several endogenously produced hormones, including jasmonic acid (JA) and ethylene. In certain defense responses, JA and ethylene signaling pathways synergize to activate a specific set of defense genes. Here, we describe the role of the Arabidopsis (Arabidopsis thaliana) APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) domain transcription factor ORA59 in JA and ethylene signaling and in defense. JA- and ethylene-responsive expression of several defense genes, including PLANT DEFENSIN1.2 (PDF1.2), depended on ORA59. As a result, overexpression of ORA59 caused increased resistance against the fungus Botrytis cinerea, whereas ORA59-silenced plants were more susceptible. Several AP2/ERF domain transcription factors have been suggested to be positive regulators of PDF1.2 gene expression based on overexpression in stably transformed plants. Using two different transient overexpression approaches, we found that only ORA59 and ERF1 were able to activate PDF1.2 gene expression, in contrast to the related proteins AtERF1 and AtERF2. Our results demonstrate that ORA59 is an essential integrator of the JA and ethylene signal transduction pathways and thereby provide new insight into the nature of the molecular components involved in the cross talk between these two hormones.
Invasion of the Arabidopsis Genome by the Tobacco Retrotransposon Tnt1 Is Controlled by Reversible Transcriptional Gene Silencing
Authors: Pérez-Hormaeche Javier , Potet Frédérique , Beauclair Linda , Le Masson Ivan , Courtial Béatrice , Bouché Nicolas , Lucas Hélène
Published: May 2008

Long terminal repeat (LTR) retrotransposons are generally silent in plant genomes. However, they often constitute a large proportion of repeated sequences in plants. This suggests that their silencing is set up after a certain copy number is reached and/or that it can be released in some circumstances. We introduced the tobacco (Nicotiana tabacum) LTR retrotransposon Tnt1 into Arabidopsis (Arabidopsis thaliana), thus mimicking the horizontal transfer of a retrotransposon into a new host species and allowing us to study the regulatory mechanisms controlling its amplification. Tnt1 is transcriptionally silenced in Arabidopsis in a copy number-dependent manner. This silencing is associated with 24-nucleotide short-interfering RNAs targeting the promoter localized in the LTR region and with the non-CG site methylation of these sequences. Consequently, the silencing of Tnt1 is not released in methyltransferase1 mutants, in contrast to decrease in DNA methylation1 or polymerase IVa mutants. Stable reversion of Tnt1 silencing is obtained when the number of Tnt1 elements is reduced to two by genetic segregation. Our results support a model in which Tnt1 silencing in Arabidopsis occurs via an RNA-directed DNA methylation process. We further show that silencing can be partially overcome by some stresses.
Inactive Methyl Indole-3-Acetic Acid Ester Can Be Hydrolyzed and Activated by Several Esterases Belonging to the AtMES Esterase Family of Arabidopsis
Authors: Yang Yue , Xu Richard , Ma Choong-je , Vlot A. Corina , Klessig Daniel F. , Pichersky Eran
Published: May 2008

The plant hormone auxin (indole-3-acetic acid [IAA]) is found both free and conjugated to a variety of carbohydrates, amino acids, and peptides. We have recently shown that IAA could be converted to its methyl ester (MeIAA) by the Arabidopsis (Arabidopsis thaliana) enzyme IAA carboxyl methyltransferase 1. However, the presence and function of MeIAA in vivo remains unclear. Recently, it has been shown that the tobacco (Nicotiana tabacum) protein SABP2 (salicylic acid binding protein 2) hydrolyzes methyl salicylate to salicylic acid. There are 20 homologs of SABP2 in the genome of Arabidopsis, which we have named AtMES (for methyl esterases). We tested 15 of the proteins encoded by these genes in biochemical assays with various substrates and identified several candidate MeIAA esterases that could hydrolyze MeIAA. MeIAA, like IAA, exerts inhibitory activity on the growth of wild-type roots when applied exogenously. However, the roots of Arabidopsis plants carrying T-DNA insertions in the putative MeIAA esterase gene AtMES17 (At3g10870) displayed significantly decreased sensitivity to MeIAA compared with wild-type roots while remaining as sensitive to free IAA as wild-type roots. Incubating seedlings in the presence of [14C]MeIAA for 30 min revealed that mes17 mutants hydrolyzed only 40% of the [14C]MeIAA taken up by plants, whereas wild-type plants hydrolyzed 100% of absorbed [14C]MeIAA. Roots of Arabidopsis plants overexpressing AtMES17 showed increased sensitivity to MeIAA but not to IAA. Additionally, mes17 plants have longer hypocotyls and display increased expression of the auxin-responsive DR5:β-glucuronidase reporter gene, suggesting a perturbation in IAA homeostasis and/or transport. mes17-1/axr1-3 double mutant plants have the same phenotype as axr1-3, suggesting MES17 acts upstream of AXR1. The protein encoded by AtMES17 had a K  m value of 13 μ  m and a K  cat value of 0.18 s−1 for MeIAA. AtMES17 was expressed at the highest levels in shoot apex, stem, and root of Arabidopsis. Our results demonstrate that MeIAA is an inactive form of IAA, and the manifestations of MeIAA in vivo activity are due to the action of free IAA that is generated from MeIAA upon hydrolysis by one or more plant esterases.
Auxin Responses in Mutants of the Arabidopsis CONSTITUTIVE PHOTOMORPHOGENIC9 Signalosome
Authors: Dohmann Esther Mirjam Natascha , Levesque Mitchell Paul , Isono Erika , Schmid Markus , Schwechheimer Claus
Published: May 2008

The CONSTITUTIVE PHOTOMORPHOGENIC9 (COP9) signalosome (CSN) is an evolutionarily conserved multiprotein complex that interacts with cullin-RING type E3 ubiquitin ligases (CRLs). CSN subunit 5 (CSN5), which, when incorporated into CSN, can deconjugate the NEDD8 modification from the cullin subunit of CRLs, is essential for CSN's role in controlling CRL activity. Whether the CSN5 monomer, which is maintained in csn mutants such as csn3 or csn4, has a functional role, remains to be established. We performed a comparative gene expression-profiling experiment with Arabidopsis (Arabidopsis thaliana) csn3, csn4, and csn5 mutants, and we show here that these mutants cannot be distinguished at the transcriptional level. Furthermore, we show that csn3 csn5 mutants are morphologically indistinguishable from csn3 or csn5 mutants. Taken together, these data suggest that the CSN5 monomer does not have a function that leads to transcriptional or morphological changes in the csn mutants. We further examined auxin responses in csn mutants. Whereas CSN had previously been shown to be required for the auxin response-regulatory E3 complexes, specifically SCFTIR1, the csn mutant phenotype suggests that CSN is not essential for auxin responses. We present physiological and genetic data that indicate that auxin responses are indeed only partially impaired in csn mutants and that this is not the result of maternally contributed CSN. Finally, we discuss these findings in the context of the current understanding of the role of neddylation and CSN-mediated deneddylation for CRL activity.
An improved SUMO fusion protein system for effective production of native proteins
Authors: Lee Chien‐Der , Sun Hui‐Chien , Hu Su‐Ming , Chiu Ching‐Feng , Homhuan Atthachai , Liang Shu‐Mei , Leng Chih‐Hsiang , Wang Ting‐Fang
Published: May 2008

Expression of recombinant proteins as fusions with SUMO (small ubiquitin‐related modifier) protein has significantly increased the yield of difficult‐to‐express proteins in Escherichia coli. The benefit of this technique is further enhanced by the availability of naturally occurring SUMO proteases, which remove SUMO from the fusion protein. Here we have improved the exiting SUMO fusion protein approach for effective production of native proteins. First, a sticky‐end PCR strategy was applied to design a new SUMO fusion protein vector that allows directional cloning of any target gene using two universal cloning sites (Sfo1 at the 5′‐end and XhoI at the 3′‐end). No restriction digestion is required for the target gene PCR product, even the insert target gene contains a SfoI or XhoI restriction site. This vector produces a fusion protein (denoted as His6‐Smt3‐X) in which the protein of interest (X) is fused to a hexahistidine (His6)‐tagged Smt3. Smt3 is the yeast SUMO protein. His6‐Smt3‐X was purified by Ni2+ resin. Removal of His6‐Smt3 was performed on the Ni2+ resin by an engineered SUMO protease, His6‐Ulp1403–621‐His6. Because of its dual His6 tags, His6‐Ulp1403–621‐His6 exhibits a high affinity for Ni2 resin and associates with Ni2+ resin after cleavage reaction. One can carry out both fusion protein purification and SUMO protease cleavage using one Ni2+‐resin column. The eluant contains only the native target protein. Such a one‐column protocol is useful in developing a better high‐throughput platform. Finally, this new system was shown to be effective for cloning, expression, and rapid purification of several difficult‐to‐produce authentic proteins.
Neutrophilic, urticaria‐like erythema associated with immunoglobulin A monoclonal gammopathy of undetermined significance
Authors: DEMITSU Toshio , KAKURAI Maki , AZUMA Ryuichi , HIRATSUKA Yuichiro , UMEMOTO Naoka , YONEDA Kozo
Published: May 2008

A 70‐year‐old‐male had suffered from non‐pruritic, erythematous eruptions on the trunk for 3 months without any general symptoms. The individual lesions lasted for several days. Laboratory investigation showed marked elevation of serum immunoglobulin A (2235 mg/dL) with monoclonal gammopathy (IgA k‐type). Monoclonal gammopathy of undetermined significance was diagnosed. Histopathological examination of the eruption revealed diffuse neutrophilic infiltration with leukocytoclasia in the dermis. There was no vasculitis. Treatment with antihistamines alone was not effective. Diaphenyl sulfone (DDS) at 75 mg/day dramatically improved the skin lesions. A similar case of urticarial erythema associated with IgA myeloma has been previously reported. We suggest that neutrophilic, urticaria‐like erythema associated with IgA monoclonal gammopathy may be regarded as a new entity.
Erythema elevatum diutinum with rare distribution as a first clinical sign of non‐Hodgkin's lymphoma: A novel association?
Authors: HATZITOLIOS Apostolos , TZELLOS Thrasivoulos George , SAVOPOULOS Christos , TZALOKOSTAS Vasileios , KAIAFA Georgia , PSOMAS Evaggelos , APOSTOLOPOULOU Martha , PAPADOPOULOS Athanasios
Published: May 2008

We present a case of a 78‐year‐old man with erythema elevatum diutinum as a first clinical sign of non‐Hodgkin's lymphoma. The patient developed erythema elevatum diutinum with an unusual distribution involving the trunk. Erythema elevatum diutinum is a rare dermatosis that is considered to be a localized, low‐grade form of leukocytoclastic vasculitis associated with neoplastic, autoimmune and infectious processes. It is probably mediated by immune complexes. Recent studies report hematological disease as the most common factor associated with erythema elevatum diutinum. Many hematological diseases, such as myeloma, myelodysplastic syndrome and immunoglobulin (Ig)A monoclonal gammopathy, have been reported in association with erythema elevatum diutinum, but none with IgM monoclonal gammopathy and only one with malignant lymphoma. We would like to add IgM monoclonal gammopathy and non‐Hodgkin's lymphoma as one of the diseases associated with erythema elevatum diutinum considering that the activity of erythema elevatum diutinum and non‐Hodgkin's lymphoma fluctuated in parallel in the present case.
Anaesthesia for Angelman syndrome
Authors: Ramanathan K. R. , Muthuswamy D. , Jenkins B. J.
Published: May 2008

We describe the administration of anaesthesia to a patient with Angelman syndrome, which is characterised by an abnormality of chromosome 15, where a subunit of the GABA receptor is coded. This has far‐reaching anaesthetic implications as many drugs used in anaesthesia are thought to act via GABA receptors. Our patient had an uneventful peri‐operative period and was discharged home on the second postoperative day.
Anaesthesia and high altitude: a history
Authors: Firth P. G. , Pattinson K. T. S.
Published: May 2008

During an expedition to climb Everest in 1933, expedition doctor Raymond Greene administered an open‐drop chloroform anaesthetic to a Tibetan patient at an altitude of more than 14 000 feet. The patient’s subsequent apparent cardiopulmonary arrest has long been attributed to the effects of altitude on anaesthetic delivery. However, anaesthetics can be safely administered at a wide variety of altitudes by adequately trained and experienced anaesthetists. The problems may have arisen from an inadequate depth of anaesthesia consequent to decreased chloroform vaporisation in a cold environment, Greene’s concern about potential depression of ventilation and the contemporary lack of a precise approach to assessing depth of anaesthesia.
Regional anaesthesia for limb surgery: a review of anaesthetists’ beliefs and practice in the Oxford region*
Authors: Feely N. M. , Popat M. T. , Rutter S. V.
Published: May 2008

We conducted a postal survey of 210 anaesthetists in the Oxford region to determine their views and practice regarding the timing of regional anaesthesia when combined with general anaesthesia for adults undergoing limb surgery and to compare the results with those obtained in a similar survey conducted in 2001. Of the 151 respondents (72% response rate), 102 (68%) regularly combined regional and general anaesthesia for adult limb surgery. Over 80% believed that central neuraxial blocks should be performed before general anaesthesia. This matched their current practice, marking a change from 2001. Significantly fewer anaesthetists believed it necessary to perform peripheral nerve blocks before general anaesthesia than in 2001, marking another significant change in practice. Overall, the results indicate an increased popularity of regional blocks in combination with general anaesthesia when compared with 2001 practice, which we believe is related to high quality advanced training modules now on offer to senior trainees in the Oxford region.
The incidence of bacteraemia associated with tracheal intubation
Authors: Valdés C. , Tomás I. , Álvarez M. , Limeres J. , Medina J. , Diz P.
Published: May 2008

Expert committees on bacterial endocarditis prophylaxis have provided differing opinions on whether tracheal intubation is an ‘at‐risk’ manipulation. We studied the incidence of bacteraemia after orotracheal and nasotracheal intubation. The study group comprised 110 patients who underwent surgery under general anaesthesia. Venous blood samples were collected from each patient at baseline and 30 s after intubation. Samples were processed with conventional microbiological techniques. Bacteraemia after tracheal intubation was detected in 13 patients (11.8%); six after orotracheal intubation and seven after nasotracheal intubation. Staphylococci and streptococci were the most commonly isolated bacterial species. Seven isolates (54%) were resistant to oxacillin. The incidence of bacteraemia was similar after orotracheal (12.0%) and nasotracheal intubation (11.7%). The recommendation for bacterial endocarditis prophylaxis with flucloxacillin when performing nasotracheal intubation, as put forward by the British Society for Antimicrobial Chemotherapy, needs further consideration.
Intravascular iodinated contrast media and the anaesthetist
Authors: Dickinson M. C. , Kam P. C. A.
Published: May 2008

The use of intravascular iodinated contrast media (ICM) in radiological investigations is common. Increasingly, anaesthetists and intensivists are involved in the care of patients undergoing these investigations. Whilst the use of ICM is generally safe there are important adverse effects that need to be recognised and measures instigated to prevent or treat these effects. In patients at risk of developing adverse reactions it is important to consider alternative modes of imaging so that ICM can be avoided. Strategies for the prevention of ICM nephropathy should be considered in all patients receiving ICM. Currently intravascular volume expansion with 0.9% saline has the strongest evidence base. The use of isotonic sodium bicarbonate combined with N‐acetylcysteine appears promising in providing further benefits. Although the use of N‐acetylcysteine alone has not been shown to significantly reduce the incidence of ICM nephropathy it is cheap, has few adverse effects and it would seem reasonable to continue its use in conjunction with intravascular volume expansion. The routine use of corticosteroid and antihistamine premedication is not always effective in preventing general adverse reactions.
A comparison of cervical spine movement during laryngoscopy using the Airtraq® or Macintosh laryngoscopes*
Authors: Hirabayashi Y. , Fujita A. , Seo N. , Sugimoto H.
Published: May 2008

The Airtraq® laryngoscope has an oropharyngeal airway‐shaped blade that provides a non‐line‐of‐sight view of the glottis. The configuration of the blade should mean that less movement of the cervical spine is required during laryngeal visualisation.

We compared the degree of cervical spine movement in laryngoscopy performed using the Airtraq and conventional Macintosh laryngoscope. In 20 patients requiring general anaesthesia and tracheal intubation, we measured cervical spine movement using radiography in the same patient during consecutive procedures using the two laryngoscopes. Although significant movement of the cervical spine from baseline was noted during all procedures (p < 0.05), cervical spinal extension with the Airtraq was 29% less than that measured during Macintosh laryngoscopy between the occiput and C4, and 44% less at the C3/C4 motion segment (p < 0.05). Anterior deviations of the vertebral bodies from baseline were 32%, 35%, 38% and 40% less at the atlas, C2, C3, and C4 vertebrae, respectively, during Airtraq laryngoscopy than those measured during Macintosh laryngoscopy (p < 0.01). Our study demonstrated that laryngoscopy using the Airtraq laryngoscope involves less movement of the cervical spine compared to conventional procedures using a Macintosh laryngoscope.
Interleukin (IL)‐17 promotes macrophages to produce IL‐8, IL‐6 and tumour necrosis factor‐α in aplastic anaemia
Authors: Gu Yan , Hu Xiaojing , Liu Chuanfang , Qv Xun , Xu Conggao
Published: May 2008

Aplastic anaemia (AA) is thought to be an autoimmune‐mediated disease with active destruction of haematopoietic cells through a T helper type 1 (Th1) cell response. Interleukin (IL)‐17 is a potent proinflammatory cytokine produced by activated memory T cells. Recent studies indicate that IL‐17 might be an essential effector cytokine in the T‐cell mediated autoimmune process. It can drive the production of tumour necrosis factor‐α (TNF‐α), IL‐1 β, IL‐6 and IL‐8 by a variety of cells. The present study investigated the genetic and protein expression of IL‐17 in patients with AA. The effect of IL‐17 on IL‐6 and IL‐8 production by macrophages was also studied. AA patients showed an elevated expression of IL17A mRNA in bone marrow mononuclear cells and peripheral blood mononuclear cells. Higher IL‐17 in bone marrow and peripheral blood plasma was also observed in AA patients compared with normal controls. IL‐17 induced the production of IL‐6 and IL‐8 by macrophages both from patients with AA and normal controls. IL‐17 stimulation also resulted in the production of TNF‐α. These results suggested that elevated expression of IL‐17 and IL‐17‐induced IL‐6, IL‐8 and TNF‐α may be involved in the mechanisms of AA.
Pan‐neurotrophin receptor p75NTR expression is strongly induced in lesional atopic mast cells
Authors: Fischer T. C. , Lauenstein H.‐D. , Serowka F. , Pilzner C. , Groneberg D. A. , Welker P.
Published: May 2008

Background
Neurotrophins such as nerve growth factor or brain‐derived neurotrophic factor influence neuronal proliferation and differentiation via the low‐affinity pan‐neurotrophin receptor p75NTR that may play a pivotal role in linking the immune with the nervous system. Because the precise regulation of p75NTR gene transcription in mast cells under states of allergic inflammation has not been investigated in detail so far, the present studies assessed the gene regulation and expression of this receptor.

Methods
Transcriptional expression of p75NTR in human skin was studied in isolated cutaneous cells by means of RT‐PCR. In situ lesional mast cell p75NTR expression was analysed by immunohistochemistry.

Results
The p75NTR mRNA expression was found in isolated human skin mast cells and keratinocytes. Lower mRNA levels were present in fibroblasts and melanocytes but no transcripts were found in endothelial cells. The p75NTR protein expression was found in situ in lesional and non‐lesional mast cells. A significantly increased expression of p75NTR protein was found in atopic dermatitis lesional mast cells when compared with control mast cell expression (P<0.05).

Conclusion
The demonstration of an increased level of p75NTR gene transcription in lesional mast cells points to an induction of low‐affinity neurotrophin receptor sensitivity of mast cells under states of allergic inflammation. Topically administered neurotrophin receptor‐modulating compounds may act as anti‐inflammatory mediators in cutaneous allergic inflammation.
Nitric oxide evaluation in upper and lower respiratory tracts in nasal polyposis
Authors: Delclaux C. , Malinvaud D. , Chevalier‐Bidaud B. , Callens E. , Mahut B. , Bonfils P.
Published: May 2008

Background
A decrease in nasal nitric oxide (NO) and an increase in exhaled NO have been demonstrated in patients with nasal polyposis (NP).

Objectives
The aims were to evaluate the flux of NO from the three compartments of the respiratory tract, namely, upper nasal, lower conducting and distal airways, and to search for relationships between NO parameters and indexes of upper and lower disease activity (bronchial reactivity and obstruction). The effect of medical treatment of polyposis was also evaluated.

Methods
Seventy patients with polyposis were recruited. At baseline, pulmonary function tests (spirometry, plethysmography, bronchomotor response to deep inspiration using forced oscillation measurement of resistance of respiratory system, methacholine challenge, multiple flow rates of exhaled NO and nasal NO measurements) were performed together with an assessment of polyposis [clinical, endoscopic and computed tomography (CT) scores].

Results
Statistical relationships were demonstrated between nasal NO flux and severity scores (clinical: ρ=−0.31, P=0.015; endoscopic: ρ=−0.57, P<0.0001; CT: ρ=−0.46, P=0.0005), and between alveolar NO concentration and distal airflow limitation (FEF25–75, ρ=−0.32, P=0.011). Thirty‐six patients were assessed after 11 [7–13] (median [interquartile]) months of medical treatment, demonstrating an improvement in clinical and endoscopic scores, an increase in nasal NO flux, a decrease in NO flux from conducting airways, an improvement in the mild airflow limitation (forced expiratory volume in 1 s, FEF25–75, even in non‐asthmatic patients) and a decrease in the bronchoconstrictor effect of deep inspiration.

Conclusions
The medical treatment of NP improves both airway reactivity and obstruction, whatever the presence of asthma, suggesting a functional link between upper and lower airway functions.
When does a protein become an allergen? Searching for a dynamic definition based on most advanced technology tools
Authors: Mari A.
Published: May 2008

Since the early beginning of allergology as a science considerable efforts have been made by clinicians and researchers to identify and characterize allergic triggers as raw allergenic materials, allergenic sources and tissues, and more recently basic allergenic structures defined as molecules. The last 15–20 years have witnessed many centres focusing on the identification and characterization of allergenic molecules leading to an expanding wealth of knowledge. The need to organize this information leads to the most important question ‘when does a protein become an allergen?’ In this article, I try to address this question by reviewing a few basic concepts of the immunology of IgE‐mediated diseases, reporting on the current diagnostic and epidemiological tools used for allergic disease studies and discussing the usefulness of novel biotechnology tools (i.e. proteomics and molecular biology approaches), information technology tools (i.e. Internet‐based resources) and microtechnology tools (i.e. proteomic microarray for IgE testing on molecular allergens). A step‐wise staging of the identification and characterization process, including bench, clinical and epidemiological aspects, is proposed, in order to classify allergenic molecules dynamically. This proposal reflects the application and use of all the new tools available from current technologies.
Cytology of benign multicystic peritoneal mesothelioma in peritoneal washings
Authors: Assaly M. , Bongiovanni M. , Kumar N. , Egger J.‐F. , Pelte M.‐F. , Genevay M. , Finci V. , Tschanz E. , Pache J.‐C.
Published: May 2008

Objective:  To describe the cytological aspect of peritoneal washings in benign multicystic peritoneal mesothelioma (BMPM).

Methods:  Three peritoneal washing specimens stained by standard cytological and histological procedures and analysed by light microscopy.

Results:  The specimens showed an abundance of monomorphous mesothelial cells devoid of atypia or mitoses. The mesothelial cells were calretinin positive. They also showed numerous squamous metaplastic cells arranged in flat sheets or isolated cells. The background contained some inflammatory cells.

Conclusion:  The combination of cytology of the peritoneal washing, histology (cell block and surgical specimen) and clinical history allow differentiation of BMPM from other cystic lesions (cystic lymphangioma and malignant mesothelioma).
The development of the referral outcome diagram and an analysis of laboratory cancer detection rates in the English NHS cervical screening programme – is there an optimum level of detection of CIN 1 and CIN 2 lesions?
Authors: Blanks R. G.
Published: May 2008

Objective:  To use routine annual data from the English cervical screening laboratories (KC61 returns) to evaluate individual laboratory return characteristics with particular reference to factors associated with sensitivity and specificity.

Methods:  A graphical technique has been developed using data on referral to colposcopy and histological outcomes called a referral outcome (ROUT) diagram. The average grade of cervical intraepithelial neoplasia (CIN) detected (the mean CIN score, MCS) is plotted against the odds of a false‐positive referral. Further analysis has been conducted to examine the relationship between the MCS and screen‐detected invasive cancer rate.

Results:  There are large variations in ROUT diagram positions of individual laboratories and the diagram can be used to identify laboratories for further investigation. These variations are strongly influenced by substantial differences in the rate of low‐grade referrals and the MCS (and positive predictive value) are inversely related to the referral rate for low‐grade cytology (P < 0.001). There is a strong association between high MCS values and increased screen‐detected cancer rates (P < 0.001) particularly above an MCS of 2.2. The data can be re‐formulated in terms of CIN 2 and CIN 3 only where it can be shown that the invasive cancer rate rapidly increases if the numbers of CIN 2 lesions detected drops below 50% of the number of CIN 3 lesions. Given the complexity of cervical screening this may best be viewed as a hypothesis generating observation, best tested by interventional studies.

Conclusions:  The ROUT diagram represents a new and potentially interesting way of presenting annual return data. The national programme in England needs to balance the prevention of cancer against too many unnecessary referrals to colposcopy and the ROUT diagram, and associated data given in this paper may help toward this. Further research is required including examining the role of referral policy and threshold criteria in influencing low‐grade referrals and the relationship between MCS and cancer detection rate.
Rapid pre‐screening of cervical smears as a method of internal quality control in a cervical screening programme
Authors: Do Nascimento Tavares S. B. , De Sousa N. L. A. , Manrique E. J. C. , De Albuquerque Z. B. P. , Zeferino L. C. , Amaral R. G.
Published: May 2008

Objective:  To evaluate the performance of rapid pre‐screening (RPS) as a method of internal quality control in the cytopathological examination of cervical smears for cervical cancer screening.

Methods:  The sample consisted of 6135 cervical smears submitted to RPS and routine screening (RS) methods. The smears classified as negative in RPS and RS were considered final diagnoses, and were not, therefore, submitted to any additional review. The smears identified as suspect or unsatisfactory according to RPS were analysed separately by two different cytologists irrespective of the diagnosis reached in RS. Smears considered abnormal or unsatisfactory at RS were also reviewed. When both cytologists issued concordant diagnoses, this was considered the final diagnosis. Discordant results were analysed by a third cytologist and a consensus meeting was held to define the final diagnosis.

Results:  Taking abnormalities detected by RS as the denominator, RPS had a sensitivity of 63.0% for the detection of all abnormal smears and 96.7% for high grade squamous intraepithelial lesion (HSIL). When compared with the final diagnosis, sensitivity of RPS for all abnormal smears was 74.9% and for HSIL 95.0%. Of the 529 abnormal smears confirmed in the final diagnosis, 2.15% were detected only by the RPS.

Conclusion:  RPS is an effective alternative method of internal quality control with high sensitivity for the detection of more severe lesions. It also permits monitoring of the laboratory rate of false‐negative results, and allows constant evaluation of the performance both of the pre‐screening and RS cytologists.
Viruses in wetland ecosystems
Authors: JACKSON EVELYN F. , JACKSON COLIN R.
Published: May 2008

1. We review studies of viruses in natural and constructed wetlands, focusing on the importance of surfaces as viral habitat, and differences in viral ecology between wetlands and other aquatic ecosystems.

2. Viruses in natural wetlands are predominantly associated with sediment, macrophytes and other submerged surfaces. In constructed wetlands, these surfaces are critical to the removal of viral pathogens and indicator organisms from wastewater.

3. Interactions between viruses and other ecosystem components have rarely been examined in wetlands, and the role of viruses in regulating wetland microbial communities is unclear. Environmental factors such as temperature and flooding regime are important abiotic controllers of viral abundances in wetlands but few studies have examined how abiotic or biotic factors affect community structure. Even basic information on wetland viral diversity is lacking.

4. Future research should include broad surveys of different types of wetlands, an emphasis on differences between microhabitats, and an increased use of molecular approaches to examine wetland viral diversity and its relationship to microbial community structure. Such studies should consider wetlands as part of the broader landscape, and emphasize interactions between wetlands and adjacent terrestrial and aquatic ecosystems.
Viriobenthos in freshwater and marine sediments: a review
Authors: DANOVARO ROBERTO , CORINALDESI CINZIA , FILIPPINI MANUELA , FISCHER ULRIKE R. , GESSNER MARK O. , JACQUET STÉPHAN , MAGAGNINI MIRKO , VELIMIROV BRANKO
Published: May 2008

1. Viruses are the most abundant biological entities on the planet, and sediments provide a highly suitable environment for them. This review presents the first comparative synthesis of information on the fresh water and marine viriobenthos and explores differences and similarities to the better known virioplankton. We present methods for studying life cycles of the viriobenthos, data on viral distribution and diversity, interactions with host microbes, and information on the role of viruses in benthic food webs and biogeochemical cycles.

2. Most approaches developed for the virioplankton are also applicable to viriobenthos, although methods for analysing benthic viruses may differ in important details.

3. Benthic viruses are very abundant in both marine and freshwater sediments, where 107–1010 can occur in 1 g of dry sediment. Although information on viral production (VP) and decay rates in freshwater sediments is very limited, the data suggest that VP and decay could also be high. These data highlight the potential ecological importance of benthic viruses, suggesting that they could play a key role in prokaryotic mortality and in biogeochemical cycles.

4. There is clear indirect evidence for the importance of viriobenthos in marine and freshwater ecosystems. However, large numbers of visibly infected cells have not been observed, suggesting limited effects on prokaryote population and community dynamics. The apparent paradox between high viral abundance and low impact is currently unresolved, while several aspects of viral life cycles in sediments (e.g. chronic infection) are almost completely unknown.

5. Studies on viriobenthic diversity and community structure are at a pioneering stage. First results from a few studies using pulsed‐field gel electrophoresis and especially from metagenomic analyses indicate, however, that viriobenthic assemblages are both highly diverse and distinct from the virioplankton.

6. Estimates of global viral abundance in the top 1 m of fresh water and marine sediments are 0.5 and 28.7 × 1028 viruses respectively. Similar rough estimates of production are 0.6 and 34.4 × 1028 viruses day−1, suggesting an average turnover time of 20 h.
Assessing streamflow characteristics as limiting factors on benthic invertebrate assemblages in streams across the western United States
Authors: KONRAD C. P. , BRASHER A. M. D. , MAY J. T.
Published: May 2008

1. Human use of land and water resources modifies many streamflow characteristics, which can have significant ecological consequences. Streamflow and invertebrate data collected at 111 sites in the western U.S.A. were analysed to identify streamflow characteristics (magnitude, frequency, duration, timing and variation) that are probably to limit characteristics of benthic invertebrate assemblages (abundance, richness, diversity and evenness, functional feeding groups and individual taxa) and, thus, would be important for freshwater conservation and restoration. Our analysis investigated multiple metrics for each biological and hydrological characteristic, but focuses on 14 invertebrate metrics and 13 streamflow metrics representing the key associations between streamflow and invertebrates.

2. Streamflow is only one of many environmental and biotic factors that influence the characteristics of invertebrate assemblages. Although the central tendency of invertebrate assemblage characteristics may not respond to any one factor across a large region like the western U.S.A., we postulate that streamflow may limit some invertebrates. To assess streamflow characteristics as limiting factors on invertebrate assemblages, we developed a nonparametric screening procedure to identify upper (ceilings) or lower (floors) limits on invertebrate metrics associated with streamflow metrics. Ceilings and floors for selected metrics were then quantified using quantile regression.

3. Invertebrate assemblages had limits associated with all streamflow characteristics that we analysed. Metrics of streamflow variation at daily to inter‐annual scales were among the most common characteristics associated with limits on invertebrate assemblages. Baseflow recession, daily variation and monthly variation, in streamflow were associated with the largest number of invertebrate metrics. Since changes in streamflow variation are often a consequence of hydrologic alteration, they may serve as useful indicators of ecologically significant changes in streamflow and as benchmarks for managing streamflow for ecological objectives.

4. Relative abundance of Plecoptera, richness of non‐insect taxa and relative abundance of intolerant taxa were associated with multiple streamflow metrics. Metrics of sensitive taxa (Ephemeroptera, Plecoptera and Trichoptera), and intolerant taxa generally had ceilings associated with flow metrics while metrics of tolerant taxa, non‐insects, dominance and chironomids generally had floors. Broader characteristics of invertebrate assemblages such as abundance and richness had fewer limits, but these limits were nonetheless associated with a broad range of streamflow characteristics.
Characterization of the shallow aquifers by high‐resolution seismic data
Authors: Giustiniani M. , Accaino F. , Picotti S. , Tinivella U.
Published: May 2008

We present the results obtained by processing high‐resolution seismic data acquired along the spring line located in the Friuli‐Venezia Giulia plain (NE of Italy), in order to characterize an important multilayered aquifer. This system is made of an unconfined layer and, at increasing depths, of several confined aquifers of variable thickness and hydraulic permeability, mainly consisting of sand and gravel material. The main targets of this study are two shallow aquifers located at about 30 m and 200 m depth respectively. The seismic method is not frequently used for this type of study but in this case, it was considered a good tool due to the depth of the targets. The detailed velocity model we obtained reveals lateral velocity variations with a maximum value of 600 m/s. The higher velocities could be associated to layers that are confined aquifers; in fact, sand and gravel are characterized by higher seismic velocity compared to clay layers. Pre‐stack depth migration using this velocity model gives a clear picture of the multilayered aquifer, highlighting lateral changes of seismic amplitude along the main reflectors. Finally, vertical variations of Poisson's ratio, computed by amplitude versus offset analysis, provide useful information about the petrophysical properties, such as the fluid content of the subsoil and lithologic changes.
Precise arrival time detection of polarized seismic waves using the spectral matrix
Authors: Moriya Hirokazu
Published: May 2008

I present a statistical method for detecting the arrival times of polarized seismic waves on three‐component seismic observations in the time and frequency domains. In this method, the polarization, which is a representation of the 3D particle motion of seismic waves, is evaluated on the basis of a spectral matrix in the time and frequency domains and the statistical parameters are defined by using the eigenvalues of the spectral matrix for detecting the arrival times of linearly and elliptically polarized waves, where the idea of a statistical test of hypothesis is introduced. An evaluation of a synthetic signal revealed that the method can detect the arrival times of linearly and elliptically polarized waves within 10 sampling points at signal‐to‐noise ratios of −7 dB. Application of the method to an earthquake suggested that it can be used to detect the arrival times of both linearly and elliptically polarized waves, which are difficult to identify manually.
Control of IL‐4 expression in T helper 1 and 2 cells
Authors: Gilmour Jane , Lavender Paul
Published: May 2008

The mechanism of differentiation of naïve T cells to a variety of effector lineages, but particularly to T helper type 1 (Th1) and Th2 cells, has been the subject of intense scrutiny over the past two decades. Studies have revealed that the expression of cytokines, receptors, signalling molecules, transcription factors, DNA methylating enzymes and histone‐modifying enzymes is altered during the process and has been shown to play a co‐ordinated role to facilitate expression of the cytokines interleukin‐4 (IL‐4), IL‐5 and IL‐13 in Th2 cells, or interferon‐γ in Th1 cells. Regulation of IL‐4 expression has been of particular interest for two main reasons: first because IL‐4 acts as a growth factor for Th2 cells, and second because of its role in the induction of immunoglobulin class switching to immunoglobulin E, which plays a critical role in mediating allergic responses. Study of the pathways that promote this tissue‐restricted expression of IL‐4 may highlight potential areas for therapeutic intervention.
Small changes in lymphocyte development and activation in mice through tissue‐specific alteration of heparan sulphate
Authors: Garner Omai B. , Yamaguchi Yu , Esko Jeffrey D. , Videm Vibeke
Published: May 2008

We have examined the role of heparan sulphate in lymphocyte development and activation in mice by conditionally deleting the genes encoding the heparan sulphate biosynthetic enzymes N‐deacetylase/N‐sulphotransferase‐1 and ‐2 (Ndst1 and Ndst2) and glucuronic acid/N‐acetylglucosamine co‐polymerase‐1 (Ext1) in T cells and B cells, respectively. Ndst1 and Ndst2 are the only Ndst isoforms in T cells. In T‐cell Ndst‐deficient mice there were normal ratios of CD4+/CD8+ cells in the blood, spleen and thymus, indicating no dramatic effect on development. However, Ndst‐deficient T cells were hyperresponsive to low‐level activation, suggesting that cell surface heparan sulphate plays a role in T‐cell proliferation. The hyperresponsive state correlated with a decrease in cell surface heparan sulphate that occurs in response to activation in wild‐type cells. There was a slight change in the number of developing B cells in B‐cell Ext1‐deficient mice, but the alteration did not cause a change in antibody production. These findings demonstrate that cell surface heparan sulphate may not play a crucial role in lymphocyte development, but can modulate the sensitivity of T cells to activation.
Serine proteases identified from a Costelytra zealandica (White) (Coleoptera: Scarabaeidae) midgut EST library and their expression through insect development
Authors: Marshall S. D. G. , Gatehouse L. N. , Becher S. A. , Christeller J. T. , Gatehouse H. S. , Hurst M. R. H. , Boucias D. G. , Jackson T. A.
Published: May 2008

Costelytra zealandica larvae are pests of New Zealand pastures causing damage by feeding on the roots of grasses and clovers. The major larval protein digestive enzymes are serine proteases (SPs), which are targets for disruption in pest control. An expressed sequence tag (EST) library from healthy, third instar larval midgut tissue was constructed and analysed to determine the composition and regulation of proteases in the C. zealandica larval midgut. Gene mining identified three trypsin‐like and 11 chymotrypsin‐like SPs spread among four major subgroups. Representative SPs were examined by quantitative PCR and enzyme activity assayed across developmental stages. The serine protease genes examined were expressed throughout feeding stages and downregulated in nonfeeding stages. The study will improve targeting of protease inhibitors and bacterial disruptors of SP synthesis.
Cloning and RNAi‐mediated functional characterization of MaLac2 of the pine sawyer, Monochamus alternatus
Authors: Niu B.‐L. , Shen W.‐F. , Liu Y. , Weng H.‐B. , He L.‐H. , Mu J.‐J. , Wu Z.‐L. , Jiang P. , Tao Y.‐Z. , Meng Z.‐Q.
Published: May 2008

Laccase, a member of a group of proteins collectively known as multicopper oxidases, is hypothesized to play an important role in insect cuticle sclerotization by oxidizing catechols in the cuticle to their corresponding quinones, which then catalyze protein cross‐linking reactions. Laccase 2 has been proved as the gene required for beetle cuticle tanning through RNA interference (RNAi) experiments on red flour beetle Tribolium castaneum. The pine sawyer beetle, Monochamus alternatus (Coleoptero: Cerambycidae) is the insect serving as a major vector of the pinewood nematode, Bursaphelenchus xylophilus, which is the causative agent for pine wilt disease. The cDNA of MaLac2 was cloned from the insect in this study. The conceptual amino‐acid sequence deduced was much conserved with other known insect laccases, particularly with the enzyme of Tribolium castaneum. Injection in hemolymph of pine sawyer larva of dsRNA targeting the laccase 2 mRNA leads to important alterations of the tanning, hardening and sclerotization of the pupal and adult cuticles. Defaults appear in a dose‐dependent manner and high loads of dsRNA are lethal. The decrease of the endogenous laccase 2 mRNA affects the procuticle which is thinner and without the characteristic piling up of successive layers. The observations reinforce the role of laccase 2 as an essential phenoloxidase for making cuticle.
Comparative study on antioxidative activity of yellow stripe trevally protein hydrolysate produced from Alcalase and Flavourzyme
Authors: Klompong Vilailak , Benjakul Soottawat , Kantachote Duangporn , Hayes Kirby Dale , Shahidi Fereidoon
Published: May 2008

Antioxidative activities of protein hydrolysates from yellow stripe trevally (Selaroides leptolepis) prepared using Alcalase 2.4 L (HA) and Flavourzyme 500 L (HF) with the degree of hydrolysis of 15% by pH‐stat method were determined. Both protein hydrolysates exhibited the antioxidative activity in a concentration dependent manner. HF generally showed the greater antioxidative activity than HA (P < 0.05) as indicated by the higher 2,2‐diphenyl‐1‐picryhydrazyl (DPPH) radical scavenging activity, reducing power and metal chelating activity. Antioxidative activity of both hydrolysates was stable when heated at 90 °C for 10 and 30 min and subjected to a wide pH range (2–12). Nevertheless, metal chelating activity decreased in very alkaline and acidic pH ranges. HA and HF at 200 ppm retarded the formation of conjugated diene and thiobarbituric acid reactive substances (TBARS) in lecithin liposome system. HF possessed the stronger antioxidative activity than HA (P < 0.05). However, α‐tocopherol at 200 ppm showed the higher antioxidative activity in the system.