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Article ; Online: Simultaneous Distinction of Monospecific and Mixed DFS70 Patterns During ANA Screening with a Novel HEp-2 ELITE/DFS70 Knockout Substrate.

Malyavantham, Kishore S / Suresh, Lakshmanan

Journal of visualized experiments : JoVE

2018 , Issue 131

Abstract: Systemic autoimmune connective tissue disorders are characterized by circulating antinuclear antibodies (ANA). Although there are several technologies available for ANA screening, indirect immunofluorescence (IIF) using Human epithelial cells-2 (HEp-2) ... ...

Abstract	Systemic autoimmune connective tissue disorders are characterized by circulating antinuclear antibodies (ANA). Although there are several technologies available for ANA screening, indirect immunofluorescence (IIF) using Human epithelial cells-2 (HEp-2) substrate remains the primary and recommended method because of its superior sensitivity. HEp-2 substrates can detect a multitude of patterns resulting from autoantibody binding to various protein and nucleic acid autoantigens distributed throughout the nucleus and cytoplasm of the cells. The great diversity of monospecific and mixed patterns resulting from positive reactions on HEp-2 substrate also complicate the interpretation and accuracy of reporting. One specific example which received utmost attention recently is the dense fine speckled 70 (DFS70) pattern resulting from autoantibodies that specifically bind to a protein called lens epithelium derived growth factor (LEDGF). Lack of clear association with a specific systemic autoimmune disease and high prevalence in healthy populations have made accurate interpretation of DFS70 pattern important. Accurate distinction of DFS70 pattern from disease-associated patterns using conventional HEp-2 substrate is challenging. Moreover, frequent co-occurrence of DFS70 pattern along with disease-associated patterns such as homogeneous, speckled, and mixed homogeneous-speckled patterns complicate the IIF interpretation. The goal of this paper is to demonstrate the utility of a novel engineered HEp-2 IIF substrate that retains all advantages of conventional HEp-2 substrate while simultaneously providing the ability to distinguish DFS70 pattern with high confidence in both monospecific and mixed ANA positive examples. The new substrate is further able to unmask disease-associated ANA patterns previously concealed by DFS70 pattern.
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/immunology ; Antibodies, Antinuclear/blood ; Antibodies, Antinuclear/immunology ; Fluorescent Antibody Technique, Indirect/methods ; Humans ; Transcription Factors/genetics ; Transcription Factors/immunology
Chemical Substances	Adaptor Proteins, Signal Transducing ; Antibodies, Antinuclear ; PSIP1 protein, human ; Transcription Factors
Language	English
Publishing date	2018-01-17
Publishing country	United States
Document type	Journal Article ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/56722
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Article: Simultaneous distinction of monospecific and mixed dfs70 patterns during ana screening with a novel hep-2 elite/dfs70 knockout substrate

Malyavantham, Kishore S / Suresh, Lakshmanan

Journal of visualized experiments. 2018 Jan. 17, , no. 131

2018

Abstract	Systemic autoimmune connective tissue disorders are characterized by circulating antinuclear antibodies (ANA). Although there are several technologies available for ANA screening, indirect immunofluorescence (IIF) using Human epithelial cells-2 (HEp-2) substrate remains the primary and recommended method because of its superior sensitivity. HEp-2 substrates can detect a multitude of patterns resulting from autoantibody binding to various protein and nucleic acid autoantigens distributed throughout the nucleus and cytoplasm of the cells. The great diversity of monospecific and mixed patterns resulting from positive reactions on HEp-2 substrate also complicate the interpretation and accuracy of reporting. One specific example which received utmost attention recently is the dense fine speckled 70 (DFS70) pattern resulting from autoantibodies that specifically bind to a protein called lens epithelium derived growth factor (LEDGF). Lack of clear association with a specific systemic autoimmune disease and high prevalence in healthy populations have made accurate interpretation of DFS70 pattern important. Accurate distinction of DFS70 pattern from disease-associated patterns using conventional HEp-2 substrate is challenging. Moreover, frequent co-occurrence of DFS70 pattern along with disease-associated patterns such as homogeneous, speckled, and mixed homogeneous-speckled patterns complicate the IIF interpretation. The goal of this paper is to demonstrate the utility of a novel engineered HEp-2 IIF substrate that retains all advantages of conventional HEp-2 substrate while simultaneously providing the ability to distinguish DFS70 pattern with high confidence in both monospecific and mixed ANA positive examples. The new substrate is further able to unmask disease-associated ANA patterns previously concealed by DFS70 pattern.
Keywords	autoantibodies ; autoantigens ; autoimmune diseases ; cytoplasm ; epithelium ; fluorescent antibody technique ; humans ; nucleic acids ; screening
Language	English
Dates of publication	2018-0117
Size	p. e56722.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/56722
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Article ; Online: Chromatin dynamics in living cells: identification of oscillatory motion.

Pliss, Artem / Malyavantham, Kishore S / Bhattacharya, Sambit / Berezney, Ronald

Journal of cellular physiology

2013 Volume 228, Issue 3, Page(s) 609–616

Abstract: ... late S-phase replicated ChrD over short time periods (<1 sec). We conclude that previously identified ... correlates with the replication timing of the ChrD with early S replicated ChrD showing the highest levels ... of motion and late S-phase chromatin the lowest. Virtually identical levels of oscillatory motion were ...

Abstract	Genomic DNA in mammalian cells is organized into ~1 Mbp chromatin domains (ChrD) which represent the basic structural units for DNA compaction, replication, and transcription. Remarkably, ChrD are highly dynamic and undergo both translational movement and configurational changes. In this study, we introduce an automated motion tracking analysis to measure, both in 2D and 3D, the linear displacement of early, mid and late S-phase replicated ChrD over short time periods (<1 sec). We conclude that previously identified large-scale transitions in the spatial position and configuration of chromatin, originate from asymmetric oscillations of the ChrD detectable in fractions of a second. The rapid oscillatory motion correlates with the replication timing of the ChrD with early S replicated ChrD showing the highest levels of motion and late S-phase chromatin the lowest. Virtually identical levels of oscillatory motion were detected when ChrD were measured during active DNA replication or during inhibition of transcription with DRB or α-amanitin. While this motion is energy independent, the oscillations of early S and mid S, but not late S replicated chromatin, are reduced by cell permeabilization. This suggests involvement of soluble factors in the regulation of chromatin dynamics. The DNA intercalating agent actinomycin D also significantly inhibits early S-labeled chromatin oscillation. We propose that rapid asymmetric oscillations of <1 sec are the basis for translational movements and configurational changes in ChrD previously detected over time spans of minutes-hours, and are the result of both the stochastic collisions of macromolecules and specific molecular interactions.
MeSH term(s)	Cell Membrane Permeability ; Chromatin/chemistry ; Chromatin/genetics ; Chromatin/physiology ; DNA/chemistry ; DNA/genetics ; DNA/physiology ; DNA Replication ; Fluorescent Dyes ; HeLa Cells ; Humans ; Imaging, Three-Dimensional ; Macromolecular Substances ; Microscopy, Fluorescence ; Models, Biological ; Movement/physiology ; S Phase ; Stochastic Processes
Chemical Substances	Chromatin ; Fluorescent Dyes ; Macromolecular Substances ; DNA (9007-49-2)
Language	English
Publishing date	2013-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	3116-1
ISSN	1097-4652 ; 0021-9541
ISSN (online)	1097-4652
ISSN	0021-9541
DOI	10.1002/jcp.24169
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Article ; Online: The architecture of functional neighborhoods within the mammalian cell nucleus.

Malyavantham, Kishore S / Bhattacharya, Sambit / Berezney, Ronald

Advances in enzyme regulation

2009 Volume 50, Issue 1, Page(s) 126–134

MeSH term(s)	Animals ; Cell Nucleus/physiology ; Cell Nucleus/ultrastructure ; Chromatin/chemistry ; Chromatin/genetics ; Chromatin/metabolism ; DNA Replication ; Gene Expression Regulation ; Mammals ; Models, Molecular ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Transcription, Genetic
Chemical Substances	Chromatin ; Nuclear Proteins
Language	English
Publishing date	2009-12-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ISSN	1873-2437 ; 0065-2571
ISSN (online)	1873-2437
ISSN	0065-2571
DOI	10.1016/j.advenzreg.2009.10.003
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Article ; Online: Chromatin dynamics is correlated with replication timing.

Pliss, Artem / Malyavantham, Kishore / Bhattacharya, Sambit / Zeitz, Michael / Berezney, Ronald

Chromosoma

2009 Volume 118, Issue 4, Page(s) 459–470

Abstract: ... strikingly higher in early S-phase replicating ChrD compared to those that replicate in mid and late S-phase ... reduced by actinomycin D treatment. Since a majority of active genes replicate in early S-phase ...

Abstract	Discrete chromatin domains (ChrD), containing an average of approximately 1 Mbp DNA, represent the basic structural units for the regulation of DNA organization and replication in situ. In this study, a bio-computational approach is employed to simultaneously measure the translational motion of large populations of ChrD in the cell nucleus of living cells. Both movement and configurational changes are strikingly higher in early S-phase replicating ChrD compared to those that replicate in mid and late S-phase. The chromatin dynamics was not sensitive to transcription inhibition by alpha-amanitin but was significantly reduced by actinomycin D treatment. Since a majority of active genes replicate in early S-phase, our results suggest a correlation between levels of chromatin dynamics and chromatin poised for active transcription. Analysis of ChrD colocalization with transcription sites and cDNA with ChrD and transcription sites further supports this proposal.
MeSH term(s)	Alpha-Amanitin/pharmacology ; Carbocyanines/chemistry ; Cell Nucleus/drug effects ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Chromatin/drug effects ; Chromatin/genetics ; Chromatin/metabolism ; Chromosome Positioning/drug effects ; DNA Replication/drug effects ; DNA Replication/genetics ; Dactinomycin/pharmacology ; Deoxyuracil Nucleotides/chemistry ; Deoxyuracil Nucleotides/metabolism ; Gene Expression ; HeLa Cells ; Humans ; In Situ Hybridization, Fluorescence ; Kinetics ; Microinjections ; Microscopy, Fluorescence ; S Phase ; Time Factors
Chemical Substances	Alpha-Amanitin ; Carbocyanines ; Chromatin ; Deoxyuracil Nucleotides ; cyanine dye 3 ; deoxyuridine triphosphate (1173-82-6) ; Dactinomycin (1CC1JFE158)
Language	English
Publishing date	2009-03-19
Publishing country	Austria
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	203083-4
ISSN	1432-0886 ; 0009-5915
ISSN (online)	1432-0886
ISSN	0009-5915
DOI	10.1007/s00412-009-0208-6
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Article ; Online: Matrin 3: chromosomal distribution and protein interactions.

Zeitz, Michael J / Malyavantham, Kishore S / Seifert, Brandon / Berezney, Ronald

Journal of cellular biochemistry

2009 Volume 108, Issue 1, Page(s) 125–133

Abstract: Matrin 3 (matr3), an abundant protein of the internal nuclear matrix, has been linked to a variety of functional events. As a step toward defining its multifunctional nature, we have studied the association of matr3 with chromosome territories and ... ...

Abstract	Matrin 3 (matr3), an abundant protein of the internal nuclear matrix, has been linked to a variety of functional events. As a step toward defining its multifunctional nature, we have studied the association of matr3 with chromosome territories and identified potential interacting proteins. A similar staining pattern of matr3 was observed in fixed WI38 fibroblast cells and in live HeLa cells using a matr3-GFP construct. Matr3 was detected throughout autosomal and the active X chromosome territories. Conversely, matr3 was strikingly excluded from the inactive X chromosome as well as within both the perinuclear and perinucleolar heterochromatin. Yeast two hybrid analysis identified matr3 interactions with 33 unique nuclear localized proteins and also revealed its propensity for self association. A majority of these proteins are involved in RNA metabolism and chromatin remodeling while others function in protein translation, DNA replication/repair and apoptosis. Further analysis of a selection of these proteins and scaffold attachment factor A (SAFA) by co-localization and co-immunoprecipitation experiments using HeLa cells confirmed their interactions with matr3.
MeSH term(s)	Binding Sites ; Chromosomes/metabolism ; Chromosomes, Human, X/metabolism ; Fibroblasts/metabolism ; HeLa Cells ; Humans ; Nuclear Matrix/metabolism ; Nuclear Matrix-Associated Proteins/analysis ; Nuclear Matrix-Associated Proteins/metabolism ; RNA-Binding Proteins/analysis ; RNA-Binding Proteins/metabolism ; Transfection
Chemical Substances	MATR3 protein, human ; Nuclear Matrix-Associated Proteins ; RNA-Binding Proteins
Language	English
Publishing date	2009-09-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	392402-6
ISSN	1097-4644 ; 0730-2312
ISSN (online)	1097-4644
ISSN	0730-2312
DOI	10.1002/jcb.22234
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Article ; Online: The search for an autoimmune origin of psychotic disorders: Prevalence of autoantibodies against hippocampus antigens, glutamic acid decarboxylase and nuclear antigens.

Hoffmann, Carolin / Zong, Shenghua / Mané-Damas, Marina / Stevens, Jo / Malyavantham, Kishore / Küçükali, Cem İsmail / Tüzün, Erdem / De Hert, Marc / van Beveren, Nico J M / González-Vioque, Emiliano / Arango, Celso / Damoiseaux, Jan G M C / Rutten, Bart P / Molenaar, Peter C / Losen, Mario / Martinez-Martinez, Pilar

Schizophrenia research

2021 Volume 228, Page(s) 462–471

Abstract: The etiology of psychotic disorders is still unknown, but in a subgroup of patients symptoms might be caused by an autoimmune reaction. In this study, we tested patterns of autoimmune reactivity against potentially novel hippocampal antigens. Serum of a ... ...

Abstract	The etiology of psychotic disorders is still unknown, but in a subgroup of patients symptoms might be caused by an autoimmune reaction. In this study, we tested patterns of autoimmune reactivity against potentially novel hippocampal antigens. Serum of a cohort of 621 individuals with psychotic disorders and 257 controls were first tested for reactivity on neuropil of rat brain sections. Brain reactive sera (67 diseased, 27 healthy) were further tested for antibody binding to glutamic acid decarboxylase (GAD) isotype 65 and 67 by cell-based assay (CBA). A sub-cohort of 199 individuals with psychotic disorders and 152 controls was tested for the prevalence of anti-nuclear antibodies (ANA) on HEp2-substrate as well as for reactivity to double-stranded DNA, ribosomal P (RPP), and cardiolipin (CL). Incubation of rat brain with serum resulted in unidentified hippocampal binding patterns in both diseased and control groups. Upon screening with GAD CBA, one of these patterns was identified as GAD65 in one individual with schizophrenia and also in one healthy individual. Two diseased and two healthy individuals had low antibody levels targeting GAD67 by CBA. Antibody reactivity on HEp-2-substrate was increased in patients with schizoaffective disorder, but only in 3 patients did antibody testing hint at a possible diagnosis of systemic lupus erythematosus. Although reactivity of serum to intracellular antigens might be increased in patients with psychotic disorder, no specific targets could be identified. GAD antibodies are very rare and do not seem increased in serum of patients with psychotic disorders.
MeSH term(s)	Antigens, Nuclear ; Autoantibodies ; Glutamate Decarboxylase ; Hippocampus ; Humans ; Prevalence ; Psychotic Disorders/epidemiology
Chemical Substances	Antigens, Nuclear ; Autoantibodies ; Glutamate Decarboxylase (EC 4.1.1.15)
Language	English
Publishing date	2021-02-11
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639422-x
ISSN	1573-2509 ; 0920-9964
ISSN (online)	1573-2509
ISSN	0920-9964
DOI	10.1016/j.schres.2020.12.038
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Article: Xerophthalmia of Sjogren's Syndrome Diagnosed with Anti-Salivary Gland Protein 1 Antibodies

Vishwanath, Sahana / Everett, Sandra / Shen, Long / Malyavantham, Kishore / Suresh, Lakshmanan / Ambrus Jr., Julian L.

Case Reports in Ophthalmology

2014 Volume 5, Issue 2, Page(s) 186–189

Abstract: Purpose: The purpose of this report is to describe 2 patients with persistent severe dry eyes, positive Schirmer tests for Sjogren's syndrome (SS) but lacking antibodies to either Ro or La. These patients were diagnosed to have SS by detecting antibodies ...

Institution	SUNY at Buffalo School of Medicine Department of Oral Diagnostic Sciences, SUNY at Buffalo School of Dental Medicine, and Immco Diagnostics, Buffalo, N.Y., USA
Abstract	Purpose: The purpose of this report is to describe 2 patients with persistent severe dry eyes, positive Schirmer tests for Sjogren's syndrome (SS) but lacking antibodies to either Ro or La. These patients were diagnosed to have SS by detecting antibodies to salivary gland protein 1 (Sp1) and parotid secretory protein (PSP). This report emphasizes the existence of patients with SS who lack antibodies to either Ro or La and may therefore be misdiagnosed. Detection of novel autoantibodies, including antibodies to Sp1 and PSP, are helpful in identifying these patients. Initial presentation may simply be dry eyes. Methods: Two patients who presented to our ophthalmology clinic are described. One of the patients underwent multiple procedures over a period of 10 years for severe xerophthalmia. The other patient had rheumatoid arthritis and xerophthalmia. However, in both patients, chronic xerophthalmia had been considered to be idiopathic because antibodies Ro and La were negative. Further serologic testing revealed antibodies to Sp1 and PSP. Results: Two patients who lacked antibodies to Ro and La but not to Sp1 and PSP were diagnosed as having SS. Conclusion: Patients presenting with unexplained dry eyes may not always show the serology markers in the current criteria for SS, anti-Ro and anti-La. In these cases, investigation for novel, early antibodies to Sp1 and PSP is of importance in the diagnosis of SS.
Keywords	Xerophthalmia ; Sjogren’s syndrome ; Autoantibodies
Language	English
Publishing date	2014-06-28
Publisher	S. Karger AG
Publishing place	Basel, Switzerland
Document type	Article
ZDB-ID	2577666-6
ISSN	1663-2699 ; 1663-2699
ISSN (online)	1663-2699
ISSN	1663-2699
DOI	10.1159/000364941
Database	Karger publisher's database

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Article ; Online: Analysis of novel Sjogren's syndrome autoantibodies in patients with dry eyes.

Everett, Sandra / Vishwanath, Sahana / Cavero, Vanessa / Shen, Long / Suresh, Lakshmanan / Malyavantham, Kishore / Lincoff-Cohen, Norah / Ambrus, Julian L

BMC ophthalmology

2017 Volume 17, Issue 1, Page(s) 20

Abstract: Background: Dry eye is a common problem in Ophthalmology and may occur for many reasons including Sjogren's syndrome (SS). Recent studies have identified autoantibodies, anti-salivary gland protein 1 (SP1), anti-carbonic anhydrase 6 (CA6) and anti- ... ...

Abstract	Background: Dry eye is a common problem in Ophthalmology and may occur for many reasons including Sjogren's syndrome (SS). Recent studies have identified autoantibodies, anti-salivary gland protein 1 (SP1), anti-carbonic anhydrase 6 (CA6) and anti-parotid secretory protein (PSP), which occur early in the course of SS. The current studies were designed to evaluate how many patients with idiopathic dry eye and no evidence of systemic diseases from a dry eye practice have these autoantibodies. Methods: Patients from a dry eye clinic and normal controls were assessed by Schirmer's test for tear flow. Sera were assessed for autoantibodies using ELISA assays. Statistics was performed with Prism 7 software and student's unpaired t test. Results: In this study 60% of the dry eye patients expressed one of these autoantibodies. Only 30% expressed one of the autoantibodies associated with long-standing SS, which are included in the diagnostic criteria for SS, anti-Ro and anti-La. Patients with disease for less than 2 years and mild dry eyes did not express anti-Ro or anti-La, while 25% expressed anti-SP1. Similar observations, with smaller numbers, were made when patients had not only dry eye but also dry mouth. Conclusions: Antibodies to SP1, CA6 and PSP occur in some patients with idiopathic dry eyes. Further studies will be needed to determine how many of these patients go on to develop systemic manifestations of SS. Testing for these autoantibodies may allow early recognition of patients with SS. This will lead to improved management of the patients and the development of new strategies to maintain normal lacrimal and salivary gland function in patients with SS.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Autoantibodies/blood ; Biomarkers/blood ; Case-Control Studies ; Dry Eye Syndromes/blood ; Dry Eye Syndromes/immunology ; Early Diagnosis ; Enzyme-Linked Immunosorbent Assay ; Female ; Humans ; Immunoglobulins/blood ; Male ; Middle Aged ; Retrospective Studies ; Sjogren's Syndrome/blood ; Sjogren's Syndrome/diagnosis ; Sjogren's Syndrome/immunology
Chemical Substances	Autoantibodies ; Biomarkers ; Immunoglobulins
Language	English
Publishing date	2017-03-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2050436-6
ISSN	1471-2415 ; 1471-2415
ISSN (online)	1471-2415
ISSN	1471-2415
DOI	10.1186/s12886-017-0412-8
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Article ; Online: Cytogenetic and cDNA microarray expression analysis of MCF10 human breast cancer progression cell lines.

Marella, Narasimharao V / Malyavantham, Kishore S / Wang, Jianmin / Matsui, Sei-ichi / Liang, Ping / Berezney, Ronald

Cancer research

2009 Volume 69, Issue 14, Page(s) 5946–5953

Abstract: We used a combination of spectral karyotyping, array comparative genomic hybridization, and cDNA microarrays to gain insights into the structural and functional changes of the genome in the MCF10 human breast cancer progression model cell lines. Spectral ...

Abstract	We used a combination of spectral karyotyping, array comparative genomic hybridization, and cDNA microarrays to gain insights into the structural and functional changes of the genome in the MCF10 human breast cancer progression model cell lines. Spectral karyotyping data showed several chromosomal aberrations and array comparative genomic hybridization analysis identified numerous genomic gains and losses that might be involved in the progression toward cancer. Analysis of the expression levels of genes located within these genomic regions revealed a lack of correlation between chromosomal gains and losses and corresponding up-regulation or down-regulation for the majority of the approximately 1,000 genes analyzed in this study. We conclude that other mechanisms of gene regulation that are not directly related to chromosomal gains and losses play a major role in breast cancer progression.
MeSH term(s)	Breast/cytology ; Breast/metabolism ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Cell Line ; Cell Line, Tumor ; Chromosome Aberrations ; Comparative Genomic Hybridization/methods ; Cytogenetics/methods ; Disease Progression ; Down-Regulation ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; Oligonucleotide Array Sequence Analysis/methods ; Spectral Karyotyping/methods ; Up-Regulation
Language	English
Publishing date	2009-07-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1432-1
ISSN	1538-7445 ; 0008-5472
ISSN (online)	1538-7445
ISSN	0008-5472
DOI	10.1158/0008-5472.CAN-09-0420
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