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Binding mode of inhibitors and Cryptosporidium parvum IMP dehydrogenase: A combined ligand- and receptor-based study

, , , , &
A combined ligand- and target-based approach was used to analyse the interaction models of Cryptosporidium parvum inosine 5’-monophosphate dehydrogenase (CpIMPDH) with selective inhibitors. First, a ligand-based pharmacophore model was generated from 20 NAD+ competitive CpIMPDH inhibitors with the HipHop module. The characteristic of the NAD+ binding site of CpIMPDH was then described, and the binding modes of the representative inhibitors were studied by molecular docking. The combination of the pharmacophore model and the docking results...

PAG Camoco Maize 2016 Poster

Robert Schaefer
Genome wide association studies (GWAS) have become the de facto approach to identify agriculturally important genes. However, complex traits such as elemental accumulation are often associated with potentially hundreds of statistically significant SNPs, many of which are located outside known gene models. Identifying causal genes for complex traits quickly become unwieldy even using straightforward marker to gene mapping such as the closest flanking gene.
Here, we present a computational framework called Camoco (Co-analysis of molecular components)...

Perineural resiniferatoxin selectively inhibits inflammatory hyperalgesia-2

John K Neubert, Andrew J Mannes, , Alan C Jenkins, , & Michael J Iadarola
Copyright information:Taken from "Perineural resiniferatoxin selectively inhibits inflammatory hyperalgesia"http://www.molecularpain.com/content/4/1/3Molecular Pain 2008;4():3-3.Published online 16 Jan 2008PMCID:PMC2242785. week (N = 6), and 2 weeks (N = 5) following application of RTX (250 ng, 50 μl) to the sciatic nerve (*P < 0.05, 1 way ANOVA). An intermediate response was seen at 1 month (N = 8), and at 3 months (N = 8). Complete recovery with a normal heat withdrawal response following inflammation was observed 6 months...

Normally distributed variation in season length and corresponding strategy response

Oliver Mitesser, Norbert Weissel, Erhard Strohm &
Copyright information:Taken from "Adaptive dynamic resource allocation in annual eusocial insects: environmental variation will not necessarily promote graded control"http://www.biomedcentral.com/1472-6785/7/16BMC Ecology 2007;7():16-16.Published online 19 Dec 2007PMCID:PMC2242787. The upper row shows the frequency distribution of season length for three cases with increasing variance (a: width standard deviation = 2.9, b: = 5.8, and c: = 8.7, mean always = 50). The lower row shows the corresponding optimal strategy transitions: the fraction of sexuals produced by the colony...

Poly I:C enhances cycloheximide-induced apoptosis of tumor cells through TLR3 pathway-3

Qun Jiang, &
Copyright information:Taken from "Poly I:C enhances cycloheximide-induced apoptosis of tumor cells through TLR3 pathway"http://www.biomedcentral.com/1471-2407/8/12BMC Cancer 2008;8():12-12.Published online 17 Jan 2008PMCID:PMC2242792.mouse TLR3 antibody at the concentration of 10 μg/ml for 4 hours before being stimulated with poly I:C (100 μg/ml)/CHX (1.5 μg/ml) for 12 hours. Apoptosis were determined as above. The data is presented as the mean ± SD.

Proportion of patients with moderate/severe pain at baseline and endpoint by response category

Eija Kalso, Karen H Simpson, Robert Slappendel, Joachim Dejonckheere & Ute Richarz
Copyright information:Taken from "Predicting long-term response to strong opioids in patients with low back pain: findings from a randomized, controlled trial of transdermal fentanyl and morphine"http://www.biomedcentral.com/1741-7015/5/39BMC Medicine 2007;5():39-39.Published online 21 Dec 2007PMCID:PMC2242794.

Expressed Sequence Tags from the oomycete , an obligate parasite of the sunflower-0

Mohamed Fouad Bouzidi, Francis Parlange, Paul Nicolas & Said Mouzeyar
Copyright information:Taken from "Expressed Sequence Tags from the oomycete , an obligate parasite of the sunflower"http://www.biomedcentral.com/1471-2180/7/110BMC Microbiology 2007;7():110-110.Published online 6 Dec 2007PMCID:PMC2242796.he ESTs tested here are: , HSP 70 [GenBank:]; , Pyruvate kinase [GenBank:]; , Superoxyde dismutase [GenBank:]; , Proteasome 26 S beta subunit [GenBank:]; protein; , Asparagine synthase; , Elicitor [GenBank:]; , Cyclophilin B [GenBank:]. : molecular marker. : negative control. The PCR products were separated on 1.5% agarose gel.

Functional, genetic and bioinformatic characterization of a calcium/calmodulin kinase gene in -1

Liz Valle-Aviles, Shirley Valentin-Berrios, Ricardo R Gonzalez-Mendez & Nuri Rodriguez-Del Valle
Copyright information:Taken from "Functional, genetic and bioinformatic characterization of a calcium/calmodulin kinase gene in "http://www.biomedcentral.com/1471-2180/7/107BMC Microbiology 2007;7():107-107.Published online 29 Nov 2007PMCID:PMC2242797. the DASQTI/WSMGVI primer pair. Fifteen μl of each reaction were resolved in a 1.2% agarose gel electrophoresis. Lanes 3 and 6, show the results obtained from the RT-PCR using total RNA extracted from yeast and mycelium cells respectively, and show the 279 bp band. Lanes 2 and 5 represent the RT-PCR control for each...

Functional, genetic and bioinformatic characterization of a calcium/calmodulin kinase gene in -2

Liz Valle-Aviles, Shirley Valentin-Berrios, Ricardo R Gonzalez-Mendez & Nuri Rodriguez-Del Valle
Copyright information:Taken from "Functional, genetic and bioinformatic characterization of a calcium/calmodulin kinase gene in "http://www.biomedcentral.com/1471-2180/7/107BMC Microbiology 2007;7():107-107.Published online 29 Nov 2007PMCID:PMC2242797.he are shown in bold and underlined, and the type and location are shown.

Functional, genetic and bioinformatic characterization of a calcium/calmodulin kinase gene in -4

Liz Valle-Aviles, Shirley Valentin-Berrios, Ricardo R Gonzalez-Mendez & Nuri Rodriguez-Del Valle
Copyright information:Taken from "Functional, genetic and bioinformatic characterization of a calcium/calmodulin kinase gene in "http://www.biomedcentral.com/1471-2180/7/107BMC Microbiology 2007;7():107-107.Published online 29 Nov 2007PMCID:PMC2242797.e shown in red, the filamentous fungi CaMKs are shown in blue. The bootstrap values for each branch are shown (maximum value 1000).

Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions-0

Tomas A Larsson, Frida Olsson, , , Sydney Brenner, & Dan Larhammar
En collapsed. Human bradykinin receptor B1 was used to root the tree.Copyright information:Taken from "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions"http://www.biomedcentral.com/1471-2148/8/184BMC Evolutionary Biology 2008;8():184-184.Published online 25 Jun 2008PMCID:PMC2453138.

Venn diagrams showing the distribution and overlap of transcript modifications in Arabidopsis plantlets transferred on sucrose medium (S), sucrose plus atrazine medium (SA) and mannitol plus atrazine medium (MA)

Fanny Ramel, Cécile Sulmon, Francisco Cabello-Hurtado, Ludivine Taconnat, , Jean-Pierre Renou, , Ivan Couée & Gwenola Gouesbet
Copyright information:Taken from "Genome-wide interacting effects of sucrose and herbicide-mediated stress in : novel insights into atrazine toxicity and sucrose-induced tolerance"http://www.biomedcentral.com/1471-2164/8/450BMC Genomics 2007;8():450-450.Published online 5 Dec 2007PMCID:PMC2242805. A statistical cut off (-value ≤ 0.05 after Bonferroni correction) was used to determine which genes were significantly differentially expressed in comparison with the mannitol treatment.

Micrographs and quantification of total colony forming units-fibroblasts (CFU-F; B), unmineralized ALP colonies (CFU-ALP; C) and mineralized ALP colonies (CFU-O; D) in bone marrow stromal cell cultures of female mutant and WT mice

Luc Malaval, , Maya Boudiffa, Jia Fei, Ralph Zirngibl, Frieda Chen, Norbert Laroche, Jean-Paul Roux, Brigitte Burt-Pichat, François Duboeuf, Georges Boivin, Pierre Jurdic, , Joëlle Amédée, Laurence Vico, Janet Rossant & Jane E. Aubin
Values are the mean ± the SEM of 8–15 wells. (E) Micrographs of and female spleen cells grown with RANKL+M-CSF and stained for TRAP activity (TRAP); (F) number of TRAP cells; (G) number of osteoclasts (TRAP cells with ≥3 nuclei) formed in spleen cell and bone marrow cultures. Values are the mean ± the SEM of 12 wells. (H) Number of resorption pits on dentine slices plated with and differentiated osteoclasts; values are the mean...

(A) Nude mice were injected subcutaneously with either MDA-EV or MDA-3B tumor cells together with 100 μg of neutralizing IL-8 antibody (MAB208) or 100 μg of control antibody (anti-CD19)

Charlotte Rolny, Lorena Capparuccia, Andrea Casazza, Massimiliano Mazzone, Antonella Vallario, Alessandro Cignetti, Enzo Medico, Peter Carmeliet, Paolo M. Comoglio & Luca Tamagnone
Antibodies were administered locally into tumors again at days 2, 5, 8, and 11 after tumor transplant. Data shown are the mean tumor volume ± SD from 10 tumors per each experimental group at the day of excision (day 15). (B) To reveal metastatic dissemination from the tumors, the lungs of mice described in A were analyzed by real-time RT-PCR using species-specific Taqman probes for mouse HPRT and human HPRT transcripts. Plotted values indicate the...

(A) Single pTα CD4CD8CD25 TCRγδ cells were sorted onto OP9-DL1 monolayers

Taras Kreslavsky, Annette I. Garbe, Andreas Krueger & Harald Von Boehmer
On day 7, the contents of each well were divided into 3 parts. One part was analyzed by FACS for surface marker expression (CD45, CD4, CD8, TCRγδ, and TCRβ), the other two parts were transferred to wells with fresh OP9-DL1 monolayers coated with TCRγδ antibodies or uncoated. On day 14 cells were again analyzed for surface marker expression, and cells from anti-TCRγδ–coated wells were further transferred to uncoated wells with fresh OP9DL1 monolayers and analyzed...

(A) Lin blood cells of heterozygous CCR9-EGFP knock-in mice were fractionated according to their CD117 and CCR9 expression

Claudia Benz, Vera C. Martins, Freddy Radtke & Conrad C. Bleul
The plot is gated on Lin cells. Percentages are indicated. (B) Lin fractions with the indicated phenotypes were isolated from blood (as shown in A) and from bone marrow, and were cultured as groups of 100 cells on OP9-DL1 stromal layers for 12 and 19 d. The fraction of wells that contained T lineage–committed DN3/4 thymocytes is plotted for each time point. At least 1,200 cells cultured as 100 cells per well were assayed for...

The LSK population was analyzed by FACS in CCR9/ //Flt3∷Cre//R26R-EYFP mice

Claudia Benz, Vera C. Martins, Freddy Radtke & Conrad C. Bleul
The top left plot is gated on LSK bone marrow cells, and the histogram plots are gated on the indicated regions of interest. The fraction of EYFP, recombined cells is shown for each subset. Percentages are indicated.Copyright information:Taken from "The stream of precursors that colonizes the thymus proceeds selectively through the early T lineage precursor stage of T cell development"The Journal of Experimental Medicine 2008;205(5):1187-1199.Published online 12 May 2008PMCID:PMC2373849.

(A) LSKs were fractionated according to their Flt3 and CCR9-EGFP expression

Claudia Benz, Vera C. Martins, Freddy Radtke & Conrad C. Bleul
The FACS plot on the left is gated on Lin cells, and the plot on the right is gated on LSK cells (as shown in the plot on the left). LSK subpopulations were sorted from the indicated regions. Percentages are indicated. (B) 100 cells of the indicated precursors were sorted onto OP9-DL1 stroma, cultured for 9 d, and analyzed by FACS. The levels of CCR9-EGFP and CD44 expression are indicative of the maturity of each...

The TAP-deficient cell TAP and the TAP-rescued cell were transduced with wild-type mMR1 or the mMR1/L chimeric molecule

, Susan Gilfillan, , Bruce Thompson, , Andrea J. Sant, , Olivier Lantz & Ted H. Hansen
(A) Thin lines indicate the background with secondary antibody only; thick lines indicate the staining with annotated antibodies. (B) Activation of MAIT cell hybridoma 6C2 (mean ± the SD) was observed with no additional antibody (No Ab), anti-MR1 blockade, or isotype-matched irrelevant Ab (34–2-12), as applied in other MAIT cell activation assays. Data are representative of two experiments.Copyright information:Taken from "MR1 uses an endocytic pathway to activate mucosal-associated invariant T cells"The Journal of Experimental Medicine...

(A) Heatmap with cluster dendrogram of the differentially expressed genes (log2 fold change vs

Philipp S. Lange, Juan C. Chavez, John T. Pinto, Giovanni Coppola, , Tim M. Townes, Daniel H. Geschwind & Rajiv R. Ratan
control) at a false discovery rate of 5%. Unsupervised clustering groups samples by genotype and by treatment. Genes are in rows and samples are in columns. Column color coding is as follows: red, ATF4 versus ATF4 untreated neurons; blue, HCA-treated ATF4 versus untreated ATF4 neurons; and green, HCA-treated ATF4 versus untreated ATF4 neurons. (B) The number of genes that are up- (red) and down-regulated (green). Shown are three different contrasts: ATF4 versus ATF4 untreated neurons,...

Calretinin and calbindin-28 kDa are distinctly distributed in the ganglion cell and nerve fiber layer as seen in retinal whole-mounts

Deb Kumar Mojumder, Theodore G. Wensel & Laura J. Frishman
Double labeling for calretinin (red) and calbindin-28 kDa (green) in the ganglion cell layer (GCL)/nerve fiber layer (NFL) shows that labeling for each was present in a distinct set of neurons. Calbindin-28 kDa positive cell bodies are indicated by arrowheads. Some calretinin-positive neurons show processes (arrow) that ascend distally. Note the discontinuous staining pattern of calretinin in the NFL in contrast to a smoother staining pattern for calbindin-28 kDa. , A single confocal optical section...

Stimulated macrophages demonstrated a nuclear retention of HMGB1 in co-cultures with oxaliplatin

Therese Östberg, Heidi Wähämaa, Karin Palmblad, Norimasa Ito, Pernilla Stridh, Maria Shoshan, Michael T Lotze, Helena Erlandsson Harris & Ulf Andersson
RAW 264.7 macrophage-like cells were cultured without exogenous stimulus or with IFN-γ and LPS alone or with IFN-γ and LPS in the presence of 0.5 μM oxaliplatin . Immunostaining for HMGB1 (green), nucleus (blue) and the cytoskeletal protein β-actin (red) was performed in fixed cells after a culture time of 24 h. Almost all nuclei demonstrated strong HMGB1 expression in resting cells , while the nuclear HMGB1 was as expected substantially reduced in IFN-γ- and...

Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets-5

&
Des and 162 edges. Colors of nodes represent Gene Ontology annotations. Supplementary Tables 2 and 3 list proteins with detailed Gene Ontology annotations, with ranking according to the degree of perturbation.Copyright information:Taken from "Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets"http://www.biomedcentral.com/1752-0509/2/56BMC Systems Biology 2008;2():56-56.Published online 30 Jun 2008PMCID:PMC2488323.

Inhibition of inflammatory mediator generation from activated human macrophages

Tina Kauss, Daniel Moynet, Jérôme Rambert, Abir Al-Kharrat, , Denis Thiolat, Rachid Ennemany, Fawaz Fawaz &
Rutoside (RU) decreased the generation of tumor necrosis factor-alpha (TNF-α), interleukin (IL)-1β, and IL-6 but not IL-10 from activated human macrophages. Inhibition of nitric oxide (NO) generation from human activated macrophages after their incubation with various RU concentrations. RU decreases both intracellular NO (upper panel) and extracellular nitrites (lower panel). Specific inducible nitric oxide synthase inhibitor (L-NIL, 1 mM) was used as control. Results from three different cell preparations ± standard deviation are shown. *value...

IL-7 causes proteoglycan release, but not nitric oxide production, in cartilage explants

David Long, Simon Blake, Xiao-Yu Song, Michael Lark & Richard F Loeser
Cartilage explants were stimulated for 72 hours with 10 ng/ml recombinant human IL-7 before media collection. Medium was analyed for sulfated glycosaminoglycan (sGAG) using the dimethylmethylene blue assay and normalized for the wet weight of the tissue. Total nitrite was measured in the media as a marker for nitric oxide production using commercially available colorimetric nitrate/nitrite assay kit. Results represent four experiments.Copyright information:Taken from "Human articular chondrocytes produce IL-7 and respond to IL-7 with increased...

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