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  • 1
    Keywords: Life sciences ; Cytology ; Cell Culture ; Life sciences ; Cell Biology ; Cell Culture ; Springer eBooks
    Description / Table of Contents: 1. Detection of Mycoplasma Contaminations -- 2. Eradication of Mycoplasma Contaminations -- 3. STR DNA Typing of Human Cell Lines: Detection of Intra- and Interspecies Cross-Contamination -- 4. Classical and Molecular Cytogenetic Analysis -- 5. Fluorescent In Situ Hybridization (FISH) of DNA Probes in the Interphase and Metaphase Stages of the Cell Cycle -- 6. The Development of T Lymphocytes in Fetal Thymus Organ Culture -- 7. Generation, Isolation, and Engraftment of In Vitro-Derived Human T Cell Progenitors -- 8. In Vitro Generation of Human T Regulatory Cells: Generation, Culture, and Analysis of FOXP3-Transduced T Cells -- 9. Simultaneous Cloning and Selection of Hybridomas and Transfected Cell Lines in Semisolid Media -- 10. Isolation and Characterization of Mouse Side Population Cells -- 11. Stem Cell Identification by DyeCycle Violet Side Population Analysis -- 12. Isolation and Characterization of Cancer Stem Cells In Vitro -- 13. Ex Vivo Differentiation of Cord Blood Stem Cells into Megakaryocytes and Platelets -- 14. Generation and Characterization of Murine Alternatively Activated Macrophages -- 15. Human Long Term Culture Initiating Cell (LTC-IC) Assay -- 16. Long Term Culture Initiating Cell (LTC-IC) Assay for Mouse Cells -- 17. Colony Forming Cell Assays for Human Hematopoietic Progenitor Cells -- 18. Studying Leukocyte Recruitment Under Flow Conditions -- 19. Generation and Establishment of Murine Adherent Cell Lines -- 20. Isolation, Enumeration, and Expansion of Human Mesenchymal Stem Cells in Culture -- 21. Isolation and Culture of Mesenchymal Stem Cells from Mouse Compact Bone -- 22. Generation of a Pool of Human Platelet Lysate (pHPL) and Efficient Use in Cell Culture -- 23. In Vitro Methods to Culture Primary Human Breast Epithelial Cells -- 24. Human Prostate Epithelial Cell Cultures -- 25. Enzymatic Dissociation, Flow Cytometric Analysis, and Culture of Normal Mouse Mammary Tissue -- 26. Isolation and Characterization of Human Hair Follicle Epithelial Cells -- 27. Co-Cultivation of Human Oral Keratinocytes and Human Osteoblast-Like Cells -- 28. Isolation and Culture of Skeletal Muscle Myofibers as a Means to Analyze Satellite Cells -- 29. Hepatic Differentiation of Embryonic Stem Cells by Murine Fetal Liver Mesenchymal Cells -- 30. Methods to Culture, Differentiate, and Characterize Neural Stem Cells from the Adult and Embryonic Mouse Central Nervous System -- 31. Feeder-Independent Culture Systems for Human Pluripotent Stem Cells -- 32. Formation of Embryoid Bodies from Human Pluripotent Stem Cells Using AggreWell™ Plates -- 33. Techniques in Embryoid Body Formation from Human Pluripotent Stem Cells
    Abstract: At some point in their careers, virtually every scientist and technician, as well as many medical professionals, regardless of their area of specialization have a need to utilize cell culture systems. Updating and significantly expanding upon the previous editions, Basic Cell Culture Protocols, Fourth Edition provides the novice cell culturist with sufficient information to perform the basic techniques, to ensure the health and identity of their cell lines, and to be able to isolate and culture specialized primary cell types. The intent of this extensive volume is to generate a valuable resource containing clear methodologies pertinent to current areas of investigation, rather than attempting to educate cell culturists on specific cell types or organ systems.℗ Written in the highly successful Methods in Molecular Biologý„Ø, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. ℗ Comprehensive and up-to-date, Basic Cell Culture Protocols, Fourth Edition compiles the essential techniques needed to approach this vital laboratory activity with full success
    Pages: XIV, 550 p. 104 illus., 44 illus. in color. : digital.
    Edition: 4th ed.
    ISBN: 9781627031288
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  • 2
    Call number: QH506:60/290a
    Keywords: Cell Culture Techniques / methods ; Culture Techniques / methods
    Description / Table of Contents: Culture of primary adherent cells and a continuously growing non-adherent cell line / Cheryl D. Helgason -- Detection of mycoplasma contaminations / Cord C. Uphoff and Hans G. Drexler -- Eradication of mycoplasma contaminations / Cord C. Uphoff and Hans G. Drexler -- Authentication of scientific human cell lines / Wilhelm G. Dirks and Hans G. Drexler -- Cytogenetic analysis of cell lines / Roderick A.F. MacLeod and Hans G. Drexler -- Human and mouse hematopoeitic colony forming cell assays / Cindy L. Miller and Becky Lai -- Isolation and culture of murine macrophages / John Q. Davies and Siamon Gordon -- Isolation and culture of human macrophages / John Q. Davies and Siamon Gordon -- The development of T lymphocytes in mouse fetal thymus organ culture / Tomoo Ueno ... [et al.] -- In vitro generation of lymphocytes from embryonic stem cells / Renée F. de Pooter, Sarah K. Cho and Juan Carlos Zúniga-Pflücker -- Hematopoietic development of human embryonic stem cells in culture / Xinghui Tian and Dan S. Kaufman -- Generation of murine stromal cell lines / Robert A.J. Oostendorp, Kirsty Harvey and Elaine E. Dzierzak -- Culture of human and mouse mesenchymal cells / Emer Clarke -- Isolation, purification, and cultivation of rat and human keratinocytes / Frizell L. Vaughan and Ludmila I. Bernstam -- Isolation and culture of primary human hepatocytes / Edward L. LeCluyse ... [et al.] -- Primary kidney proximal tubule cells / Mary Taub -- Enzymatic dissociation and culture of normal human mammary tissue to detect progenitor activity / John Stingl, Joanne T. Emerman, and Connie J. Eaves -- Generation and differentiation of neurospheres from murine embryonic day 14 central nervous system tissue / Sharon A. Louis and Brent A. Reynolds -- Isolation and culture of skeletal muscle myofibers as a means to analyze satellite cells / Gabi Shefer and Zipora Yablonka-Reuveni -- Adult ventricular cardiomyocytes / Klaus-Dieter Schlüter and Daniela Schreiber -- Isolation and culture of primary endothelial cells / Bruno Larrivée and Aly Karsan -- Studying leukocyte rolling and adhesion in vitro under flow conditions / Susan L. Cuvelier and Kamala D. Patel -- Isolation and characterization of side population cells / Margaret A. Goodell, Shannon McKinney-Freeman and Fernando D. Camargo -- Scalable production of embryonic stem cell-derived cells / Stephen M. Dang and Peter W. Zandstra
    Notes: 2nd ed. edited by Jeffrey W. Pollard and John M. Walker.
    Pages: xii, 371 p. : ill. + 1 CD-ROM
    Edition: 3rd ed.
    ISBN: 1588292843
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  • 3
    Publication Date: 2012-08-24
    Description: Mutations generate sequence diversity and provide a substrate for selection. The rate of de novo mutations is therefore of major importance to evolution. Here we conduct a study of genome-wide mutation rates by sequencing the entire genomes of 78 Icelandic parent-offspring trios at high coverage. We show that in our samples, with an average father's age of 29.7, the average de novo mutation rate is 1.20 x 10(-8) per nucleotide per generation. Most notably, the diversity in mutation rate of single nucleotide polymorphisms is dominated by the age of the father at conception of the child. The effect is an increase of about two mutations per year. An exponential model estimates paternal mutations doubling every 16.5 years. After accounting for random Poisson variation, father's age is estimated to explain nearly all of the remaining variation in the de novo mutation counts. These observations shed light on the importance of the father's age on the risk of diseases such as schizophrenia and autism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548427/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548427/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kong, Augustine -- Frigge, Michael L -- Masson, Gisli -- Besenbacher, Soren -- Sulem, Patrick -- Magnusson, Gisli -- Gudjonsson, Sigurjon A -- Sigurdsson, Asgeir -- Jonasdottir, Aslaug -- Jonasdottir, Adalbjorg -- Wong, Wendy S W -- Sigurdsson, Gunnar -- Walters, G Bragi -- Steinberg, Stacy -- Helgason, Hannes -- Thorleifsson, Gudmar -- Gudbjartsson, Daniel F -- Helgason, Agnar -- Magnusson, Olafur Th -- Thorsteinsdottir, Unnur -- Stefansson, Kari -- MH071425/MH/NIMH NIH HHS/ -- R01 MH071425/MH/NIMH NIH HHS/ -- England -- Nature. 2012 Aug 23;488(7412):471-5. doi: 10.1038/nature11396.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland. kong@decode.is〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22914163" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Autistic Disorder/epidemiology/etiology/*genetics ; Chromosomes, Human/genetics ; Female ; *Genetic Predisposition to Disease ; Genome, Human/genetics ; Humans ; Iceland/epidemiology ; Male ; Middle Aged ; Mothers ; *Mutation Rate ; Ovum/metabolism ; *Paternal Age ; Pedigree ; Polymorphism, Single Nucleotide/genetics ; Risk Factors ; Schizophrenia/epidemiology/etiology/*genetics ; Selection, Genetic/genetics ; Sequence Analysis, DNA ; Spermatozoa/metabolism ; Young Adult
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Keywords: RECEPTOR ; CANCER ; POPULATION ; RISK ; SITE ; DISTINCT ; GENE ; GENES ; GENOME ; RESOLUTION ; BINDING ; SEQUENCE ; ASSOCIATION ; SUSCEPTIBILITY ; SUSCEPTIBILITY LOCUS ; ALPHA ; BREAST ; breast cancer ; BREAST-CANCER ; genetics ; SNP ; POPULATIONS ; PROJECT ; ESTROGEN-RECEPTOR ; HETEROGENEITY ; ORIGIN ; TAMOXIFEN ; ASSOCIATIONS ; SNPs ; SCIENCE ; ESTROGEN ; HAPLOTYPE ; LOCUS ; TRAITS ; estrogen receptor ; BINDING-SITE ; CHINESE POPULATION ; GENOME-WIDE ASSOCIATION ; AFRICAN-AMERICAN ; ESTROGEN-RECEPTOR-ALPHA ; CONFER SUSCEPTIBILITY ; BINDING SITE ; Genetic ; COMMON VARIANTS ; ANCESTRY ; PANEL ; CAUSAL VARIANTS
    Abstract: We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case: control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2x10(-3)), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9x10(-4)) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9x10(-7)), was without significant heterogeneity between ancestries (P-het = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[ T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping
    Type of Publication: Journal article published
    PubMed ID: 20661439
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  • 5
    Keywords: EXPRESSION ; DISEASES ; RISK ; POLYMORPHISMS ; DNA-REPAIR GENES ; METAANALYSIS ; UROTHELIAL CELL-CARCINOMA ; imputation ; CONFERS SUSCEPTIBILITY ; SEQUENCE VARIANT
    Abstract: Genome-wide association studies (GWAS) of urinary bladder cancer (UBC) have yielded common variants at 12 loci that associate with risk of the disease. We report here the results of a GWAS of UBC including 1670 UBC cases and 90 180 controls, followed by replication analysis in additional 5266 UBC cases and 10 456 controls. We tested a dataset containing 34.2 million variants, generated by imputation based on whole-genome sequencing of 2230 Icelanders. Several correlated variants at 20p12, represented by rs62185668, show genome-wide significant association with UBC after combining discovery and replication results (OR = 1.19, P = 1.5 x 10(-11) for rs62185668-A, minor allele frequency = 23.6%). The variants are located in a non-coding region approximately 300 kb upstream from the JAG1 gene, an important component of the Notch signaling pathways that may be oncogenic or tumor suppressive in several forms of cancer. Our results add to the growing number of UBC risk variants discovered through GWAS.
    Type of Publication: Journal article published
    PubMed ID: 24861552
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  • 6
    Keywords: EXPRESSION ; BREAST-CANCER ; REDUCED RISK ; SKIN-CANCER ; CASP8 GENE ; GENOME-WIDE ASSOCIATION ; COMMON VARIANTS ; SEQUENCE VARIANTS ; INACTIVATING MUTATIONS ; GENETIC-VARIANTS
    Abstract: In an ongoing screen for DNA sequence variants that confer risk of cutaneous basal cell carcinoma (BCC), we conduct a genome-wide association study (GWAS) of 24,988,228 SNPs and small indels detected through whole-genome sequencing of 2,636 Icelanders and imputed into 4,572 BCC patients and 266,358 controls. Here we show the discovery of four new BCC susceptibility loci: 2p24 MYCN (rs57244888[C], OR=0.76, P=4.7 x 10(-12)), 2q33 CASP8-ALS2CR12 (rs13014235[C], OR=1.15, P=1.5 x 10(-9)), 8q21 ZFHX4 (rs28727938[G], OR=0.70, P=3.5 x 10(-12)) and 10p14 GATA3 (rs73635312[A], OR=0.74, P=2.4 x 10(-16)). Fine mapping reveals that two variants correlated with rs73635312[A] occur in conserved binding sites for the GATA3 transcription factor. In addition, expression microarrays and RNA-seq show that rs13014235[C] and a related SNP rs700635[C] are associated with expression of CASP8 splice variants in which sequences from intron 8 are retained.
    Type of Publication: Journal article published
    PubMed ID: 25855136
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  • 7
    Abstract: The timing of puberty is a highly polygenic childhood trait that is epidemiologically associated with various adult diseases. Using 1000 Genomes Project-imputed genotype data in up to approximately 370,000 women, we identify 389 independent signals (P 〈 5 x 10-8) for age at menarche, a milestone in female pubertal development. In Icelandic data, these signals explain approximately 7.4% of the population variance in age at menarche, corresponding to approximately 25% of the estimated heritability. We implicate approximately 250 genes via coding variation or associated expression, demonstrating significant enrichment in neural tissues. Rare variants near the imprinted genes MKRN3 and DLK1 were identified, exhibiting large effects when paternally inherited. Mendelian randomization analyses suggest causal inverse associations, independent of body mass index (BMI), between puberty timing and risks for breast and endometrial cancers in women and prostate cancer in men. In aggregate, our findings highlight the complexity of the genetic regulation of puberty timing and support causal links with cancer susceptibility.
    Type of Publication: Journal article published
    PubMed ID: 28436984
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  • 8
    Keywords: carcinoma ; CELL ; DISEASE ; EPIDEMIOLOGY ; NEW-YORK ; RISK ; GENE ; GENES ; SAMPLE ; TIME ; RISK-FACTORS ; SEQUENCE ; ASSOCIATION ; SIGNAL ; VARIANTS ; NO ; HEALTH ; genetics ; SNP ; risk factors ; MELANOMA ; HUMAN HOMOLOG ; INDIVIDUALS ; EUROPE ; heredity ; SKIN-CANCER ; basal cell carcinoma ; CELL CARCINOMA ; VARIANT ; SNPs ; CANDIDATE GENES ; EUROPEANS ; USA ; PIGMENTATION ; CANDIDATE ; RISK-FACTOR ; SIGNALS ; COMMON VARIANT ; SET ; NOV ; association study ; BASAL-CELL ; GENOME-WIDE ; CITRULLINATION ; GENETIC-DETERMINANTS ; PEPTIDYLARGININE DEIMINASE
    Abstract: To search for new sequence variants that confer risk of cutaneous basal cell carcinoma (BCC), we conducted a genome-wide SNP association study of 930 Icelanders with BCC and 33,117 controls. After analyzing 304,083 SNPs, we observed signals from loci at 1p36 and 1q42, and replicated these associations in additional sample sets from Iceland and Eastern Europe. Overall, the most significant signals were from rs7538876 on 1p36 (OR = 1.28, P = 4.4 x 10(-12)) and rs801114 on 1q42 (OR = 1.28, P = 5.9 x. 10(-12)). The 1p36 locus contains the candidate genes PADI4, PADI6, RCC2 and ARHGEF10L, and the gene nearest to the 1q42 locus is the ras-homolog RHOU. Neither locus was associated with fair pigmentation traits that are known risk factors for BCC, and no risk was observed for melanoma. Approximately 1.6% of individuals of European ancestry are homozygous for both variants, and their estimated risk of BCC is 2.68 times that of noncarriers
    Type of Publication: Journal article published
    PubMed ID: 18849993
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  • 9
    Keywords: CANCER ; SURVIVAL ; CLASSIFICATION ; DIAGNOSIS ; FOLLOW-UP ; DEATH ; DISEASE ; POPULATION ; PROTEIN ; PROTEINS ; PATIENT ; MARKER ; prognosis ; BIOMARKERS ; CYCLE ; STAGE ; IDENTIFICATION ; colorectal cancer ; COLORECTAL-CANCER ; mass spectrometry ; SPECTROMETRY ; chemotherapy ; MARKERS ; MASS-SPECTROMETRY ; SURFACE ; NETHERLANDS ; PROTEOMIC ANALYSIS ; ONCOLOGY ; monitoring ; overall survival ; MS ; biomarker ; PROFILES ; colorectal ; PROFILE ; STAGE OVARIAN-CANCER ; TREATMENT RESPONSE ; transthyretin ; Follow up ; APOLIPOPROTEIN A1 ; prognostic ; proteomic
    Abstract: Colorectal cancer (CRC) is the second most common cause of cancer related death. Prognosis is highly dependent on stage at diagnosis making early detection mandatory. This study aimed to identify novel disease specific biomarkers of CRC, validate our previously identified biomarkers of CRC and identify serum biomarkers predicting treatment response and for monitoring. Serum of patients with metastatic CRC was collected, according to a predefined schedule, prior to start of standard first-line chemotherapy with oxaliplatin and capecitabine and serially before each 3 weekly treatment cycle and analyzed for proteomic profile by standardized SELDI-TOF MS. Serum proteomic mass spectrometry data of all subjects were processed using the tbimass R-package and proteomic profiles of CRC patients were compared with those of matched normal control subjects. Furthermore, changes in proteomic profiles during the course of chemotherapy were recorded according to treatment response. In total, 42 patients with advanced CRC were treated and mean follow-up was 13.5 months. The response rate was 50% and the median overall survival 19.5 months (95% CI: 16-23). By comparing CRC patients and healthy controls we identified 13 potential biomarkers of CRC (m/z 2.0-31.9 kDa) whereas two proteins, m/z 14060 and 28100 Da (apolipoprotein A-I), were highly significant (p〈0.0001). Comparison of responding and non-responding patients identified 6 proteins potentially predicting response, where of m/z 3330 Da was significant (p=0.007). Serial analysis identified 2 proteins, m/z 2022 and 28100 Da, that changed during chemotherapy in accordance with response. We identified 13 m/z values discriminating between CRC patients and healthy controls, including the previously identified apolipoprotein A-I as a candidate biomarker for CRC and treatment monitoring
    Type of Publication: Journal article published
    PubMed ID: 20514444
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  • 10
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