Journal: Orphanet Journal of Rare Diseases

Article Title: Comprehensive characterization of malignant phyllodes tumor by whole genomic and proteomic analysis: biological implications for targeted therapy opportunities

doi: 10.1186/1750-1172-8-112

Figure Lengend Snippet: Summary of molecular profiling analyses from various CLIA certified methods in a patient with malignant phyllodes sarcoma

Article Snippet: Whole-genome array-based comparative genomic hybridization (array CGH) was performed by using the CLIA-certified DNAarrayTM (CombiMatrix Diagnostics, Irvine, CA).

Techniques: Sequencing, Hybridization, Immunohistochemistry, Staining

Journal: Orphanet Journal of Rare Diseases

Article Title: Comprehensive characterization of malignant phyllodes tumor by whole genomic and proteomic analysis: biological implications for targeted therapy opportunities

doi: 10.1186/1750-1172-8-112

Figure Lengend Snippet: Imaging studies, histopathology and FISH studies: UA and B: CT of the chest showing metastatic masses in the lung. C Hematoxylin and Eosin stained section of the tumor from the right mastectomy shows a malignant sarcoma/malignant phyllodes tumor that has high stromal cellularity and a mitotic index of 11 per 10 high power fields. D HER - 2 / neu by Fluorescence in Situ Hybridization (FISH) HER-2 gene amplification was assessed utilizing the PathVysion assay (Vysis Corp., Downers Grove, Illinois). The identification probes for the HER-2 (SpectrumOrange) and alpha satellite DNA sequence at the centromeric region of chromosome 17 (SpectrumGreen) were hybridized according to the manufacturer’s guidelines. At least twenty non-overlapping nuclei containing at least one orange and one green signal were enumerated. The ratio of orange signals (HER-2 gene) to green signals (chromosome 17) was calculated. A ratio greater than or equal to 2.0 is considered as amplified based on the FDA approval in this kit. The CAP HER-2 consensus conference 2002 suggested that a ratio of 1.8-2.2 be considered as borderline.

Article Snippet: Whole-genome array-based comparative genomic hybridization (array CGH) was performed by using the CLIA-certified DNAarrayTM (CombiMatrix Diagnostics, Irvine, CA).

Techniques: Imaging, Histopathology, Staining, Fluorescence, In Situ Hybridization, Amplification, Sequencing

Journal: PLoS ONE

Article Title: Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut

doi: 10.1371/journal.pone.0044229

Figure Lengend Snippet: Panel a displays a Venn diagram of homologs shared between sequenced bifidobacterial- Gardnella genomes. Panel b shows the percentage of amino acid identity of the top-scoring self-matches for protein-coding genes in the analysed bacteria using the predicted proteome of B. asteroides PRL2011 as a reference. For each bacterium, the deduced protein-coding regions for each gene were compared with those derived from the B. asteroides PRL2011 genome. Panel c depicts a phylogenetic supertree based on the sequences of Bifidobacterium-Gardnella core proteins. Panel d indicates the generated phylogenetic tree based on 16S rRNA gene sequences from the same set of bacteria. Three other members of the Actinobacteria phylum, N. farcinia , T. whipplei and L. xyli , were also included in the analyses depicted in panels c and d, while the trees were rooted using L. salivarius as outgroup.

Article Snippet: Hybridization of labeled cDNA to B. asteroides PRL2011 arrays was performed according to CombiMatrix protocols ( http://www.combimatrix.com/support_docs.htm ).

Techniques: Bacteria, Derivative Assay, Generated

Journal: PLoS ONE

Article Title: Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut

doi: 10.1371/journal.pone.0044229

Figure Lengend Snippet: Panel a represents a circular genome atlas of B. asteroides PRL2011 (circle 1) with mapped orthologs (defined as reciprocal best FastA hits with more than 30% identity over at least 80% of both protein lengths) in seven publicly available Bifidobacterium genomes. From the outer circle, circle (2) shows B. breve UCC2003, circle (3) B. animalis subsp. lactis DSM 10140, circle (4) B. longum subsp. infantis ATCC 15697, circle (5) B. dentium Bd1, circle (6) B. longum NCC2705, circle (7) B. bifidum PRL2010, circle (8) B. adolescentis ATCC 15703. Circle(9) illustrates B. asteroides PRL2011 G+C% deviation followed by circle (10) that highlights B. asteroides PRL2011 GC skew (G−C/G+C). Moreover, the outer insets indicate the main genetic loci encoding enzymes involved in respiratory metabolism, which are mapped on the circular genome atlas of B. asteroides PRL2011. Panel b shows a schematic representation of a cell and metabolic pathways for respiration. The different ORFs of B. asteroides PRL2011 encoding the presumed enzymes involved in the respiratory chain are indicated.

Article Snippet: Hybridization of labeled cDNA to B. asteroides PRL2011 arrays was performed according to CombiMatrix protocols ( http://www.combimatrix.com/support_docs.htm ).

Techniques:

Journal: PLoS ONE

Article Title: Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut

doi: 10.1371/journal.pone.0044229

Figure Lengend Snippet: Panel a shows the comparative genomic hybridization data obtained using different members of the B. asteroides species. Each horizontal row corresponds to a probe on the array, and genes are ordered vertically according to their position on the PRL2011 genome. The columns represent the analysed strains, and strains are indicated by their strain codes. The colour code corresponding to the presence/absence is given at the top right of the figure: the gradient goes from black to yellow to indicate the presence, divergence or absence of a gene sequence. The predicted function of particular genes is shown on the right-hand margin. Black typed descriptions relate to most significant DNA regions that are absent in the investigated strains. Red typed descriptions represent DNA regions that encode enzymes predicted to be involved in respiration in PRL2011. Panel b details the presence (black) or absence (yellow) of key genes predicted to be involved in respiration within the B. asteroides phylogenetic group as well as in other genome sequenced bifidobacteria based on genomic data.

Article Snippet: Hybridization of labeled cDNA to B. asteroides PRL2011 arrays was performed according to CombiMatrix protocols ( http://www.combimatrix.com/support_docs.htm ).

Techniques: Hybridization, Sequencing

Journal: PLoS ONE

Article Title: Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut

doi: 10.1371/journal.pone.0044229

Figure Lengend Snippet: Panel a displays the global transcription profiling of PRL2011 cells under different growth conditions. Panel b shows the whole genome transcriptome-based clustering data analysis. Panel c represents a heat-map indicating the change in transcription levels of putative respiratory chain-encoding genes upon cultivation of PRL2011 cells under different cultivation conditions. Lane 1, transcriptome of PRL2011 cells cultivated in the absence of oxygen and protoporphyrin; lane 2, transcriptome of PRL2011 cells in the presence of oxygen and protoporphyrin; lane 3, transcriptome of PRL2011 cells in the absence of oxygen and hemin; lane 4, transcriptome of PRL2011 cells in the presence of oxygen and hemin; lane 5, transcriptome of PRL2011 cells in the absence of oxygen and glucuronic acid; lane 6, transcriptome of PRL2011 cells in the presence of oxygen and glucuronic acid; lane 7, transcriptome of PRL2011 cells in the presence of iron chloride (3 mM) and under anaerobic conditions; lane 8, transcriptome of PRL2011 cells in the presence of iron chloride (3 mM) and under aerobic conditions. Each row represents a separate transcript and each column represents a separate sample. Colour legend is on the bottom of the figure. Green indicates DNA regions which are actively transcribed, while black represents DNA regions that exhibit no or very low transcriptional activity. In panel a, the arrows indicate the change in the transcription of PRL2011 genes encoding for putative respiratory chain.

Article Snippet: Hybridization of labeled cDNA to B. asteroides PRL2011 arrays was performed according to CombiMatrix protocols ( http://www.combimatrix.com/support_docs.htm ).

Techniques: Activity Assay