High frequency of inadequate test requests for antiphospholipid antibodies in daily clinical practice

Abstract Background: We have empirically noted that many physicians routinely request anti-phospholipid antibodies (aPL) without a correct clinical indication. The aim of this study was to evaluate retrospectively whether aPL testing at our Thrombosis Centre was justified. Methods: Medical records from 520 subjects for aPL screening tests for various clinical conditions were reviewed. The aPL screening tests were: lupus anticoagulant (LA), anti-cardiolipin antibodies (aCL) and anti-β(2) glycoptotein I (aβ(2) GPI). Requests for aPL screening were divided into justified, potentially justified or not adequately justified. Results: aPL testing requests were considered justified in 358 (69%) patients, potentially justified in 66 (12.6%) and not adequately justified in 96 (18.4%). LA was positive in 65 (18%) of justified requests and in only one (1%) of the 96 potentially justified requests. None of the 66 not adequately justified for aPL testing was positive for LA. aβ(2) ..

Isotope correlations as a probe for freeze-out characterization: central 124Sn+64Ni, 112Sn+58Ni collisions

124Sn+64Ni and 112Sn+58Ni reactions at 35 AMeV incident energy were studied with the forward part of CHIMERA multi-detector. The most central collisions were selected by means of a multidimensional analysis. The characteristics of the source formed in the central collisions, as size, temperature and volume, were inspected. The measured isotopes of light fragments (3 <= Z <=8) were used to examine isotope yield ratios that provide information on the free neutron to proton densities.Comment: 4 pages, Contribution to 8th International Conference on Nucleus-Nucleus Collisions, Moscow 200

Histone deacetylases as new therapy targets for platinum-resistant epithelial ovarian cancer

Introduction: In developed countries, ovarian cancer is the fourth most common cancer in women. Due to the nonspecific symptomatology associated with the disease many patients with ovarian cancer are diagnosed late, which leads to significantly poorer prognosis. Apart from surgery and radiotherapy, a substantial number of ovarian cancer patients will undergo chemotherapy and platinum based agents are the mainstream first-line therapy for this disease. Despite the initial efficacy of these therapies, many women relapse; therefore, strategies for second-line therapies are required. Regulation of DNA transcription is crucial for tumour progression, metastasis and chemoresistance which offers potential for novel drug targets. Methods: We have reviewed the existing literature on the role of histone deacetylases, nuclear enzymes regulating gene transcription. Results and conclusion: Analysis of available data suggests that a signifant proportion of drug resistance stems from abberant gene expression, therefore HDAC inhibitors are amongst the most promising therapeutic targets for cancer treatment. Together with genetic testing, they may have a potential to serve as base for patient-adapted therapies

De Novo assembly and transcriptome analysis of the mediterranean fruit fly ceratitis capitata early embryos

The agricultural pest Ceratitis capitata, also known as the Mediterranean fruit fly or Medfly, belongs to the Tephritidae family, which includes a large number of other damaging pest species. The Medfly has been the first non-drosophilid fly species which has been genetically transformed paving the way for designing geneticbased pest control strategies. Furthermore, it is an experimentally tractable model, in which transient and transgene-mediated RNAi have been successfully used. We applied Illumina sequencing to total RNA preparations of 8-10 hours old embryos of C. capitata, This developmental window corresponds to the blastoderm cellularization stage. In summary, we assembled 42,614 transcripts which cluster in 26,319 unique transcripts of which 11,045 correspond to protein coding genes; we identified several hundreds of long ncRNAs; we found an enrichment of transcripts encoding RNA binding proteins among the highly expressed transcripts, such as CcTRA-2, known to be necessary to establish and, most likely, to maintain female sex of C. capitata. Our study is the first de novo assembly performed for Ceratitis capitata based on Illumina NGS technology during embryogenesis and it adds novel data to the previously published C. capitata EST databases. We expect that it will be useful for a variety of applications such as gene cloning and phylogenetic analyses, as well as to advance genetic research and biotechnological applications in the Medfly and other related Tephritidae

The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain

[EN] Phytophthora is one of the most important and aggressive plant pathogenic genera in agriculture and forestry. Early detection and identification of its pathways of infection and spread are of high importance to minimize the threat they pose to natural ecosystems. eDNA was extracted from soil and water from forests and plantations in the north of Spain. Phytophthora-specific primers were adapted for use in high-throughput Sequencing (HTS). Primers were tested in a control reaction containing eight Phytophthora species and applied to water and soil eDNA samples from northern Spain. Different score coverage threshold values were tested for optimal Phytophthora species separation in a custom-curated database and in the control reaction. Clustering at 99% was the optimal criteria to separate most of the Phytophthora species. Multiple Molecular Operational Taxonomic Units (MOTUs) corresponding to 36 distinct Phytophthora species were amplified in the environmental samples. Pyrosequencing of amplicons from soil samples revealed low Phytophthora diversity (13 species) in comparison with the 35 species detected in water samples. Thirteen of the MOTUs detected in rivers and streams showed no close match to sequences in international sequence databases, revealing that eDNA pyrosequencing is a useful strategy to assess Phytophthora species diversity in natural ecosystems.This project has been supported by the Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (EUPHRESCO-CEP: "Current and Emerging Phytophthoras: Research Supporting Risk Assessment And Risk Management"). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Català, S.; Pérez Sierra, AM.; Abad Campos, P. (2015). The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain. 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Pyrosequencing enumerates and contrasts soil microbial diversity. The ISME Journal, 1(4), 283-290. doi:10.1038/ismej.2007.53Acosta-Martínez, V., Dowd, S., Sun, Y., & Allen, V. (2008). Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biology and Biochemistry, 40(11), 2762-2770. doi:10.1016/j.soilbio.2008.07.022Jumpponen, A., & Jones, K. L. (2009). Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperateQuercus macrocarpaphyllosphere. New Phytologist, 184(2), 438-448. doi:10.1111/j.1469-8137.2009.02990.xNilsson, R. H., Ryberg, M., Abarenkov, K., Sjökvist, E., & Kristiansson, E. (2009). The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiology Letters, 296(1), 97-101. doi:10.1111/j.1574-6968.2009.01618.xCoince, A., Caël, O., Bach, C., Lengellé, J., Cruaud, C., Gavory, F., … Buée, M. (2013). Below-ground fine-scale distribution and soil versus fine root detection of fungal and soil oomycete communities in a French beech forest. Fungal Ecology, 6(3), 223-235. doi:10.1016/j.funeco.2013.01.002Vannini, A., Bruni, N., Tomassini, A., Franceschini, S., & Vettraino, A. M. (2013). Pyrosequencing of environmental soil samples reveals biodiversity of thePhytophthoraresident community in chestnut forests. FEMS Microbiology Ecology, 85(3), 433-442. doi:10.1111/1574-6941.12132Jerde, C. L., Mahon, A. R., Chadderton, W. L., & Lodge, D. M. (2011). «Sight-unseen» detection of rare aquatic species using environmental DNA. Conservation Letters, 4(2), 150-157. doi:10.1111/j.1755-263x.2010.00158.xMonchy, S., Sanciu, G., Jobard, M., Rasconi, S., Gerphagnon, M., Chabé, M., … Sime-Ngando, T. (2011). Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing. Environmental Microbiology, 13(6), 1433-1453. doi:10.1111/j.1462-2920.2011.02444.xJobard, M., Rasconi, S., Solinhac, L., Cauchie, H.-M., & Sime-Ngando, T. (2012). Molecular and morphological diversity of fungi and the associated functions in three European nearby lakes. Environmental Microbiology, 14(9), 2480-2494. doi:10.1111/j.1462-2920.2012.02771.xLivermore, J. A., & Mattes, T. E. (2013). Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high-throughput sequencing sets. Environmental Microbiology, 15(8), 2333-2341. doi:10.1111/1462-2920.12106NAKAYAMA, J., JIANG, J., WATANABE, K., CHEN, K., NINXIN, H., MATSUDA, K., … LEE, Y.-K. (2013). Up to Species-level Community Analysis of Human Gut Microbiota by 16S rRNA Amplicon Pyrosequencing. Bioscience of Microbiota, Food and Health, 32(2), 69-76. doi:10.12938/bmfh.32.69CREER, S., & SINNIGER, F. (2012). Cosmopolitanism of microbial eukaryotes in the global deep seas. Molecular Ecology, 21(5), 1033-1035. doi:10.1111/j.1365-294x.2012.05437.xDavey, M. L., Heegaard, E., Halvorsen, R., Kauserud, H., & Ohlson, M. (2012). Amplicon-pyrosequencing-based detection of compositional shifts in bryophyte-associated fungal communities along an elevation gradient. Molecular Ecology, 22(2), 368-383. doi:10.1111/mec.12122Weber, C. F., Vilgalys, R., & Kuske, C. R. (2013). Changes in Fungal Community Composition in Response to Elevated Atmospheric CO2 and Nitrogen Fertilization Varies with Soil Horizon. Frontiers in Microbiology, 4. doi:10.3389/fmicb.2013.00078Bergmark, L., Poulsen, P. H. B., Al-Soud, W. A., Norman, A., Hansen, L. H., & Sørensen, S. J. (2012). Assessment of the specificity of Burkholderia and Pseudomonas qPCR assays for detection of these genera in soil using 454 pyrosequencing. FEMS Microbiology Letters, 333(1), 77-84. doi:10.1111/j.1574-6968.2012.02601.xLi, L., Abu Al-Soud, W., Bergmark, L., Riber, L., Hansen, L. H., Magid, J., & Sørensen, S. J. (2013). Investigating the Diversity of Pseudomonas spp. in Soil Using Culture Dependent and Independent Techniques. Current Microbiology, 67(4), 423-430. doi:10.1007/s00284-013-0382-xSCHENA, L., HUGHES, K. J. D., & COOKE, D. E. L. (2006). Detection and quantification ofPhytophthora ramorum,P. kernoviae,P. citricolaandP. quercinain symptomatic leaves by multiplex real-time PCR. Molecular Plant Pathology, 7(5), 365-379. doi:10.1111/j.1364-3703.2006.00345.xTooley, P. W., Martin, F. N., Carras, M. M., & Frederick, R. D. (2006). Real-Time Fluorescent Polymerase Chain Reaction Detection ofPhytophthora ramorumandPhytophthora pseudosyringaeUsing Mitochondrial Gene Regions. Phytopathology, 96(4), 336-345. doi:10.1094/phyto-96-0336Pavón, C. F., Babadoost, M., & Lambert, K. N. (2008). Quantification of Phytophthora capsici Oospores in Soil by Sieving-Centrifugation and Real-Time Polymerase Chain Reaction. Plant Disease, 92(1), 143-149. doi:10.1094/pdis-92-1-0143Than, D. J., Hughes, K. J. D., Boonhan, N., Tomlinson, J. A., Woodhall, J. W., & Bellgard, S. E. (2013). A TaqMan real-time PCR assay for the detection ofPhytophthora‘taxon Agathis’ in soil, pathogen of Kauri in New Zealand. Forest Pathology, 43(4), 324-330. doi:10.1111/efp.12034Chen, W., Djama, Z. R., Coffey, M. D., Martin, F. N., Bilodeau, G. J., Radmer, L., … Lévesque, C. A. (2013). Membrane-Based Oligonucleotide Array Developed from Multiple Markers for the Detection of Many Phytophthora Species. Phytopathology, 103(1), 43-54. doi:10.1094/phyto-04-12-0092-rScibetta, S., Schena, L., Chimento, A., Cacciola, S. O., & Cooke, D. E. L. (2012). A molecular method to assess Phytophthora diversity in environmental samples. Journal of Microbiological Methods, 88(3), 356-368. doi:10.1016/j.mimet.2011.12.012Català S, Pérez-Sierra A, Berbegal M, Abad-Campos P. First approach into the knowledge of the Phytophthora species diversity in Mediterranean holm oak forests based on 454 parallel amplicon pyrosequencing of soil samples. Phytophthora in Forest and Natural Ecosystems 6th International IUFRO Working Party 7.02.09 Meeting, Córdoba, Spain, pp 34; 2012.Català S, Pérez-Sierra A, Beltrán A, Abad-Campos P. Next Generation Sequencing shows Phytophthora species diversity in soil samples of Macaronesian laurel forests from the Canary Islands. Phytophthora in Forest and Natural Ecosystems 6th International IUFRO Working Party 7.02.09 Meeting, Córdoba, Spain, pp. 86; 2012.Cooke, D. E. L., Drenth, A., Duncan, J. M., Wagels, G., & Brasier, C. M. (2000). A Molecular Phylogeny of Phytophthora and Related Oomycetes. Fungal Genetics and Biology, 30(1), 17-32. doi:10.1006/fgbi.2000.1202Andrews S. FastQC: a quality control tool for high throughput sequence data. Available: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/Chou, H.-H., & Holmes, M. H. (2001). DNA sequence quality trimming and vector removal. Bioinformatics, 17(12), 1093-1104. doi:10.1093/bioinformatics/17.12.1093Altschul, S. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389-3402. doi:10.1093/nar/25.17.3389Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792-1797. doi:10.1093/nar/gkh340Gouy, M., Guindon, S., & Gascuel, O. (2009). SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building. Molecular Biology and Evolution, 27(2), 221-224. doi:10.1093/molbev/msp259Park, J., Park, B., Veeraraghavan, N., Jung, K., Lee, Y.-H., Blair, J. E., … Kang, S. (2008). Phytophthora Database: A Forensic Database Supporting the Identification and Monitoring of Phytophthora. Plant Disease, 92(6), 966-972. doi:10.1094/pdis-92-6-0966Vettraino, A. M., Bonants, P., Tomassini, A., Bruni, N., & Vannini, A. (2012). Pyrosequencing as a tool for the detection ofPhytophthoraspecies: error rate and risk of false Molecular Operational Taxonomic Units. Letters in Applied Microbiology, 55(5), 390-396. doi:10.1111/j.1472-765x.2012.03310.xJung, T., & Burgess, T. I. (2009). Re-evaluation of Phytophthora citricola isolates from multiple woody hosts in Europe and North America reveals a new species, Phytophthora plurivora sp. nov. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 95-110. doi:10.3767/003158509x442612Deagle, B. E., Eveson, J. P., & Jarman, S. N. (2006). Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces. Frontiers in Zoology, 3(1). doi:10.1186/1742-9994-3-11Dejean, T., Valentini, A., Duparc, A., Pellier-Cuit, S., Pompanon, F., Taberlet, P., & Miaud, C. (2011). Persistence of Environmental DNA in Freshwater Ecosystems. PLoS ONE, 6(8), e23398. doi:10.1371/journal.pone.0023398Guha Roy S, Grunwald NJ. The plant destroyer genus Phytophthora in the 21st century. In book: Review of Plant Pathology, Edition: Volume 6, Publisher: Scientific Publishers (India), Jodhpur, Editors: B.N.Chakraborty, B.B.L.Thakore, pp. In press; 2014.Brasier, C. M., Cooke, D. E. L., Duncan, J. M., & Hansen, E. M. (2003). Multiple new phenotypic taxa from trees and riparian ecosystems in Phytophthora gonapodyides-P. megasperma ITS Clade 6, which tend to be high-temperature tolerant and either inbreeding or sterile. Mycological Research, 107(3), 277-290. doi:10.1017/s095375620300738xHüberli, D., Hardy, G. E. S. J., White, D., Williams, N., & Burgess, T. I. (2013). 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Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Comparison between recombinant and rabbit thromboplastin in the management of patients on oral anticoagulant therapy

Abstract The aim of this study was to compare recombinant thromboplastin (rTF, ISI = 0.82) with rabbit thromboplastin (RT, ISI = 1.46) in order to evaluate which performed better in our thrombosis centre. To this purpose we randomized 67 patients to be double-blind monitored in two groups for three months either with PT performed with RT or with PT performed with rTF. After this period each patient was shifted to the other group. We considered the following as end points of the study: percentages of PT results within the therapeutic range, number of visits and therapeutic dose adjustments per patient. The &quot;last check in file&quot; method was used to evaluate the laboratory quality of oral anticoagulation for both thromboplastins. The results show that there was no difference in the number of visits per patient between the two groups: 6.9 +/- 1.7 in the rTF group versus 7.3 +/- 1.9 in the RT group (p = 0.19). The variations of therapeutic dose per patient were not different in the two gr..