88,778 Works

Substrates for helicase assays generated by PCR

Jae-Ho Shin, John N. Reeve & Zvi Kelman
Copyright information:Taken from "Use of a restriction enzyme-digested PCR product as substrate for helicase assays"Nucleic Acids Research 2005;33(1):e8-e8.Published online 13 Jan 2005PMCID:PMC546180.© 2005, the authors © A PCR product and its restriction fragment derivatives are shown. PCR reactions were performed as described in Materials and Methods with P-labeled primer, and products were purified using the QIAquick PCR purification kit (Qiagen) (lane 1) and digest with PstI (lane 2), EcoRI (lane 3) and SmaI (lane 4)...

Xenoestrogen-Induced ERK-1 and ERK-2 Activation via Multiple Membrane-Initiated Signaling Pathways-1

Nataliya N. Bulayeva & Cheryl S. Watson
Copyright information:Taken from "Xenoestrogen-Induced ERK-1 and ERK-2 Activation via Multiple Membrane-Initiated Signaling Pathways"Environmental Health Perspectives 2004;112(15):1481-1487.Published online 28 Jul 2004PMCID:PMC1325963.This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original DOI.

A Case Study in Software Product Lines - The Case of the Mobile Game Domain

Leandro Nascimento, Eduardo Almeida & Silvio Meira
Software Product Lines (SPL) processes aregradually being adopted by many companies in severaldomains. A particular domain where the adoption ofsuch processes may bring relevant benefits is themobile applications domain given the big diversity ofhandsets, although the characteristics of this domainusually create barriers to apply these processes inpractice, such as, restrictions of memory size andprocessing power and different API implementationsby different manufacturers. In this context, this workpresents briefly a practical approach to implementcore assets in a...

Lecture notes in population genetics

Kent Holsinger
Lecture notes from my graduate course in population genetics. Topics covered include basic principles of Hardy-Weinberg, population structure, drift, mutation, selection, quantitatitve genetics, molecular evolution, and phylogeography. Please contact me if you find errors or places where the explanations are unclear or incomplete. The first link below will take you to the course website. The second will take you to a Github repository in which you'll find the LaTeX source and associated files needed to...

(A) Net K and H flux kinetics measured in 6-d-old seedlings of Baart 46 cultivar following 80 mM NaCl treatment

Tracey Ann Cuin, Stewart A. Betts, Rémi Chalmandrier & Sergey Shabala
Fluxes were measured in the mature zone, about 10 mm from the root tip. Means ±SE (=6). (B) Mean net K flux from each of the four cultivars over the first 60 min after NaCl application (80 mM). Means ±SE (=6). (C) Peak H efflux values measured 2 min after NaCl stress onset in four wheat cultivars. Means ±SE (=6). In all MIFE measurements, the sign convention is efflux negative.Copyright information:Taken from "A root's ability...

Reactivity of GS-I and VVA lectins with an array of carbohydrate probes was tested by a standard ELISA

Soheila Korourian, Eric Siegel, Thomas Kieber-Emmons & Behjatolah Monzavi-Karbassi
Carbohydrate probes include: 1, GalNAcα 1→3GalNAcα-PAA; 2, Galβ1→4GlcNAcβ-PAA; 3, Galβ1→3GalNAcα-PAA; 4, GlcNAcβ1→3Galβ-PAA; 5, Galα1→3Galβ-PAA; 6, GlcNAcβ1→4GlcNAcβ-PAA; 7, β-GalNAc-PAA. The starting concentration of each lectin was 10 μg/ml that was further serially diluted. The assay was repeated three times with similar results. SD is shown for reactive sugars only.Copyright information:Taken from "Expression analysis of carbohydrate antigens in ductal carcinoma of the breast by lectin histochemistry"http://www.biomedcentral.com/1471-2407/8/136BMC Cancer 2008;8():136-136.Published online 14 May 2008PMCID:PMC2394536.

MetHb levels in room air and argon chamber.

Melissa A Qazi, Fabiola G Rizzatti, Barbora Piknova, Nathawut Sibmooh, David F. Stroncek & Alan N. Schechter
Change in MetHb levels in room air (6A) and chamber (6B) samples over 42 days of storage; number of donors, n=2 (A), n=2 (B). To view the data behind the graphs, access 'show all items' above.

Bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of N-acetylated intermediates in prokaryotes-2

Ying Xu, Nicolas Glansdorff & Bernard Labedan
Copyright information:Taken from "Bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of N-acetylated intermediates in prokaryotes"BMC Genomics 2006;7():4-4.Published online 12 Jan 2006PMCID:PMC1382215.Copyright © 2006 Xu et al; licensee BioMed Central Ltd.information concerning genes; refers to the gene for phosphoenolpyruvate carboxylase, adjacent to in many of these organisms; nd: not determined. On the left-hand side, the putative content of the ancestral gene clusters are...

Cos7 and NIH3T3 cells containing a single integrated copy of the pBABE

Qing Lin, Daewoong Jo, Kassatihun D Gebre-Amlak & H Earl Ruley
Copyright information:Taken from "Enhanced cell-permeant Cre protein for site-specific recombination in cultured cells"BMC Biotechnology 2004;4():25-25.Published online 22 Oct 2004PMCID:PMC529453.Copyright © 2004 Lin et al; licensee BioMed Central Ltd.lox.stp.EGFP retrovirus and murine embryonic stem (ES) cells containing a floxed IKK γ gene were treated with 0, 0.5, 1.0, 2.0, 5.0, and 10 μM HNC (Cos7 and NIH3T3) or with 0, 0.25, 0.5, 1.0, 2.0, and 5.0 μM HNC (ES cells) for two hours. Cellular DNA was...

The incremental cost-effectiveness plane

Elisabeth Fenwick, Deborah A Marshall, Adrian R Levy & Graham Nichol
Copyright information:Taken from "Using and interpreting cost-effectiveness acceptability curves: an example using data from a trial of management strategies for atrial fibrillation"BMC Health Services Research 2006;6():52-52.Published online 19 Apr 2006PMCID:PMC1538588. NE = northeast quadrant; NW = northwest quadrant; SE = southeast quadrant; SW = southwest quadrant; QALY = quality adjusted life year

Potential value of PTEN in predicting cetuximab response in colorectal cancer: An exploratory study-4

Evangelia Razis, Evangelos Briasoulis, Eleni Vrettou, Dimosthenis V Skarlos, Dimitrios Papamichael, Ioannis Kostopoulos, Epaminontas Samantas, Ioannis Xanthakis, Mattheos Bobos, Eleni Galanidi, Maria Bai, Ioanna Gikonti, Alona Koukouma, Georgia Kafiri, Pavlos Papakostas, Konstantine T Kalogeras, Paris Kosmidis & George Fountzilas
Green signals) accompanied by extra copies of EGFR gene (arrows). Five copies of chromosome 7 in one tumor cell are also visible (arrowhead); c. & d. Trisomy chromosome 10 (green signals) and extra copies of PTEN gene (red signals), (arrowhead), PTEN gene homozygous deletion (stealth arrow), heterozygous deletion (arrow).Copyright information:Taken from "Potential value of PTEN in predicting cetuximab response in colorectal cancer: An exploratory study"http://www.biomedcentral.com/1471-2407/8/234BMC Cancer 2008;8():234-234.Published online 13 Aug 2008PMCID:PMC2527615.

Heterologous expression in of functional AP65 adhesin-2

Ashwini S Kucknoor, Vasanthakrishna Mundodi & JF Alderete
Copyright information:Taken from "Heterologous expression in of functional AP65 adhesin"BMC Molecular Biology 2005;6():5-5.Published online 4 Mar 2005PMCID:PMC1079839.10% SDS-PAGE and blotted onto Hybond-P membranes for probing with mAb DM116 specific for AP65, as before (Garcia ., 2003). The AP65 protein was readily detected in total protein blots of transfected (lane 2) and (lane 4), but not in wt (lane 1) and in transfected with the control pBS-plasmid (lane 3). The migration of detected AP65 was ~65-kDa...

The evolutionary conservation of the core components necessary for the extrinsic apoptotic signaling pathway, in Medaka fish-3

Kazuhiro Sakamaki, Masami Nozaki, Katsuya Kominami & Yutaka Satou
Copyright information:Taken from "The evolutionary conservation of the core components necessary for the extrinsic apoptotic signaling pathway, in Medaka fish"http://www.biomedcentral.com/1471-2164/8/141BMC Genomics 2007;8():141-141.Published online 1 Jun 2007PMCID:PMC1903365.ains. Human, chicken and zebrafish TRADD were used as the outgroup proteins for rooting the tree. The number noted at branches indicates the percentage of times that a node was supported in 1000 bootstrap pseudoreplications and are shown only greater than 50% for the bootstrap value. The scale bar indicates...

Comparison of the precision of FAST LCS with that of Clustal-W on sequence sets of different lengths

Yixin Chen, Andrew Wan & Wei Liu
Copyright information:Taken from "A fast parallel algorithm for finding the longest common sequence of multiple biosequences"BMC Bioinformatics 2006;7(Suppl 4):S4-S4.Published online 12 Dec 2006PMCID:PMC1780122.

Association of genetic variants with renal function in Africans and in Caucasians-4

Murielle Bochud, Chin B Eap, Marc Maillard, Toby Johnson, Peter Vollenweider, Pascal Bovet, Robert C Elston, Sven Bergmann, Jacques S Beckmann, Dawn M Waterworth, Vincent Mooser, Anne Gabriel & Michel Burnier
End across genotypes using the ASSOC program in S.A.G.E. in models without additional covariates. GFR: glomerular filtration rate measured using inulin clearance. ERPF: effective renal plasma flow measured using PAH clearance. RVR: renal vascular resistance.Copyright information:Taken from "Association of genetic variants with renal function in Africans and in Caucasians"http://www.biomedcentral.com/1755-8794/1/21BMC Medical Genomics 2008;1():21-21.Published online 2 Jun 2008PMCID:PMC2424071.

Transcriptome profiling of human hepatocytes treated with Aroclor 1254 reveals transcription factor regulatory networks and clusters of regulated genes-0

Susanne Reymann & Jürgen Borlak
Copyright information:Taken from "Transcriptome profiling of human hepatocytes treated with Aroclor 1254 reveals transcription factor regulatory networks and clusters of regulated genes"BMC Genomics 2006;7():217-217.Published online 26 Aug 2006PMCID:PMC1590027.ons of Aroclor 1254 (10 μM, 20 μM, and 50 μM) for 72 h, respectively. Lane 1: control, untreated; lane 2: 10 μM Aroclor 1254; lane 3: 20 μM Aroclor 1254; lane 4: 50 μM Aroclor 1254. B: EROD-enzyme activity. Enzyme activity of CYP1A1 in cultures of human...

Synthesis of minus strong stop DNA, begins with t-RNA (clover-leaf structure) binding to the primer binding site (pbs), followed by RNA-templated polymerization of minus strong stop DNA (dashed arrow)

Mario Clemente Estable
Copyright information:Taken from "In search of a function for the most frequent naturally-occurring length polymorphism (MFNLP) of the HIV-1 LTR: Retaining functional coupling, of Nef and RBF-2, at RBEIII?"International Journal of Biological Sciences 2007;3(5):318-327.Published online 11 Jun 2007PMCID:PMC1893116.© Ivyspring International Publisher. This is an open-access article distributed under the terms of the Creative Commons License (http://creativecommons.org/licenses/by-nc-nd/3.0/). Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. RNase...

FRAP analysis of EGFP-tagged Pol II

C. Lux, H. Albiez, R. D. Chapman, M. Heidinger, M. Meininghaus, R. Brack-Werner, A. Lang, M. Ziegler, T. Cremer & D. Eick
Copyright information:Taken from "Transition from initiation to promoter proximal pausing requires the CTD of RNA polymerase II"Nucleic Acids Research 2005;33(16):5139-5144.Published online 12 Sep 2005PMCID:PMC1214543.© The Author 2005. Published by Oxford University Press. All rights reserved () Pol II wt and Pol II Δ5 were tagged with EGFP at the carboxy-terminus. () Pol II-EGFP and H2B-MRFP signals of exemplary nuclei subjected to FRAP analysis were shown: fixed Pol II wt-EGFP (panel 1); live Pol II wt-EGFP...

Categories of data models

SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall & ME Clamp
Copyright information:Taken from "Apollo: a sequence annotation editor"Genome Biology 2002;3(12):research0082.1-82.14.Published online 23 Dec 2002PMCID:PMC151184.Copyright © 2002 Lewis et al., licensee BioMed Central Ltd The Apollo data models fall into one of two broad categories (or are a descriptive auxiliary class, for example, Comment): a location on a sequence; or a sequence. The corresponding Java superclasses are Range and AbstractSequence, respectively. The inheritance hierarchy from these two central classes is shown here, but some minor classes...

Performance of our algorithm on publicly available Chipdata 2 is evaluated using the Yeast Proteome Database collection of transcription factor targets 28,29 and compared with another popular means of computing values 2

Francis D Gibbons, Markus Proft, Kevin Struhl & Frederick P Roth
Copyright information:Taken from "Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization"Genome Biology 2005;6(11):R96-R96.Published online 1 Nov 2005PMCID:PMC1297652.Copyright © 2005 Gibbons et al.; licensee BioMed Central Ltd. Receiver-operating characteristic curves for our method (black, 'Chipper') and that of Lee . [2] (green, 'Lee') using three replicate experiments for the transcription factor Ino4, made publicly available by Lee Sensitivity as a function of significance threshold. The broken line represents the performance of choosing potential...

Gene expressivity (CAI) values and log2 gene expression values between , and genes in different genome organizations

Wagied Davids & Zhaolei Zhang
Copyright information:Taken from "The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment"http://www.biomedcentral.com/1471-2148/8/23BMC Evolutionary Biology 2008;8():23-23.Published online 24 Jan 2008PMCID:PMC2259305. Box plot of CAI values between , and genes in operons; Box plot of gene CAI values between , and genes in protein interaction network (PIN); Box plot of log2 gene expression values between , and genes in operons; Box plot of log2 gene expression values...

Effect of intracellular siRNA half-life on the duration of siRNA-mediated gene silencing

Derek W. Bartlett & Mark E. Davis
Copyright information:Taken from "Insights into the kinetics of siRNA-mediated gene silencing from live-cell and live-animal bioluminescent imaging"Nucleic Acids Research 2006;34(1):322-333.Published online 12 Jan 2006PMCID:PMC1331994.© The Author 2006. Published by Oxford University Press. All rights reserved Curves represent model predictions for luciferase knockdown after transfection with 100 nM siRNA against luciferase on day 0 with a cell doubling time of 1 day ( = 0.0.029 h) and intracellular siRNA half-lives of 24, 48 and 72 h...

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