Lectin microarray profiling of metastatic breast cancers

Altered protein glycosylation compared with the disease-free state is a universal feature of cancer cells. It has long been established that distinct glycan structures are associated with specific forms of cancer, but far less is known about the complete array of glycans associated with certain tumors. The cancer glycome has great potential as a source of biomarkers, but progress in this field has been hindered by a lack of available techniques for the elucidation of disease-associated glycosylation. In the present study, lectin microarrays consisting of 45 lectins with different binding preferences covering N- and O-linked glycans were coupled with evanescent-field activated fluorescent detection in the glycomic analysis of primary breast tumors and the serum and urine of patients with metastatic breast cancer. A single 50 μm section of a primary breast tumor or <1 μL of breast cancer patient serum or urine was sufficient to detect glycosylation alterations associated with metastatic breast cancer, as inferred from lectin-binding patterns. The high-throughput, sensitive and relatively simple nature of the simultaneous analysis of N- and O-linked glycosylation following minimal sample preparation and without the need for protein deglycosylation makes the lectin microarray analysis described a valuable tool for discovery phase glycomic profiling.     

Systematic detection of polygenic cis-regulatory evolution

The idea that most morphological adaptations can be attributed to changes in the cis-regulation of gene expression levels has been gaining increasing acceptance, despite the fact that only a handful of such cases have so far been demonstrated. Moreover, because each of these cases involves only one gene, we lack any understanding of how natural selection may act on cis-regulation across entire pathways or networks. Here we apply a genome-wide test for selection on cis-regulation to two subspecies of the mouse Mus musculus. We find evidence for lineage-specific selection at over 100 genes involved in diverse processes such as growth, locomotion, and memory. These gene sets implicate candidate genes that are supported by both quantitative trait loci and a validated causality-testing framework, and they predict a number of phenotypic differences, which we confirm in all four cases tested. Our results suggest that gene expression adaptation is widespread and that these adaptations can be highly polygenic, involving cis-regulatory changes at numerous functionally related genes. These coordinated adaptations may contribute to divergence in a wide range of morphological, physiological, and behavioral phenotypes.     

Detection and discovery of RNA modifications using microarrays

Using a microarray that tiles all known yeast non-coding RNAs, we compared RNA from wild-type cells with RNA from mutants encoding known and putative RNA modifying enzymes. We show that at least five types of RNA modification (dihydrouridine, m1G, m2(2)G, m1A and m6(2)A) catalyzed by 10 different enzymes (Trm1p, Trm5, Trm10p, Dus1p-Dus4p, Dim1p, Gcd10p and Gcd14p) can be detected by virtue of differential hybridization to oligonucleotides on the array that are complementary to the modified sites. Using this approach, we identified a previously undetected m1A modification in GlnCTG tRNA, the formation of which is catalyzed by the Gcd10/Gcd14 complex. complex.     

Network theory and SARS: predicting outbreak diversity

Many infectious diseases spread through populations via the networks formed by physical contacts among individuals. The patterns of these contacts tend to be highly heterogeneous. Traditional "compartmental" modeling in epidemiology, however, assumes that population groups are fully mixed, that is, every individual has an equal chance of spreading the disease to every other. Applications of compartmental models to Severe Acute Respiratory Syndrome (SARS) resulted in estimates of the fundamental quantity called the basic reproductive number R0--the number of new cases of SARS resulting from a single initial case--above one, implying that, without public health intervention, most outbreaks should spark large-scale epidemics. Here we compare these predictions to the early epidemiology of SARS. We apply the methods of contact network epidemiology to illustrate that for a single value of R0, any two outbreaks, even in the same setting, may have very different epidemiological outcomes. We offer quantitative insight into the heterogeneity of SARS outbreaks worldwide, and illustrate the utility of this approach for assessing public health strategies.     

Thin-film coupled fluid-solid analysis of flow through the Ahmed glaucoma drainage device

The Ahmed glaucoma valve (AGV) is a popular glaucoma drainage device, allowing maintenance of normal intraocular pressure in patients with reduced trabecular outflow facility. The uniquely attractive feature of the AGV, in contrast to other available drainage devices, is its variable resistance in response to changes in flow rate. As a result of this variable resistance, the AGV maintains a pressure drop between 7 and 12 mm Hg for a wide range of aqueous humor flow rates. In this paper, we demonstrate that the nonlinear behavior of the AGV is a direct result of the flexibility of the valve material. Due to the thin geometry of the system, the leaflets of the AGV were modeled using the von Kármán plate theory coupled to a Reynolds lubrication theory model of the aqueous humor flow through the valve. The resulting two-dimensional coupled steady-state partial differential equation system was solved by the finite element method. The Poisson's ratio of the valve was set to 0.45, and the modulus was regressed to experimental data, giving a best-fit value 4.2 MPa. Simulation results compared favorably with previous experimental studies and our own pressure-drop/flow-rate data. For an in vitro flow of 1.6 microL/min, we calculated a pressure drop of 5.8 mm Hg and measured a pressure drop of 5.2 +/- 0.4 mm Hg. As flow rate was increased, pressure drop rose in a strongly sublinear fashion, with a flow rate of 20 microL/min giving a predicted pressure drop of only 10.9 mm Hg and a measured pressure drop of 10.5 +/- 1.1 mm Hg. The AGV model was then applied to simulate in vivo conditions. For an aqueous humor flow rate of 1.5-3.0 microL/min, the calculated pressure drops were 5.3 and 6.3 mm Hg.     

Regulatory mechanism of histidine-tagged homocitrate synthase from Saccharomyces cerevisiae. I. Kinetic studies

Homocitrate synthase (HCS) catalyzes one of the regulated steps of the alpha-aminoadipate pathway for lysine biosynthesis in fungi. The kinetic mechanism of regulation of HCS from Saccharomyces cerevisiae by Na+ and the feedback inhibitor lysine was studied by measuring the initial rate in the absence and presence of the effectors. The data suggest that Na+ is an activator at low concentrations and an inhibitor at high concentrations and that these effects occur as a result of the monovalent ion binding to two different sites in the free enzyme. Inhibition and activation by Na+ can occur simultaneously, with the net rate of the enzyme determined by Na+/K(iNa+) and Na+/K(act), where K(iNa+) and K(act) are the inhibition and activation constants, respectively. The inhibition by Na+ was eliminated at high concentrations of acetyl-CoA, the second substrate bound, but the activation remained. Fluorescence binding studies indicated that lysine bound with high affinity to its binding site as an inhibitor. The inhibition by lysine was competitive versus alpha-ketoglutarate and linear in the physiological range of lysine concentrations up to 5 mm. The effects of Na+ and lysine were independent of one another. A model is developed for regulation of HCS that takes into account all of the effects discussed above.     

Cutting edge: CpG oligonucleotides induce splenic CD19+ dendritic cells to acquire potent indoleamine 2,3-dioxygenase-dependent T cell regulatory functions via IFN Type 1 signaling

CpG oligodeoxynucleotides (CpG-ODNs) stimulate innate and adaptive immunity by binding to TLR9 molecules. Paradoxically, expression of the immunoregulatory enzyme indoleamine 2,3-dioxygenase (IDO) is induced following i.v. CpG-ODN administration to mice. CpG-ODNs induced selective IDO expression by a minor population of splenic CD19+ dendritic cells (DCs) that did not express the plasmacytoid DC marker 120G8. Following CpG-ODN treatment, CD19+ DCs acquired potent IDO-dependent T cell suppressive functions. Signaling through IFN type I receptors was essential for IDO up-regulation, and CpG-ODNs induced selective activation of STAT-1 in CD19+ DCs. Thus, CpG-ODNs delivered systemically at relatively high doses elicited potent T cell regulatory responses by acting on a discrete, minor population of splenic DCs. The ability of CpG-ODNs to induce both stimulatory and regulatory responses offers novel opportunities for using them as immunomodulatory reagents but may complicate therapeutic use of CpG-ODNs to stimulate antitumor immunity in cancer patients.     

Cytologic findings of a pleomorphic adenoma of the breast: a case report

BACKGROUND: Pleomorphic adenoma of the breast is a rare benign tumor. Only a few cases have been reported. The histologic features have been described well. However, the cytologic findings have been described in only a few papers. CASE: A 47-year-old female presented with a left breast mass of several months' duration. The clinical and mammographic findings were highly suspicious for malignancy. Following an aspiration biopsy diagnosis of "positive for malignancy," the mass was excised. The histologic diagnosis was pleomorphic adenoma (mixed tumor of salivary gland type) rather than carcinoma. CONCLUSION: The cytologic presentation of pleomorphic adenoma of the breast can masquerade as that of a malignant tumor, in this case colloid carcinoma. This case delineates the cytomorphologicfeatures of pleomorphic adenoma, which may mimic carcinoma.