We have established a highly sensitive and quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) method to detect axillary lymph node metastases of breast cancer. Amplifying cytokeratin 19 (CK19) mRNA transcripts using real-time TaqMan PCR made it possible to quantify axillary metastatic burden. Metastases in 358 axillary lymph nodes obtained from 23 breast cancers of 22 patients were investigated by conventional haematoxylin and eosin (H&E) staining, immunohistochemical staining and quantitative RT-PCR assay. The detection rates of axillary lymph node metastasis using H&E staining, immunohistochemistry and RT-PCR assay were 4.5, 5.9 and 13.1%, respectively. RT-PCR assay was the most sensitive of these three methods for detecting lymph node metastases. Cytokeratin 19 mRNA expression values of both histologically and immunohistochemically positive lymph nodes were significantly higher than the values for lymph nodes judged to be negative by both histological and immunohistochemical methods (P<0.0001), and those of histologically negative, but immunohistochemically positive lymph nodes were significantly higher than the values for lymph nodes judged to be negative by both histological and immunohistochemical methods (P<0.0001). Furthermore, metastatic rates of sentinel nodes were higher than the rates of nonsentinel lymph nodes as measured by all three methods. These results indicate that quantitative RT-PCR assay is a sensitive and reliable method for detecting lymph node metastasis. Furthermore, quantification of metastases in sentinel lymph nodes by quantitative RT-PCR assay may be useful to assess the entire axillary burden of breast cancer patients.

In this report, we have analyzed the effects of left and right STN stimulation separately on different aspects of speech. Significant differences were found between left and right stimulation. It appears that selective left-sided stimulation has a profoundly negative effect on prosody, articulation and hence intelligibility. Right-sided stimulation does not display this side-effect. There is no significant difference in speech characteristics between bilateral stimulation on and off. We suggest that a balanced tuning of bilateral basal ganglia networks is necessary for speech, and that the left circuit is probably dominant.

Angiogenic defects in Id mutant mice inhibit the growth of tumor xenografts, providing a genetic model for antiangiogenic stress. Our work tests the consequences of such stress on progression of more physiological Pten+/- tumors. While tumor growth occurs despite impaired angiogenesis, disruption of vasculature by Id loss causes tumor cells to experience hypoxia and necrosis, the extent of which is tumor dependent. We show that bone-marrow-derived endothelial precursors contribute functionally to neovasculature of some but not all Pten+/- tumors, partially rescuing Id mutant phenotype. We demonstrate that loss of Id1 in tumor endothelial cells results in downregulation of several proangiogenic genes, including alpha6 and beta4 integrins, matrix metalloprotease-2, and fibroblast growth factor receptor-1. Inhibition of these factors phenocopies loss of Id in in vivo angiogenesis assays.

The objective of this study was to determine whether centrally administered leptin decreased liver and adipose SCD1 expression or adipose resistin expression, and whether these effects were mediated by central melanocortin receptors. Male Sprague-Dawley rats were injected into the lateral cerebral ventricle (i.c.v.) once daily for 4 days with artificial cerebrospinal fluid (aCSF, 5 microl), leptin (10 microg) or MTII (0.1 nmol); two other groups were pretreated icv with the melanocortin antagonist, SHU9119 (1.0 nmol), followed by leptin or MTII. Epididymal and inguinal adipose tissue and liver were collected after rats were killed and mRNA expression of SCD1 and resistin was measured. Both leptin and MTII reduced SCD1 expression and pretreatment with SHU9119 reversed their effects. Neither leptin nor MTII affected resistin expression, but it was increased by SHU9119. These results show that CNS melanocortin receptors are likely mediators of leptin's effects on SCD1 expression in liver and adipose tissue, The findings were inconclusive concerning the effects of leptin and melanocortins on adipose resistin expression.

It is generally believed that significant ribosomal frameshifting during translation does not occur without a functional purpose. The distribution of two frameshift-prone sequences, A_AAA_AAG and CCC_TGA, in coding regions of Escherichia coli has been analyzed. Although a moderate level of selection against the first sequence is evident, 68 genes contain A_AAA_AAG and 19 contain CCC_TGA. The majority of those tested in their genomic context showed >1% frameshifting. Comparative sequence analysis was employed to assess a potential biological role for frameshifting in decoding these genes. Two new candidates, in pheL and ydaY, for utilized frameshifting have been identified in addition to those previously known in dnaX and nine insertion sequence elements. For the majority of the shift-prone sequences no functional role can be attributed to them, and the frameshifting is likely erroneous. However, none of frameshift sequences is in the 306 most highly expressed genes. The unexpected conclusion is that moderate frameshifting during expression of at least some other genes is not sufficiently harmful for cells to trigger strong negative evolutionary pressure.

Several theories have been proposed to explain the phenomenon of tissue restoration in amphibians and higher order animals. These theories include dedifferentiation of damaged tissues, transdifferentiation of lineage-committed stem cells, and activation of quiescent stem cells. Young and colleagues demonstrated that connective tissues throughout the body contain multiple populations of quiescent lineage-committed progenitor stem cells and lineage-uncommitted pluripotent stem cells. Subsequent cloning and cell sorting studies identified quiescent lineage-uncommitted pluripotent mesenchymal stem cells, capable of forming any mesodermal cell type, and pluripotent epiblastic-like stem cells, capable of forming any somatic cell type. Based on their studies, they propose at least 11 categories of quiescent reserve stem cells resident within postnatal animals, including humans. These categories are pluripotent epiblastic-like stem cells, pluripotent ectodermal stem cells, pluripotent epidermal stem cells, pluripotent neuronal stem cells, pluripotent neural crest stem cells, pluripotent mesenchymal (mesodermal) stem cells, pluripotent endodermal stem cells, multipotent progenitor stem cells, tripotent progenitor stem cells, bipotent progenitor stem cells, and unipotent progenitor stem cells. Thus, activation of quiescent reserve stem cells, i.e., lineage-committed progenitor stem cells and lineage-uncommitted pluripotent stem cells, resident within the connective tissues could provide for the continual maintenance and repair of the postnatal organism after birth.

The role of lysophosphatidylcholine (LPC) in the induction of MCP-1, IL-8 and RANTES, which are chemotactic factors to monocytes, neutrophils and lymphocytes, respectively, by human vascular endothelial cells (EC), was examined. LPC induced the expression of MCP-1 and IL-8 in a concentration- and time-dependent manner in microvascular EC (MVEC) and in large vessel EC from aorta, pulmonary artery and umbilical vein. LPC also induced RANTES in MVEC but not in large vessel EC. Signaling pathways responsible for LPC induction of chemokines were examined in MVEC. LPC and TNFalpha, a cytokine secreted in sites of inflammation, additively stimulated RANTES expression. LPC did not augment TNFalpha induction of MCP-1 or IL-8. A platelet-activating factor receptor antagonist (BN52021) failed to block LPC induction of MVEC chemokines, but the G(i)-protein inhibitor pertussis toxin partially blocked LPC induction of RANTES and IL-8. LPC activated multiple kinases in MVEC; it increased the phosphorylation of ERK1/2, AKT and p38 MAP kinase in a time-dependent manner. An inhibitor of the MAPK/ERK pathway, PD98059, blocked the phosphorylation of ERK1/2 and RANTES induction by LPC, but augmented IL-8 induction. LY294002, a specific inhibitor of phosphoinositide 3 kinase (PI3 kinase), blunted the phosphorylation of AKT and inhibited LPC induction of RANTES more strongly than IL-8. Inhibition of p38 MAP kinase pathway by SB202190 also blocked LPC-induced expression of IL-8 and RANTES. Our results suggest that LPC induction of chemokines in MVEC is distinct from that in large vessel EC, and required the activities of MAP kinases and PI3 kinase for the induction of RANTES and IL-8. We speculate that the presence of LPC, a bioactive lipid product of phospholipase A(2) (PLA(2)) and a constituent of oxidized low-density lipoprotein, can differentially influence the chemotaxis of particular leukocyte subpopulations during inflammation.

The cerebral cortex (CX), cingulate CX (cgCX), and striatum (STR) play an important role in locomotion, cognition, emotion, and reward-motivated behaviors, and are altered by prenatal morphine exposure. We have demonstrated that delta-opioid receptors in the CX and STR of adult male and female rats are altered by prenatal morphine exposure and gonadal hormonal treatment. Because morphine binds with greater affinity to mu- than delta-opioid receptors, the present study examined the effect of prenatal morphine exposure on mu-opioid receptor density in the CX, cgCX, and STR of adult male and female rats using receptor autoradiography. In Experiment 1, three groups of adult male rats were analyzed: intact, gonadally intact; GNX, gonadectomized; and TP, GNX and testosterone propionate (TP)-treated. In Experiment 2, four groups of adult females were analyzed: OVX, ovariectomized; EB, OVX and estradiol benzoate (EB)-treated; P, OVX and progesterone (P)-treated; and EB+P, OVX and EB- and P-treated. In male rats, GNX and TP males had lower mu-opioid receptor densities in all three brain regions than gonadally intact males regardless of prenatal drug exposure. In female rats, OVX, EB+P-treated females had lower mu-opioid receptor density in the STR than OVX only females regardless of prenatal drug exposure. There were no drug or gonadal hormone effects in the CX or in the cgCX of female rats. Thus, the present study demonstrates that gonadal hormones, and not prenatal morphine exposure, alter the density of mu-opioid receptors in the CX, cgCX, and STR of adult male and female rats.

We have previously shown that abstinence from morphine by either abrupt (AW) or precipitated (PW) withdrawal induces greater than 80% suppression in the capacity to mount an in vitro plaque-forming cell (PFC) response to sheep red blood cells at 24-h post withdrawal. Present studies on the mechanisms of immunosuppression showed that addition of normal unfractionated spleen cells, macrophage-enriched adherent cells, or CD11b(+) purified macrophages, to spleen cells taken from withdrawn mice, restored immune responses. Spleen cells from mice undergoing withdrawal also had decreased splenic mRNA and/or protein levels of IL-1beta, IL-1Ra, TNF-alpha, IL-12, and IFN-gamma. Addition of IL-1beta or IFN-gamma to AW cultures was able to reverse their immunosuppression. These results strongly suggest that morphine withdrawal results in a deficit of macrophage function.

Interleukin-1 (IL-1) exerts numerous effects in the central nervous system and has been implicated in synaptic plasticity. The objective of this study was to investigate the role of endogenous as well as exogenous IL-1 on long-term potentiation (LTP). Hippocampal slices incubated at 34-36 degrees C show enhanced levels of IL-1alpha and IL-1beta compared to slices incubated at 21-24 degrees C. IL-1 inhibits LTP induced by theta-burst stimulation (TBS) at either temperature. IL-1 receptor antagonist (IL-1ra) had no effect on LTP at 21-24 degrees C, but displayed a concentration-dependent inhibition of LTP at 34-36 degrees C. Under control conditions, the magnitude of LTP was not temperature dependent. These data suggest that IL-1 is required for LTP under physiological conditions but at higher doses, as encountered in pathological conditions, IL-1 inhibits LTP.

Normalization means to adjust microarray data for effects which arise from variation in the technology rather than from biological differences between the RNA samples or between the printed probes. This paper describes normalization methods based on the fact that dye balance typically varies with spot intensity and with spatial position on the array. Print-tip loess normalization provides a well-tested general purpose normalization method which has given good results on a wide range of arrays. The method may be refined by using quality weights for individual spots. The method is best combined with diagnostic plots of the data which display the spatial and intensity trends. When diagnostic plots show that biases still remain in the data after normalization, further normalization steps such as plate-order normalization or scale-normalization between the arrays may be undertaken. Composite normalization may be used when control spots are available which are known to be not differentially expressed. Variations on loess normalization include global loess normalization and two-dimensional normalization. Detailed commands are given to implement the normalization techniques using freely available software.

In the past several years, oligonucleotide microarrays have emerged as a widely used tool for the simultaneous, non-biased measurement of expression levels for thousands of genes. Several challenges exist in successfully utilizing this biotechnology; principal among these is analysis of microarray data. An experiment to measure differential gene expression can consist of a dozen microarrays, each consisting of over a hundred thousand data points. Previously, we have described the use of a novel algorithm for analyzing oligonucleotide microarrays and assessing changes in gene expression. This algorithm describes changes in expression in terms of the statistical significance (S-score) of change, which combines signals detected by multiple probe pairs according to an error model characteristic of oligonucleotide arrays. Software is available that simplifies the use of the application of this algorithm so that it may be applied to improving the analysis of oligonucleotide microarray data. The application of this method to problems of the central nervous system is discussed.

DNA array technology now allows an enormous amount of expression data to be obtained. For large-scale gene profiling enterprises, this is of course welcome. However, the scientist interested in follow-up studies of a handful of differentially expressed genes may find it hard to sift through the vast datasets to pinpoint genes with the most desirable and reliable behaviors. Here, we present the methodology we have employed to discover genes differentially expressed in the adult mouse brain. We first used Affymetrix microarrays to compare gene expression from five different brain regions: the amygdala, cerebellum, hippocampus, olfactory bulb, and periaqueductal gray. Second, we identified genes differentially expressed within three distinct amygdala subnuclei. In this case, the tissue was microdissected by laser-capture to minimize contamination from adjacent subnuclei, and extracted RNA was subjected to three rounds of linear amplification prior to hybridization to the microarrays. To select candidate genes, we developed a custom algorithm to identify those genes with the most robust changes in expression across different replicate samples. Confirmation of expression patterns with in situ hybridization uncovered further criteria to consider in the selection process.

Topoisomerase I (Topo I) is mostly known for its role in DNA relaxation, which is required for duplication and transcription. Topo I acts as a protein kinase mainly directed to the mRNA splicing factor SC35. Camptothecin is one of the specific Topo I inhibitors and is effective on the two functions of the enzyme. In this study we demonstrated that treatment of KB cells with camptothecin for only 30 min induced the 3D reorganization and redistribution of three proteins involved in the nucleus machinery, P 120, pKi-67, and SC 35, and this occurred in a cell cycle-dependent manner. Our data were obtained from confocal microscopic studies after immunolabeling, 3D reconstruction, and measurement of the nuclear components volumes. In the presence of camptothecin, P 120, which occupied the nucleolar volume, lost its reticulation and pKi-67 was redistributed within the nucleoplasm and even into the cytoplasm. Finally, for SC 35 the fusion of its dots into bigger volumes was observed specifically during the G1 phase. Variations of volumes were also observed for the nucleolus and for the nucleus. These results pointed out that, depending on the cell cycle phase, Topo I functions were selective toward the three different proteins.

Chemokines are implicated in tumor pathogenesis, although it is unclear whether they affect human cancer progression positively or negatively. We found that activation of the chemokine receptor CCR5 regulates p53 transcriptional activity in breast cancer cells through pertussis toxin-, JAK2-, and p38 mitogen-activated protein kinase-dependent mechanisms. CCR5 blockade significantly enhanced proliferation of xenografts from tumor cells bearing wild-type p53, but did not affect proliferation of tumor xenografts bearing a p53 mutation. In parallel, data obtained in a primary breast cancer clinical series showed that disease-free survival was shorter in individuals bearing the CCR5Delta32 allele than in CCR5 wild-type patients, but only for those whose tumors expressed wild-type p53. These findings suggest that CCR5 activity influences human breast cancer progression in a p53-dependent manner.

Systemic autoimmune disease is frequently characterized by the production of autoantibodies against widely expressed intracellular self-antigens, whereas B cell tolerance to ubiquitous and highly expressed extracellular antigens is strictly enforced. To test for differences in the B cell response to intracellular and extracellular self-antigens, we sequestered a tolerogenic cell surface antigen intracellularly by addition of a two amino acid endoplasmic reticulum (ER) retention signal. In contrast to cell surface antigen, which causes the deletion of autoreactive B cells, the intracellularly sequestered self-antigen failed to induce B cell tolerance and was instead autoimmunogenic. The intracellular antigen positively selected antigen-binding B cells to differentiate into B1 cells and induced large numbers of IgM autoantibody-secreting plasma cells in a T-independent manner. By analyzing the impact of differences in subcellular distribution independently from other variables, such as B cell receptor affinity, antigen type, or tissue distribution, we have established that intracellular localization of autoantigen predisposes for autoantibody production. These findings help explain why intracellular antigens are targeted in systemic autoimmune diseases.

Synaptic signaling comprises a complex molecular network. Such networks carry out diverse operations such as molecular logic, signal amplification, memory and other aspects of cellular decision-making. The synapse in particular encounters complex input patterns that have different temporal sequences. Different input patterns to the synapse are known to give rise to a range of synaptic responses, including facilitation, depression and various forms of short and long-term potentiation. In many cases the stimuli that generate these disparate responses are tens of seconds or more in length, much greater than the typical time-courses of calcium dynamics. In this paper I propose that the synaptic signaling network can perform temporal computation operations such as tuning for stimulus duration or interval. Using simulation methods I show that the simple time-courses of individual signaling pathways combine in the network to give rise to different temporally selective responses. Downstream pathways that exhibit temporal integration or amplitude thresholding select different input patterns and thus perform temporal computation.

Changes in the genetic makeup of an organism can extend lifespan significantly if they promote tolerance to environmental insults and thus prevent the general deterioration of cellular function that is associated with aging. Here, we introduce the Jun N-terminal kinase (JNK) signaling pathway as a genetic determinant of aging in Drosophila melanogaster. Based on expression profiling experiments, we demonstrate that JNK functions at the center of a signal transduction network that coordinates the induction of protective genes in response to oxidative challenge. JNK signaling activity thus alleviates the toxic effects of reactive oxygen species (ROS). In addition, we show that flies with mutations that augment JNK signaling accumulate less oxidative damage and live dramatically longer than wild-type flies. Our work thus identifies the evolutionarily conserved JNK signaling pathway as a major genetic factor in the control of longevity.

In the presented studies HBcAg-specific cytokine production (IFN-gamma, IL-2, IL-4, IL-5 and IL-10) was evaluated, by Th lymphocytes isolated from peripheral blood of children with acute or chronic B hepatitis. Moreover, effect of IL-10 neutralization was examined on HBcAg-induced secretory response of Th lymphocytes obtained from children with chronic B hepatitis. The studies were performed on 12 children with acute self-limited B hepatitis and 20 children with chronic active B hepatitis. CD4 T cells were isolated from peripheral blood of the patients, cultured for 48h in presence of rHBcAg or in its absence (control). Production of studied cytokines was monitored using ELISPOT and ELISE assays. The course of acute self-limited B hepatitis was associated with preferential Th1-type response, manifested by elevated production of IFN-gamma and IL-2. On the other hand, in chronic B hepatitis a diminished response to HBcAg of both Th1 and Th2 types was disclosed, characterized by very low secretion of IFN-gamma, IL-2, IL-4 and IL-5. In parallel, preferential antigen-specific production of IL-10 was noted and its suppressive effect on HBcAg-induced response of Th1 cells. The results permitted to conclude that in children with acute self-limited B hepatitis preferential HBcAg-specific activation of Th1 lymphocytes may be of significance for efficient anti-HBV immune response. On the other hand, development of chronic B infection in children seems to be determined by disturbed HBcAg-specific functions of both Th1 and Th2 cells whereas activity of the disease may be controlled by anti-inflammatory response of antigen-presenting cells and/or of regulatory CD4 T lymphocytes, involving IL-10 production.

Steroid hormones fulfil important functions in animal development. In Drosophila, ecdysone triggers moulting and metamorphosis through its effects on gene expression. Ecdysone works by binding to a nuclear receptor, EcR, which heterodimerizes with the retinoid X receptor homologue Ultraspiracle. Both partners are required for binding to ligand or DNA. Like most DNA-binding transcription factors, nuclear receptors activate or repress gene expression by recruiting co-regulators, some of which function as chromatin-modifying complexes. For example, p160 class coactivators associate with histone acetyltransferases and arginine histone methyltransferases. The Trithorax-related gene of Drosophila encodes the SET domain protein TRR. Here we report that TRR is a histone methyltransferases capable of trimethylating lysine 4 of histone H3 (H3-K4). trr acts upstream of hedgehog (hh) in progression of the morphogenetic furrow, and is required for retinal differentiation. Mutations in trr interact in eye development with EcR, and EcR and TRR can be co-immunoprecipitated on ecdysone treatment. TRR, EcR and trimethylated H3-K4 are detected at the ecdysone-inducible promoters of hh and BR-C in cultured cells, and H3-K4 trimethylation at these promoters is decreased in embryos lacking a functional copy of trr. We propose that TRR functions as a coactivator of EcR by altering the chromatin structure at ecdysone-responsive promoters.