Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data

<p>Abstract</p> <p>Background</p> <p>Time-course microarray experiments are being increasingly used to characterize dynamic biological processes. In these experiments, the goal is to identify genes differentially expressed in time-course data, measured between different biological conditions. These differentially expressed genes can reveal the changes in biological process due to the change in condition which is essential to understand differences in dynamics.</p> <p>Results</p> <p>In this paper, we propose a novel method for finding differentially expressed genes in time-course data and across biological conditions (say <it>C</it>₁and <it>C</it>₂). We model the expression at <it>C</it>₁using Principal Component Analysis and represent the expression profile of each gene as a linear combination of the dominant Principal Components (PCs). Then the expression data from <it>C</it>₂is projected on the developed PCA model and scores are extracted. The difference between the scores is evaluated using a hypothesis test to quantify the significance of differential expression. We evaluate the proposed method to understand differences in two case studies (1) the heat shock response of wild-type and HSF1 knockout mice, and (2) cell-cycle between wild-type and Fkh1/Fkh2 knockout Yeast strains.</p> <p>Conclusion</p> <p>In both cases, the proposed method identified biologically significant genes.</p

Redirecting T Cells to Ewing's Sarcoma Family of Tumors by a Chimeric NKG2D Receptor Expressed by Lentiviral Transduction or mRNA Transfection

We explored the possibility to target Ewing's sarcoma family of tumors (ESFT) by redirecting T cells. To this aim, we considered NKG2D-ligands (NKG2D-Ls) as possible target antigens. Detailed analysis of the expression of MICA, MICB, ULBP-1, -2, and -3 in fourteen ESFT cell lines revealed consistent expression of at least one NKG2D-L. Thus, for redirecting T cells, we fused a CD3ζ/CD28-derived signaling domain to the ectodomain of NKG2D, however, opposite transmembrane orientation of this signaling domain and NKG2D required inverse orientation fusion of either of them. We hypothesized that the particularly located C-terminus of the NKG2D ectodomain should allow reengineering of the membrane anchoring from a native N-terminal to an artificial C-terminal linkage. Indeed, the resulting chimeric NKG2D receptor (chNKG2D) was functional and efficiently mediated ESFT cell death triggered by activated T cells. Notably, ESFT cells with even low NKG2D-L expression were killed by CD8pos and also CD4pos cells. Both, mRNA transfection and lentiviral transduction resulted in high level surface expression of chNKG2D. However, upon target-cell recognition receptor surface levels were maintained by tranfected RNA only during the first couple of hours after transfection. Later, target-cell contact resulted in strong and irreversible receptor down-modulation, whereas lentivirally mediated expression of chNKG2D remained constant under these conditions. Together, our study defines NKG2D-Ls as targets for a CAR-mediated T cell based immunotherapy of ESFT. A comparison of two different methods of gene transfer reveals strong differences in the susceptibility to ligand-induced receptor down-modulation with possible implications for the applicability of RNA transfection

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

Ambulatory EEG

Ambulatory EEG (A-EEG) allows long-term EEG monitoring under dynamic conditions: patients, therefore, are not confined to a small room, but they are free to perform their normal daily activities. This method is fairly comfortable for the patient and relatively inexpensive as it does not require hospitalisation. The usefulness of an A-EEG includes a wide spectrum of advantages, the detection of epileptiform activity not evidenced during standard EEG being one of the main ones. Other important A-EEG advantages is its utility in the differential diagnosis between epileptic and non-epileptic manifestations, in the confirmation of drug efficacy or in the detection of epileptiform activity during slee

The dispersal of vascular plants in a forest mosaic by a guild of mammalian herbivores

Endozochorous seed dispersal by herbivores can affect plant spatial dynamics and macroecological patterns. We have investigated the number and species composition of viable seeds deposited in faeces of a full guild of macroherbivores (four deer and two lagomorph species) in a forest in eastern Britain. One hundred and one plant species germinated from faecal pellet material, 85 of which were among the 247 vascular plant species recorded in the forest. However, three species – Chenopodium album, Urtica dioica and Agrostis stolonifera – comprised 56% of the seedlings recorded. Of the species recorded in faecal samples, 36% had no recognised dispersal mechanism, while very few (7%) were adapted to endozoochorous dispersal (fleshy fruit or nut). The number of species dispersed by the herbivores was ranked Cervus elaphus and Dama dama (96) > Capreolus capreolus (40) > Muntiacus reevesi (31) > Oryctolagus cuniculus (21) > Lepus europaeus (19), with the other taxa dispersing subsets of those dispersed by C. elpahus and D. dama. The invasive M. reevesi deposited the fewest seeds per gram of faecal pellet material (0.4 g−1) and hence fewer seeds per unit area than other deer species despite their numerical dominance, while C. elaphus/D. dama deposited the most (0.43 seeds m−2 year−1). Due to differences in faecal seed density among habitats combined with the ranging behaviour of animals, more seeds were deposited in younger stands, enhancing the potential contribution of macroherbivores to population persistence by dispersal and colonisation in a successional mosaic