Expression profiling of cancer-related long non-coding RNAs revealed upregulation and biomarker potential of HAR1B and JPX in colorectal cancer

Molecular Biology Reports - Aberrant expressions of long non-coding RNAs promote cancer development including colorectal cancer. Expression profiling of cancer-related lncRNAs may introduce new...     

Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood

MOTIVATION: In two-color microarray experiments, well-known differences exist in the labeling and hybridization efficiency of Cy3 and Cy5 dyes. Previous reports have revealed that these differences can vary on a gene-by-gene basis, an effect termed gene-specific dye bias. If uncorrected, this bias can influence the determination of differentially expressed genes. RESULTS: We show that the magnitude of the bias scales multiplicatively with signal intensity and is dependent on which nucleotide has been conjugated to the fluorescent dye. A method is proposed to account for gene-specific dye bias within a maximum-likelihood error modeling framework. Using two different labeling schemes, we show that correcting for gene-specific dye bias results in the superior identification of differentially expressed genes within this framework. Improvement is also possible in related ANOVA approaches. AVAILABILITY: A software implementation of this procedure is freely available at http://cellcircuits.org/VERA     

Excitation of System I and System II in Photosynthesis as a Possible Control Mechanism of Glycolate Metabolism in the Blue-Green Alga Anacystis nidulans

Photosynthetic enhancement studies performed at 619 nm (excitation of Systems I and II) and at 446 nm (mainly excitation of System I) revealed an 18% photosynthetic enhancement simultaneously with a 31% reduction in glycolate excretion. This observation supports the hypothesis that some glycolate may be consumed in an oxidation process associated with System I when System II is poorly excited and the supply of electrons from the water splitting process of photosynthesis is low.     

Repeated immunostaining of the same tissue section using alkaline phosphatase as a reporter

One can determine the best dilution of a primary antibody for immunohistochemistry that uses horseradish peroxidase conjugated to a secondary antibody by testing increasing concentrations sequentially on the same tissue section. When the same tissue section is incubated repeatedly with increasing concentrations of primary antibodies to epithelial membrane antigen, smooth muscle α-actin, or vimentin using alkaline phosphatase conjugated to a secondary antibody as the reporter, the best staining was obtained with a less concentrated primary antibody than was optimal for a single staining test. The best concentration of primary antibody for single run staining using an alkaline phosphatase reporting system is usually four times the best concentration for staining with multiple runs. The optimal concentration can be determined by denaturing the residual alkaline phosphatase and extracting residual stain by incubating the section in 4:1 diglyme:phosphate buffered saline for 20 min at 80^o C between tests of primary antibody concentrations. I tested the method for four chromogens from one supplier and one chromogen from a different supplier.     

Inventing Engineered Organoids for end-stage liver failure patients

Journal of Molecular Histology - End-stage liver disease (ESLD) is a term used clinically in reference to a group of liver diseases with liver transplantation as the choice of treatment. Due to the...     

人肿瘤浸润淋巴细胞的克隆化

肿瘤组织经机械剪切和酶消化分离肿瘤浸润淋巴细胞(TIL)。TIL在含1000U/ml重组人白细胞介素-2(rhIL-2)的培养液中培养6d后,植入含1000U/ml rhIL-2的软琼脂半固体培养基中培养,7d后将形成的克隆转移到含rhIL-2的培养液中培养。~(51)Cr释放法测定结果表明,约30％的克隆对NK敏感的K562细胞和对NK不敏感的H7402肝癌细胞有细胞毒性,为具有杀瘤活性的TIL杀伤克隆(TIL-K)。60％以上TIL-K克隆在含IL-2的培养液中可持续地增殖2～3个月,其细胞数可扩增至10~8～10~9,并始终保持对肿瘤细胞的细胞毒性。TIL-K克隆的表型为CD3~ 、CD4~-、CD8~ 、CD16~-,有T细胞抗原受体β链基因的表达,说明其属T细胞系统。采用半固体-液体两步培养法可获取大量高纯度具有广谱杀瘤活性的TIL,本研究有助于TIL的深入研究和临床应用。     

Differing reactions of monoclonal anti-A antibodies with oligosaccharides related to blood group A

Inhibition radioimmunoassays with blood group A-related oligosaccharides have been used to investigate the specificities of six monoclonal anti-A antibodies, three of which had been intentionally generated by immunization of mice with blood group A erythrocytes and A-active blood group substance, and three were incidentally produced following immunization of mice with human tonsil cell membranes or a human colon cancer cell line. By hemagglutination, these antibodies are highly specific for human blood group A erythrocytes. However, they differ from one another in their reaction patterns with mono- and difucosyl A antigen structures and the corresponding afucosyl sequences on Type 1 and Type 2 backbone structures. The six antibodies, together with four previously characterized anti-A monoclonal antibodies (originally raised against the receptor for epidermal growth factor) have been classified into five groups. The first two groups consist of antibodies with broad specificities for A-related structures. There are five antibodies in the first group (TL5, 29.1, A17/3D1, MH2/6D4, and MH1/5D1) reacting to varying degrees with the mono- and difucosyl A antigen structures on either type of backbone sequence. In the second group are two antibodies (A15/3D4 and A15/3D3) which are difficult to inhibit with the oligosaccharides tested, but they reacted best with monofucosyl A structure on either type of backbone. Each of the remaining three antibodies had a distinct and more restricted reaction pattern, with a specificity for the difucosyl A antigen on both types of backbone (antibody EGR/G49) or the Type 1-based mono- and difucosyl A antigen structures (antibody MAS 016c) or the Type 2-based monofucosyl A antigen structure (antibody 455). The reactions of four of the antibodies with N-acetylgalactosamine or with oligosaccharides containing the afucosyl sequence GalNAc alpha 1-3Gal suggest that they may react with certain glycoconjugates with alpha-N-acetylgalactosaminyl termini ("A-like" structures) that are unrelated to the products of the blood group A gene-specified alpha-N-acetylgalactosaminyl-transferase. Knowledge of the differing reactions of these monoclonal antibodies is important for interpreting their reactions with glycoproteins and glycolipids of diverse origins.     

Purification and some catalytic properties of phosphoglucomutase from maize leaves

Phosphoglucomutase (EC 2.7.5.1, PGM) was purified to homogeneity from maize (Zea mays L.) leaves. The enzyme had specific activity 11. 7 U/mg protein and molecular mass (determined by gel-chromatography) of 133 +/- 4 kD. The molecular mass of PGM subunits determined by SDS-electrophoresis was 66 +/- 3 kD. The enzyme had Km for glucose-1-phosphate and glucose-1,6-diphosphate of 20.0 +/- 0.9 and 16.0 +/- 0.8 &mgr;M, respectively. Concentrations of glucose-1-phosphate and glucose-1,6-diphosphate above 3 and 0.4 mM, respectively, cause substrate inhibition. The enzyme activity was maximal at pH 8.0 and temperature 35 degreesC. Magnesium ions activate the enzyme and manganese ions inhibit it. 3-Phosphoglycerate is an uncompetitive inhibitor of the enzyme (Ki = 1.22 +/- 0.05 mM). Fructose-6-phosphate, 6-phosphogluconate, and ADP activate PGM, whereas ATP, UTP, and AMP inhibit the enzyme. Citrate was also a potent inhibitor, inhibitory effects of isocitrate and cis-aconitate being less pronounced.     

Altered Receptor Specificity and Cell Tropism of D222G Hemagglutinin Mutants Isolated from Fatal Cases of Pandemic A(H1N1) 2009 Influenza Virus

Mutations in the receptor-binding site of the hemagglutinin of pandemic influenza A(H1N1) 2009 viruses have been detected sporadically. An Asp222Gly (D222G) substitution has been associated with severe or fatal disease. Here we show that 222G variants infected a higher proportion of ciliated cells in cultures of human airway epithelium than did viruses with 222D or 222E, which targeted mainly nonciliated cells. Carbohydrate microarray analyses showed that 222G variants bind a broader range of α2-3-linked sialyl receptor sequences of a type expressed on ciliated bronchial epithelial cells and on epithelia within the lung. These features of 222G mutants may contribute to exacerbation of disease.Although the majority of disease cases have been mild, the pandemic influenza A(H1N1) 2009 (H1N1pdm) virus has caused a substantial number of severe and fatal infections (2). Mutants with a D222G or D222E substitution (D225G or D225E in the H3 numbering system) in the receptor-binding site of the virus hemagglutinin (HA) have been detected sporadically (1), and the D222G substitution has been observed to correlate with cases of severe or fatal disease (1, 3, 9, 14). Cell surface receptors for influenza viruses are sialyl glycans (α2-3 Sia or α2-6 Sia) with terminal sialic acid linked α2-3 or α2-6, respectively, to a penultimate galactose. These differ in distribution in the tissues and cells of different species. The sialyl glycans are differentially recognized by the HAs of human and animal influenza viruses and are critical determinants of host range and tissue tropism (16). Using an experimental system of differentiated cultures of human tracheobronchial epithelial cells (HTBE) for studying influenza virus cell tropism, we and others have established that in the initial stages of infection, seasonal human influenza viruses which recognize α2-6 Sia receptors infect mainly nonciliated cells, whereas avian viruses which recognize α2-3 Sia receptors predominantly infect ciliated cells (8, 17, 22).Previous analyses of human and swine influenza H1N1 viruses (5, 15, 21) and preliminary studies of H1N1pdm viruses (24) have indicated that amino acid substitutions in the HA at position 222 may affect the specificity of receptor binding. This, in turn, would be predicted to determine the range of cell types in human respiratory tissues infected by the viruses (17, 20, 22, 23). We have therefore examined the influence of the D222G and D222E substitutions on the cell tropism of H1N1pdm viruses in HTBE cultures (Table ​(Table1).1). Five viruses were isolated from clinical material in MDCK cells and passaged solely in these cells. Two of these, A/Hamburg/5/2009 (Ham) (4) isolated from a case of mild infection and A/Moldova/G186/2009 (Mol) from a serious but nonfatal infection, had 222D. A/Dakar/37/2009 (Dak) isolated from a mild case of the disease had 222E. Two isolates from fatal cases, A/Lviv/N6/2009 (Lvi) and A/Norway/3206-3/2009 (Nor), had 222G. A sixth virus tested, A/Hamburg/5/2009-e (Ham-e), was derived from Ham by egg passage and plaque purification in MDCK cells and differed by a single substitution, D222G.

TABLE 1.

Differences in amino acid sequence of the HAs of the H1N1pdm viruses and cell tropism in HTBE cultures