Current challenges in software solutions for mass spectrometry-based quantitative proteomics

This work was in part supported by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme; The Netherlands Proteomics Centre, embedded in The Netherlands Genomics Initiative; The Netherlands Bioinformatics Centre; and the Centre for Biomedical Genetics (to S.C., B.B. and A.J.R.H); by NIH grants NCRR RR001614 and RR019934 (to the UCSF Mass Spectrometry Facility, director: A.L. Burlingame, P.B.); and by grants from the MRC, CR-UK, BBSRC and Barts and the London Charity (to P.C.

Design and Integration of All-Silicon Fiber-Optic Receivers for Multi-Gigabit Chip-to-Chip Links

This paper presents a top-down approach to the design of all-silicon CMOS-based fully integrated optical receivers. From the system-level requirements, we determine the optimum block-level specifications, based on which the individual building blocks are designed. Measurement results of the manufactured design show operation at data rates exceeding 2.5-Gbps/channel for the detector, the amplification and the clock and data recovery circuits. This proof of concept is the first step towards design optimized, completely integrated, multi-channel optical receivers for high-bandwidth short-distance chip-to-chip interconnects

Demonstration of the histopathological and immunohistochemical effects of a novel hemostatic agent, ankaferd blood stopper, on vascular tissue in a rat aortic bleeding model

Background: Ankaferd Blood Stopper®(ABS) is a folkloric medicinal plant extract used as a hemostatic agent in traditional Turkish medicine. This experimental study investigated the histopathological and immunohistochemical effects of ABS on vascular tissue in a rat model of aortic bleeding.Methods: Four groups of 11 Wistar albino rats were used. The abdominal aortas of the rats were wounded; an ABS-soaked tampon was applied to rats in Groups 1 and 3, and a plain gauze tampon was applied to rats in Groups 2 and 4 until the bleeding stopped. The bleeding time was recorded. Immediately following sacrificing, the arteriotomy sites from Groups 1 and 2 were removed. The abdominal incisions in Groups 3 and 4 were closed following hemostasis. On Day 7 of the study, Group 3 and 4 rats were sacrificed and the abdominal aorta arteriotomy sites were removed for histopathological and immunohistochemical evaluation.Results: The mean bleeding time in 15 animals in Groups 2 and 4 was 4.9 ± 0.6 s, and in 22 animals in Groups 1 and 3 was 3.1 ± 0.6 s. Distal aortic occlusion was not observed on either Day 1 or 7 in any group. Significantly more widespread and dense endothelial nitric oxide synthase (eNOS) staining was observed in Group 1 animals than Group 2. On Days 1 and 7 after application of ABS, histopathological changes, consisting of necrosis, inflammation, and endothelial cell loss, in the rat abdominal aortas did not differ between Groups 1 and 2. The basophilic discoloration in the ABS group on the operation day was a result of a foreign body reaction and hemosiderin-loaded histiocyte accumulation, which occurred on Day 7.Conclusions: In this study, hemostasis was successfully achieved with ABS in rat abdominal aortas. No histopathological change was found in the rat abdominal aortas between the ABS and control groups on Days 1 and 7. Further studies on the long-term effects of foreign body reactions and hemosiderin-loaded histiocyte accumulation are required. © 2010 Kandemir et al; licensee BioMed Central Ltd

The state of the art in the analysis of two-dimensional gel electrophoresis images

Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments. Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments. We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results. Challenges for analysis software as well as good practices are highlighted. We emphasize image warping and related methods that are able to overcome the difficulties that are due to varying migration positions of spots between gels. Spot detection, quantitation, normalization, and the creation of expression profiles are described in detail. The recent development of consensus spot patterns and complete expression profiles enables one to take full advantage of statistical methods for expression analysis that are well established for the analysis of DNA microarray experiments. We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field

Composição química e toxicidade de óleos essenciais para o pulgão-verde Schizaphis graminum (Rondani, 1852)

Este trabalho teve como objetivo identificar e quantificar os constituintes dos óleos essenciais de Illicum verum, Ageratum conyzoides, Piper hispidinervum e Ocotea odorifera, bem como avaliar a toxicidade para o pulgão-verde Schizaphis graminum. A qualificação dos constituintes foi realizada por meio de um cromatógrafo gasoso + espectrômetro de massas, e a quantificação, por um cromatógrafo gasoso + detector de ionização de chama, ambos com uma coluna DB5. O método de hidrodestilação promoveu um rendimento (p/p) de 3,81% para I. verum, 0,46% para A. conyzoides, 2,85% para P. hispidinervum e 0,68% para O. odorífera. Já os componentes majoritários foram: precoceno (87,0%) e (E)-cariofileno (7,1%) para A. conyzoides; (E)-anetol (90,4%), limoneno (2,6%) e metil-chavicol (1,3%) para I. verum; metil-eugenol (81,2%) e safrol (10,6%) para Ocotea odorífera; e safrol (82,5%) e α-terpinoleno (13,4%) para P. hispidinervum. Pelos testes de toxicidade aguda (24 horas) com folhas de sorgo ou papel-filtro contaminados, verificou-se que o óleo de A. conyzoides foi o mais tóxico para o pulgão, com CL50 de 7,13 e 7,08 µL óleo/cm2 respectivamente, seguido por O. odorifera com CL50 de 11,80 e 103,00 µL óleo/cm2 respectivamente; I. verum de 51,80 µL óleo/cm2 em ambos os substratos; e o menos tóxico foi o óleo essencial de P. hispidinervum, com CL50 de 62,50 e 143,00 µL óleo/cm2, respectivamente. Dessa maneira, sugere-se que o uso dos óleos essenciais pode representar uma nova ferramenta em programas de manejo integrado de pragas.The aim of this study was to assess the chemical composition of essential oils of Illicum verum, Ageratum conyzoides, Piper hispidinervum and Ocotea odorífera, as well as their toxicity to the green-aphid Schizaphis graminum. Compound identification was carried out with gas chromatography + mass spectrometry, and quantification with gas chromatography + flame ionization detector, both with DB5 column. The hydrodistillation process promoted oil yield of 3.81% for I. verum; 0.46% for A. conyzoides; 2.85 % for P. hispidinervum; and 0.68 % for O. odorífera. The major components from the oils of A. conyzoides was precocene (87.0%) and (E)-caryophyllene (7.1%); (E)-anethol (90.4%), limonene (2.6%) and methyl-chavicol (1.3%) for I. verum; methyleugenol (81.2%) and safrole (10.6%) for O. odorifera; and safrole (82.5%) and α-terpinolene (13.4%) for P. hispidinervum. The acute toxicity test (24 hours) performed by contact in sorghum leaves or contaminated filter-paper showed that the higher toxicity occur with essential oils of A. conyzoides, with LC50 of 7.01 and 7.01 µg oil/cm2, respectively; followed by O. odorifera, with LC50 of 17.10 and 66.70 µg oil/cm2, respectively; I. verum, with LC50 of 66.40 and 65.40 µg oil/cm2, respectively; and low toxicity was observed for the P. hispidinervum essential oil, with LC50 of 64.00 and 143.00 oil/cm2, respectively. With the results obtained in this research, we can state that the use of these essential oils can be a new tool in integrated pest management.Universidade Federal de São João Del Rei Departamento de Ciências NaturaisUniversidade Federal de Lavras Departamento de QuímicaUFLA Departamento de EntomologiaUniversidade Estadual Paulista Júlio de Mesquita FilhoUniversidade Estadual Paulista Júlio de Mesquita Filh