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At least 1,225 records · Page 68Linked to original sources
PubMed1996

Comparative genomic hybridization analysis of archival formalin-fixed paraffin-embedded uveal melanomas.

Comparative genomic hybridization (CGH) was used to analyze seven autologous uveal melanomas with both formalin-fixed, paraffin-embedded and fresh-frozen specimens. In addition, DNA from two archival formalin-fixed tumors more than 45 years old were also analyzed. The most frequent genetic changes were loss of chromosome 3; increase in copy number of 6p and loss of 6q; and increase in copy number of 8q. A comparison of CGH data from the fresh-frozen tumors and their autologous formalin-fixed tumors revealed a correlation coefficient of 0.83. Comparative genomic hybridization (CGH) analysis of 45-year-old specimens identified genetic changes similar to those found in more recent tumors including loss of chromosome 3 and increase in copy numbers of 6p and 8q. The results indicate that there is a good agreement between data obtained from formalin-fixed and fresh-frozen specimens using CGH. Furthermore, the results demonstrate the applicability of this technique in analyzing archival formalin-fixed tumors that were previously not accessible to cytogenetic analysis.

Analysis of Variance↗
PubMed2004

[A comparative analysis of genomes of virulent and avirulent strains of Vibrio cholerae O139].

A comparative analysis of the genome of V. cholerae O139 strains isolated in Russia's territory from patients with cholera and from the environment showed essential differences in their structures. The genome of clinical strains possessed all tested genes associated with virulence (ctxAB, zot, ace, rstC, rtxA, hap, toxR and toxT) and the at-tRS site for the CTXp phage DNA integration. As for the O139 V. cholerae chromosome strains isolated from water, 70% of the studied genes (ctxAB, zot, ace, rstC, tcpA, and toxT) and the attRS sequence were not detected in them. A lack of the key virulence genes in O139-serogroup "water" vibrios, including genes of toxin-coregulated adhesion pili. (that are receptors for the CTXp phage), and of the attachment site of the above phage are indicative of that the O139 V. cholerae strains isolated from open water sources located in different Russia's regions are epidemically negligible.

Adenosine Triphosphatases↗
PubMed1988

Characterization of a latent protein encoded by the large internal repeats and the BamHI Y fragment of the Epstein-Barr virus (EBV) genome.

Analysis of EBV nuclear antigen 1 (EBNA 1) encoding transcripts by cDNA characterization revealed a potentially polycistronic message generated by long-range splicing of several exons (Speck, S., and Strominger, J., Proc. Natl. Acad. Sci. USA 82, 8305-8309, 1985). Besides the open reading frame encoding EBNA 1, two other open reading frames are found in the EBNA 1-specific cDNA. The first reading frame consists of several exons from BamHI W and Y viral genome fragments (W1, W2, Y1, and Y2). In our experiments, the W1 exon was expressed in the tryptophan-regulated expression vector pATH11. Rabbit sera, raised against the bacterial fusion protein, recognized one or two proteins of molecular weights between 30,000 and 100,000 in several EBV genome harboring Burkitt lymphoma and EBV immortalized peripheral blood cell lines. Although, in a few cell lines from both groups no specific protein could be detected. Immunofluorescence analysis and characterization of subcellular distribution demonstrated that this W/Y fragment encoded latent protein is located, in part, in the cytoskeleton fraction, and in the chromatin. In addition, 2-D immunoblot analysis revealed post-translational modifications of this latent protein, probably due to phosphorylation. In DNA-binding studies on DNA cellulose columns, this W/Y encoded latent protein exhibited specific DNA binding activities.

Amino Acid Sequence↗
PubMed2004

[Analysis of genomic polymorphism of typical and atypical strains of the plague pathogen using polymerase chain reaction with universal primers].

An analysis of genome polymorphism of the Y. pestis strains by using the method of polymerase chain reaction (PCR) for the tandem repeats of bacteriophage M13 DNA revealed a species similarity of both typical and atypical (according to diagnostic signs) plague-microbe strains. Strain Y. pestis A-1726 with the atypical differential-and-diagnostic properties, without the amplicon specified for Y. pestis and sized 1000 b.p., was identified among 27 analyzed Y. pestis strains. The amplicon profiles of the basic Y. pestis subtype were found to be different from such profiles of other Y. pestis subtypes.

Bacteriophage M13↗
PubMed2004

Transition metal transport in the green microalga Chlamydomonas reinhardtii--genomic sequence analysis.

Uptake and export systems play a major role in transition metal homeostasis. The objective of this study was to identify potential metal transport mechanisms in the green microalga Chlamydomonas reinhardtii. We concentrated on the four major transition metal transporter families found in plants and other organisms: the ZIP, CDF and Nramp families, and the CPx-ATPases. Using the information available for these protein families we performed comparative sequence analysis in the recently released genome of C. reinhardtii. Using this approach we were able to identify members of all four transporter families (four ZIPs, one CDF, two CPx-ATPases, and five Nramps). These findings advance our current knowledge of the metal transport processes present in C. reinhardtii. In addition, by subsequent in silico splicing of the genomic sequence we obtained cDNA sequences which led to the identification of ESTs (expressed sequence tags) in the C. reinhardtii EST database. These identified ESTs will be valuable for the cloning and characterization of several metal transporters utilized by the alga.

Amino Acid Sequence↗
PubMed2003

A case of nasal leiomyosarcoma: the first comparative genomic hybridization analysis.

Leiomyosarcomas are rare in the head and neck region. The treatment of choice is surgical resection. We present a case of leiomyosarcoma in a 50-year-old female patient, arising from the inferior turbinate. The tumor was resected by a transnasal microendoscopic approach and no evidence for tumor recurrence was found during an endoscopic and radiologic follow-up of two years. Cytogenetic analysis by means of comparative genomic hybridization revealed chromosomal gains at 4p13p15, 6p21p22, 7q22qter, 9q22qter and chromosomal losses at 10q22qter and 19p12p13.1. With augmented experience, the transnasal approach may be appropriate to resect circumscribed malignant tumors located in the nasal cavity.

Chromosome Aberrations↗
PubMed1995

Molecular epidemiology of bovine rotaviruses. Characterization of rotaviruses isolated from diarrhoeic calves by genome profile analysis.

Fifteen bovine rotavirus group A strains were isolated in several Italian regions over the period 1981-1989 from calves in ten neonatal diarrhoea outbreaks. The electrophoretical analysis of the genoma showed genomic variations and five different profiles were observed, including one with thirteen dsRNA segments. The finding of extra RNA fragments, with respect to the regular eleven genome segments, suggests the possibility of simultaneous or sequential infection by more than one electropherotype or a modification in the length of RNA segments during infection.

Animals↗
PubMed1995

Detection of p53 gene mutations in aspiration biopsy specimens from suspected breast cancers by polymerase chain reaction-single strand conformation polymorphism analysis.

Genomic DNA was extracted from aspiration biopsy specimens taken from 15 suspected cases of breast cancer, including 7 known cases of breast cancer, and the p53 gene was studied for evidence of mutation by using a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. In 5 of the 15 cases (33%), p53 gene mutation was identified and these tumors were subsequently histologically diagnosed as malignant. Further, DNA flow cytometry of the 15 tumors demonstrated that 6 (40%) were aneuploid and malignant, whereas 9 (60%) were diploid and benign. It was also found that the tumor cells in 5 aspirated cases that showed p53 gene mutations were all aneuploid, the p53 protein expression was positive, and the tumors were proved to be histologically malignant. It was thus concluded that the detection of p53 gene mutation by PCR-SSCP analysis of aspirated biopsy specimens from suspected breast cancers is a helpful method for achieving a more accurate diagnosis.

Adult↗
PubMed2004

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs.

Several widely used methods for predicting functional associations between proteins are based on the systematic analysis of genomic context. Efforts are ongoing to improve these methods and to search for novel aspects in genomes that could be exploited for function prediction. Here, we use gene expression data to demonstrate two functional implications of genome organization: first, chromosomal proximity indicates gene coregulation in prokaryotes independent of relative gene orientation; and second, adjacent bidirectionally transcribed genes (that is,'divergently' organized coding regions) with conserved gene orientation are strongly coregulated. We further demonstrate that such bidirectionally transcribed gene pairs are functionally associated and derive from this a novel genomic context method that reliably predicts links between >2,500 pairs of genes in approximately 100 species. Around 650 of these functional associations are supported by other genomic context methods. In most instances, one gene encodes a transcriptional regulator, and the other a nonregulatory protein. In-depth analysis in Escherichia coli shows that the vast majority of these regulators both control transcription of the divergently transcribed target gene/operon and auto-regulate their own biosynthesis. The method thus enables the prediction of target processes and regulatory features for several hundred transcriptional regulators.

Amino Acid Sequence↗
PubMed2006

Array comparative genomic hybridization analysis in first-trimester spontaneous abortions with 'normal' karyotypes.

Array comparative genomic hybridization (array CGH) analysis was conducted in chorionic villous samples from 20 first-trimester spontaneous abortions with G-banding normal chromosomes. A microarray, containing 2,173 BAC clones and covering the whole genome with a 1.5-Mb resolution, was constructed and used in the analysis. Two deletions were identified: a 1.4-Mb deletion at 3p26.2-p26.3 and a 13.7-Mb deletion at 13q32.3-qter. Reexamination of chromosome preparations from the sample with the 13.7-Mb deletion documented a mixture of cells with the 13q- chromosome and those with 46,XX chromosomes, the latter of which are likely to have been derived from contaminating decidual cells. This left the 1.4-Mb 3p deletion as the only instance with submicroscopic imbalance detected, giving a frequency of 1 in 19 (5%) G-banding normal abortions.

Abortion, Spontaneous↗
PubMed1985

Application of molecular biology to mental illness. Analysis of genomic DNA and brain mRNA.

Techniques in molecular biology and genetics have made it possible to systematically study gene effects in human disease. The number of gene clusters specifically encoding human brain structure and function is probably about 1,600 or half of all clusters. Evolutionary effects such as linkage disequilibrium and conservation of exons (DNA encoding structural proteins) as well as the fact that there are a tractable number of gene clusters involved, tend to make it quite likely that DNA pathology or DNA variation (polymorphism) predisposing to mental illness can be detected. Genes involved in mental illness can be detected either by studying DNA obtained from blood samples (genomic DNA) directly or by the analysis of mRNA and proteins from suitable cell or tissue preparations. The study of gene expression in the human brain is still in its infancy, nevertheless there are some hints that non-poly-adenylated mRNAs may be important in brain development and certain transcribed sequences may have a specific role in gene expression of the brain. The advantage of studying genomic DNA by the use of linkage and association analysis in multiply affected families is that it will, in the end, almost certainly yield a positive result for a disease with a substantial genetic input. Analysis of gene products from tissues such as brain could in theory detect specific disease genes but the approach will also identify genes secondarily affected by the disease process. Differentiation of genes that are primarily causing mental illness from those that are secondarily affected can be carried out by using such candidate genes as linkage markers in multiply affected families.

Animals↗
PubMed2005

[Libraries of large-insert genomic clones as a tool for molecular cytogenetic analysis of avian genome].

Integration of molecular and cytegenetic levels of investigation results in complex understanding of structural and functional genome organization. Gridded libraries of large-insert genomic clones represent a powerful tool of the genome analysis. Their utilization provides coordination of data on molecular organization of nucleic acids with cytogenetic data on the chromosome structure. These libraries played an important role in sequencing of genomes of human, mouse, and other organisms as an instrument linking molecular biological and cytogenetic data via construction of contigs and their localization on the chromosomes. They also enabled analysis of orthology between the mammalian genomes. The existing avian libraries fit molecular cytogenetic analysis of the class Aves genome, and can be successfully used for the isolation and characterization of large genomic fragments. This provides utilization of these libraries not only for the chromosome mapping, but also for positional cloning and search for candidate genes for quantitative traits.

Animals↗
PubMed1996

Molecular characterization of Echinostoma caproni and E. paraensei by random amplification of polymorphic DNA (RAPD) analysis.

Genomic DNA from Echinostoma caproni and Echinostoma paraensei was amplified by the polymerase chain reaction using primers (5'-TCGTAGCCAA and 5'-TCACGATGCA), originally found to differentiate species and strain of Schistosoma. The 2 putative species of Echinostoma produced distinct banding patterns clearly distinguishable from one another, thereby suggesting that RAPD (random amplification of polymorphic DNA) analysis may be useful for the identification of echinostome strains and species previously misunderstood or undescribed, and that primers developed for species within a given genus, e.g., Schistosoma, may have broader application in identifying other trematodes.

Animals↗
PubMed2004

Genome wide analysis of common and specific stress responses in adult drosophila melanogaster.

BACKGROUND: During their life, multicellular organisms are challenged with oxidative stress. It is generated by several reactive oxygen species (ROS), may limit lifespan and has been related to several human diseases. ROS can generate a wide variety of defects in many cellular components and thus the response of the organism challenged with oxidative stress may share some features with other stress responses. Conversely, in spite of recent progress, a complete functional analysis of the transcriptional responses to different oxidative stresses in model organisms is still missing. In addition, the functional significance of observed transcriptional changes is still elusive. RESULTS: We used oligonucleotide microarrays to address the specificities of transcriptional responses of adult Drosophila to different stresses induced by paraquat and H2O2, two oxidative stressors, and by tunicamycin which induces an endoplasmic reticulum (ER) stress. Both specific and common responses to the three stressors were observed and whole genome functional analysis identified several important classes of stress responsive genes. Within some functional classes, we observed that isozymes do not all behave similarly, which may reflect unsuspected functional specificities. Moreover, genetic experiments performed on a subset of lines bearing mutations in genes identified in microarray experiments showed that a significant number of these mutations may affect resistance of adult Drosophila to oxidative stress. CONCLUSIONS: A long term common stress response to paraquat- or H2O2-induced oxidative stresses and ER stress is observed for a significant number of genes. Besides this common response, the unexpected complexity of the stress responses to oxidative and ER stresses in Drosophila, suggest significant specificities in protective properties between genes associated to the same functional classes. According to our functional analysis, a large part of the genome may play a role in protective mechanisms against oxidative stress in Drosophila.

Animals↗
PubMed2005

Identification of a novel homozygous deletion region at 6q23.1 in medulloblastomas using high-resolution array comparative genomic hybridization analysis.

PURPOSE: The aim of this study is to comprehensively characterize genome copy number aberrations in medulloblastomas using high-resolution array comparative genomic hybridization. EXPERIMENTAL DESIGN: High-density genomic arrays containing 1,803 BAC clones were used to define recurrent chromosomal regions of gains or losses throughout the whole genome of medulloblastoma. A series of 3 medulloblastoma cell lines and 16 primary tumors were investigated. RESULTS: The detected consistent chromosomal aberrations included gains of 1q21.3-q23.1 (36.8%), 1q32.1 (47.4%), 2p23.1-p25.3 (52.6%), 7 (57.9%), 9q34.13-q34.3 (47.4%), 17p11.2-q25.3 (89.5%), and 20q13.31-q13.33 (42.1%), as well as losses of 3q26.1 (57.9%), 4q31.23-q32.3 (42.1%), 6q23.1-25.3 (57.9%), 8p22-23.3 (79%), 10q24.32-26.2 (57.9%), and 16q23.2-q24.3 (63.2%). One of the most notable aberrations was a homozygous deletion on chromosome 6q23 in the cell line DAOY, and single copy loss on 30.3% primary tumors. Further analyses defined a 0.887 Mbp minimal region of homozygous deletion at 6q23.1 flanked by markers SHGC-14149 (6q22.33) and SHGC-110551 (6q23.1). Quantitative reverse transcription-PCR analysis showed complete loss of expression of two genes located at 6q23.1, AK091351 (hypothetical protein FLJ34032) and KIAA1913, in the cell line DAOY. mRNA levels of these genes was reduced in cell lines D283 and D384, and in 50% and 70% of primary tumors, respectively. CONCLUSION: Current array comparative genomic hybridization analysis generates a comprehensive pattern of chromosomal aberrations in medulloblastomas. This information will lead to a better understanding of medulloblastoma tumorigenesis. The delineated regions of gains or losses will indicate locations of medulloblastoma-associated genes. A 0.887 Mbp homozygous deletion region was newly identified at 6q23.1. Frequent detection of reduced expression of AK091351 and KIAA1913 genes implicates them as suppressors of medulloblastoma tumorigenesis.

Adolescent↗
PubMed2000

High resolution comparative genomic hybridisation analysis reveals imbalances in dyschromosomal patients with normal or apparently balanced conventional karyotypes.

A sensitive technique is needed for screening whole genome imbalances in dyschromosomal patients when G-banding shows normal karyotypes or apparently balanced translocations. In this study we performed highly sensitive comparative genomic hybridisation analysis on a number of such cases and revealed chromosomal imbalances in all.

Chromosome Aberrations↗
PubMed2005

Microarray comparative genomic hybridisation analysis of intraocular uveal melanomas identifies distinctive imbalances associated with loss of chromosome 3.

Defining regions of genomic imbalance can identify genes involved in tumour development. Conventional cytogenetics has identified several nonrandom copy number alterations (CNA) in uveal melanomas (UVM), which include monosomy 3, chromosome 6 abnormalities and gain of 8q. To gain further insight into the CNAs and define the regions involved more precisely we analysed 18 primary UVMs using 1 Mb BAC microarray comparative genomic hybridisation (CGH). Our analysis showed that the most common genomic imbalances were 8q gain (78%), 6p gain (67%) and monosomy 3 (56%). Two distinct CGH profiles could be delineated on the basis of the chromosome 3 status. The most common genetic changes in monosomy 3 tumours, in our study, were gain of 8q11.21-q24.3, 6p25.1-p21.2, 21q21.2-q21.3 and 21q22.13-q22.3 and loss of 1p36.33-p34.3, 1p31.1-p21.2, 6q16.2-q25.3 and 8p23.3-p11.23. In contrast, disomy 3 tumours showed recurrent gains of only 6p25.3-p22.3 and 8q23.2-q24.3. Our approach allowed definition of the smallest overlapping regions of imbalance, which may be important in the development of UVM.

Adult↗
PubMed1978

Adenovirus type 2 early proteins synthesized in vitro and in vivo: identification in infected cells of the 38,000- to 50,000- molecular-weight protein encoded by the left end of the adenovirus type 2 genome.

Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of protein synthesized early after injection of human cells with adenovirus type 2 (Ad2) showed that polypeptides of 11,000 (11K), 12K, 14K, 15K, 19K, 21K, 24K, and 72k molecular weight were present in infected but not in mock-infected cells. These polypeptides corresponded in electrophoretic mobility to the following polypeptides synthesized in vitro by using mRNA complementary to specific regions of the Ad2 genome: 11K, 19K, 21K (91.5 to 96.8 map units), 14K (78.2 to 83.4 map units), 72K (62.4 to 67.9 map units), and 15K (4.9 to 11.0 map units). Polypeptides of 25K, 17K, 15.5K, and 13K were also synthesized in vitro, but have not yet been detected in infected cells. In addition, six adeno-specific polypeptides of 38 to 50K molecular weight could be discerned in infected cells if two-dimensional isoelectric focusing-polyacrylamide gel electrophoresis was used to compare extracts from infected and mock-infected cells. Partial protease digestion showed these 38 to 50K polypeptides to be related in sequence to each other and to the 40 to 50K polypeptide made in vitro (1.3 to 4.0 map units).

Adenoviruses, Human↗