16 research outputs found
Transient expression assays in tobacco protoplasts
No full textThe sequence information generated through genome and transcriptome analysis from plant tissues has reached unprecedented sizes. Sequence homology-based annotations may provide hints for the possible function and roles of particular plant genes, but the functional annotation remains nonexistent or incomplete for many of them. To discover gene functions, transient expression assays are a valuable tool because they can be done more rapidly and at a higher scale than generating stably transformed tissues. Here, we describe a transient expression assay in protoplasts derived from suspension cells of tobacco (Nicotiana tabacum) for the study of the transactivation capacities of transcription factors. To enhance throughput and reproducibility, this method can be automated, allowing medium-throughput screening of interactions between large compendia of potential transcription factors and gene promoters
Analysis of the leprosy literature indexed in Medline (1950-2007)
No full textSome 19,201 leprosy-related articles were identified in the Medline database for the period 1950-2007. These were analysed for distribution and evolution of a number of variables: publication years, languages, document types, journals, authors, major aspects and countries involved, and author addresses. Next to a number of tables presenting the actual results, some noteworthy trends and possible pitfalls in the interpretation of these results are discussed. The analysis shows that the number of leprosy-related articles peaked in the 1980s and has been in decline ever since, as well in absolute as in relative numbers. Coverage of non-English language literature has decreased far more strongly than that of English language articles. The scholarly input of a number of countries where the leprosy burden is the highest, such as India and Brazil, is clearly visible in the distribution of journals, authors, and for some, language, but this is certainly not the case for all countries afflicted
Inflammatory markers in younger vs elderly normal volunteers and in patients with Alzheimer's disease
No full textIt has been reported that activation of the inflammatory response system (IRS) may play a role in the aging process and in the pathogenesis of the degenerative changes associated with dementia of the Alzheimer type (DAT). This study examined the peripheral IRS in 31 normally aging Ss (age 22-91 yrs) and 15 DAT patients (age 56-94 yrs)
Multidisciplinary interobserver agreement in the diagnosis of idiopathic pulmonary fibrosis
No full textThe purpose of the present study was to evaluate the accuracy of the diagnosis of idiopathic pulmonary fibrosis (IPF) by respiratory physicians in six European countries, and to calculate the interobserver agreement between high-resolution computed tomography reviewers and histology reviewers in IPF diagnosis.The diagnosis of usual interstitial pneumonia (UIP) was assessed by a local investigator, following the American Thoracic Society/European Respiratory Society consensus statement, and confirmed when a minimum of two out of three expert reviewers from each expert panel agreed with the diagnosis. The level of agreement between readers within each expert panel was calculated by weighted kappa.The diagnosis of UIP was confirmed by the expert panels in 87.2% of cases. A total of 179 thoracic high-resolution computed tomography scans were independently reviewed, and an interobserver agreement of 0.40 was found. Open or thoracoscopic lung biopsy was performed in 97 patients, 82 of whom could be reviewed by the expert committee. The weighted kappa between histology readers was 0.30.It is concluded that, although the level of agreement between the readers within each panel was only fair to moderate, the overall accuracy of a clinical diagnosis of idiopathic pulmonary fibrosis in expert centres is good (87.2%).The members of the Idiopathic Pulmonary Fibrosis International Group Exploring N-Acetylcysteine I Annual
(IFIGENIA) study group are as follows.
Steering committee: J. Behr (Grosshadern Clinic, Ludwig Maximilian University, Munich, Germany); R. Buhl (Johannes
Gutenberg University Clinic, Mainz, Germany); U. Costabel (Ruhrland Clinic, Essen, Germany); R. Dekhuijzen (Radboud
University Nijmegen Medical Centre, Nijmegen, The Netherlands); M. Demedts (Chairman) and M. Thomeer
(University Hospitals, Catholic University of Leuven, Leuven, Belgium); H.M. Jansen (Academic Medical Centre,
Amsterdam, The Netherlands); W. MacNee (University of Edinburgh Medical School, Edinburgh, UK); and B. Wallaert
TABLE 4 Overview of studies addressing interobserver agreement on thoracic computed tomography (CT) in various forms of
pulmonary fibrosis
First author [Ref.] Year Interobserver agreement k coefficient Study population Subjects n Observers n Comments
GRENIER [10] 1991 0.64–0.78 Sarcoidosis 53 3 Definition of IPF unclear Pulmonary fibrosis 33 Histiocytosis X 17
Other ILD 37 WELLS [19] 1993 0.58–0.76 Systemic sclerosis 35 2 Interobserver agreement for grading CT appearance
IPF 21 and change in nature and extent of disease COLLINS [8] 1994 0.48 Systemic sclerosis 63 4 Interobserver agreement for CT pattern type
IPF 63 KAZEROONI [20] 1997 0.51–0.83 UIP; DIP 24; 1 4 Interobserver agreement for pattern type in different lobes
MACDONALD [9] 2001 0.40 NSIP 21 4 Interobserver agreement for NSIP and UIP UIP 32
HUNNINGHAKE [7] 2001 0.54 IPF 54 4 Interobserver agreement for IPF versus non-IPF;
Non-IPF 37 criteria for IPF diagnosis not mentioned FLAHERTY [3] 2003 0.43 NSIP 23 2 Interobserver agreement for NSIP and UIP
UIP 73 AZIZ [21] 2004 0.50 DPLD 131 11 Interobserver agreement for first-choice diagnosis of IPF
Present study 0.40 UIP 156 3 Interobserver agreement for IPF versus non-IPF; Non-UIP 23 IPF patients included following ATS/ERS criteria
ILD: interstitial lung disease; IPF: idiopathic pulmonary fibrosis; UIP: usual interstitial pneumonia; DIP: desquamative interstitial pneumonia; NSIP: nonspecific interstitial
pneumonia; DPLD: diffuse parenchymal lung disease; ATS: American Thoracic Society; ERS: European Respiratory Society.
M. THOMEER ET AL. INTEROBSERVER AGREEMENT IN IPF DIAGNOSIS c EUROPEAN RESPIRATORY JOURNAL VOLUME 31 NUMBER 3 589
(Calmette Hospital, Lille Regional University Hospital, Lille, France).
Country coordinators: P. de Vuyst (Erasmus University Hospital, Brussels, Belgium); B. Wallaert (France); J. Behr
(Germany); S. Petruzzelli (Cardiothoracic Dept, Pisa University, Pisa, Italy); J.M.M. van den Bosch (St Antonius
Hospital, Nieuwegein, The Netherlands); E. Rodrı´guez-Becerra (Virgen del Rocı´o University Hospital, Seville, Spain); W.
MacNee (UK).
Radiology review committee: C.D.R. Flower (Evelyn Hospital, Cambridge, UK); J. Verschakelen (University Hospitals,
Catholic University of Leuven, Leuven, Belgium); F. Laurent (Cardiological Hospital, Bordeaux University Hospital,
Bordeaux, France).
Histology review committee: A.G. Nicholson (Royal Brompton Hospital, London, UK); E.K. Verbeken (University Hospitals,
Catholic University of Leuven, Leuven); F. Capron (Pitie-Salpetriere Hospital, Paris, France).
Local investigators. Belgium: M. Demedts, P. de Vuyst, E. Michiels (East Limburg Hospital, Genk), H. Slabbynck
(Middelheim General Hospital, Antwerp), M. Thomeer.
France: A. Bourdin and P. Chanez (Arnaud de Villeneuve Hospital, Montpellier), J. Cadranel (Tenon Hospital, Paris), P.
Camus (Le Bocage University Hospital, Dijon), P. Delaval (Pontchaillou Hospital, Rennes), N. Just and B. Wallaert
(Calmette Hospital, Lille Regional University Hospital, Lille, France), J.F. Muir (Bois Guillaume Hospital, Rouen). Germany:
U. Costabel, R. Baumgartner (Grosshadern Clinic, Ludwig Maximilian University, Munich), J. Behr, R. Bonnet and I
Ma¨der (Bad Berka Central Clinic, Bad Berka), R. Buhl, A.M. Kirsten (Johannes Gutenberg University Clinic, Mainz), R.
Loddenkemper (Heckeshorn Lung Clinic, Zehlendorf Clinic, Berlin), A. Meyer (Eppendorf University Hospital, Hamburg),
J. Mu¨ ller-Quernheim (Borstel Research Centre, Medical Clinic, Borstel), H. Steveling (Ruhrland Clinic, Essen, Germany), T.
Welte (Magdeburg University Clinic, Magdeburg), H. Worth (Clinic Fu¨ rth, Fu¨ rth). Italy: G. Anzalone (Prato Hospital, Prato),
G.B. Bottino (DIMI, Genoa University, Genoa), G. Bustacchini (S. Maria delle Croci Hospital, Ravenna), M. Dottorini (R.
Silvestrini Hospital, Perugia), S. Gasparini (Torrette Hospital, Torrette di Ancona), C. Giuntini (Cardiothoracic Dept, Pisa
University, Pisa), A. Rossi (IRCCS S. Matteo General Hospital, Pavia), G. Simon (Azienda Ospedaliera Villa Sofia, Palermo).
The Netherlands: F. Beaumont (Bosch Medicentrum, Locatie Grootziekengasthuis, Hertogenbosch), M. Drent (Maastricht
University Hospital, Maastricht), H.M. Jansen, J.M.M. van den Bosch, and F.J.J. van den Elshout (Rijnstate Hospital, Arnheim).
Spain: J. Ancochea Bermudez (Hospital Universitario de la Princesa, Madrid), L. Callol Sanchez (Hospital Universitario Del
Aire, Madrid), J.L. Llorente (Hospital De Cruces, Baracaldo-Bilbao), J.M. Rodriguez-Arias and I. Vigil (Hospital Sant Pau,
Barcelona), E. Rodrı´quez-Becerra (Hospital Universitario Virgen del Rocı´o, Seville).
Zambon personnel and consultants: A. Ardia (consultant), M. Sardina, G. Corvasce, and I. Lankhorst (consultant)
Current concepts on oxidative/carbonyl stress, inflammation and epigenetics in pathogenesis of chronic obstructive pulmonary disease
No full textChronic obstructive pulmonary disease (COPD) is a global health problem. The current therapies for COPD are poorly effective and the mainstays of pharmacotherapy are bronchodilators. A better understanding of the pathobiology of COPD is critical for the development of novel therapies. In the present review, we have discussed the roles of oxidative/aldehyde stress, inflammation/immunity, and chromatin remodeling in the pathogenesis of COPD. An imbalance of oxidants/antioxidants caused by cigarette smoke and other pollutants/biomass fuels plays an important role in the pathogenesis of COPD by regulating redox-sensitive transcription factors (e.g., NF-κB), autophagy and unfolded protein response leading to chronic lung inflammatory response. Cigarette smoke also activates canonical/alternative NF-κB pathways and their upstream kinases leading to sustained inflammatory response in lungs. Recently, epigenetic regulation has been shown to be critical for the development of COPD because the expression/activity of enzymes that regulate these epigenetic modifications have been reported to be abnormal in airways of COPD patients. Hence, the significant advances made in understanding the pathophysiology of COPD as described herein will identify novel therapeutic targets for intervention in COPD
Expression of SofLAC, a new laccase in sugarcane, restores lignin content but not S:G ratio of Arabidopsis lac17 mutant
No full textFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Lignin is a complex phenolic heteropolymer deposited in the secondarily thickened walls of specialized plant cells to provide strength for plants to stand upright and hydrophobicity to conducting cells for long-distance water transport. Although essential for plant growth and development, lignin is the major plant cell-wall component responsible for biomass recalcitrance to industrial processing. Peroxidases and laccases are generally thought to be responsible for lignin polymerization, but, given their broad substrate specificities and large gene families, specific isoforms involved in lignification are difficult to identify. This study used a combination of co-expression analysis, tissue/cell-type-specific expression analysis, and genetic complementation to correlate a sugarcane laccase gene, SofLAC, to the lignification process. A co-expression network constructed from 37 cDNA libraries showed that SofLAC was coordinately expressed with several phenylpropanoid biosynthesis genes. Tissue-specific expression analysis by quantitative RT-PCR showed that SofLAC was expressed preferentially in young internodes and that expression levels decrease with stem maturity. Cell-type-specific expression analysis by in situ hybridization demonstrated the localization of SofLAC mRNA in lignifying cell types, mainly in inner and outer portions of sclerenchymatic bundle sheaths. To investigate whether SofLAC is able to oxidize monolignols during lignification, the Arabidopsis lac17 mutant, which has reduced lignin levels, was complemented by expressing SofLAC under the control of the Arabidopsis AtLAC17 promoter. The expression of SofLAC restored the lignin content but not the lignin composition in complemented lac17 mutant lines. Taken together, these results suggest that SofLAC participates in lignification in sugarcane.64617691781Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)FAPESP [BIOEN 08/58035-6]CAPES [201660/2010-5]FAPESP [Ghent University Multidisciplinary Research Partnership 'Biotechnology for a Sustainable Economy'
Expression of SofLAC, a new laccase in sugarcane, restores lignin content but not S:G ratio of Arabidopsis lac17 mutant
No full textLignin is a complex phenolic heteropolymer deposited in the secondarily thickened walls of specialized plant cells to provide strength for plants to stand upright and hydrophobicity to conducting cells for long-distance water transport. Although essential for plant growth and development, lignin is the major plant cell-wall component responsible for biomass recalcitrance to industrial processing. Peroxidases and laccases are generally thought to be responsible for lignin polymerization, but, given their broad substrate specificities and large gene families, specific isoforms involved in lignification are difficult to identify. This study used a combination of co-expression analysis, tissue/cell-type-specific expression analysis, and genetic complementation to correlate a sugarcane laccase gene, SofLAC, to the lignification process. A co-expression network constructed from 37 cDNA libraries showed that SofLAC was coordinately expressed with several phenylpropanoid biosynthesis genes. Tissue-specific expression analysis by quantitative RT-PCR showed that SofLAC was expressed preferentially in young internodes and that expression levels decrease with stem maturity. Cell-type-specific expression analysis by in situ hybridization demonstrated the localization of SofLAC mRNA in lignifying cell types, mainly in inner and outer portions of sclerenchymatic bundle sheaths. To investigate whether SofLAC is able to oxidize monolignols during lignification, the Arabidopsis lac17 mutant, which has reduced lignin levels, was complemented by expressing SofLAC under the control of the Arabidopsis AtLAC17 promoter. The expression of SofLAC restored the lignin content but not the lignin composition in complemented lac17 mutant lines. Taken together, these results suggest that SofLAC participates in lignification in sugarcane
