Tuning of magnetization in vertical graphenes by plasma-enabled chemical conversion of organic precursors with different oxygen content

Different magnetization in vertical graphenes fabricated by plasma-enabled chemical conversion of organic precursors with various oxygen atom contents and bonding energies was achieved. The graphenes grown from fat-like precursors exhibit magnetization up to 8 emu g−1, whereas the use of sugar-containing precursors results in much lower numbers. A relatively high Curie temperature exceeding 600 K was also demonstrated.

Molecular network analysis using reverse phase protein microarrays for patient tailored therapy.

The practice of medicine has always aimed at individualized treatment of disease. The relationship between patient and physician has always been a personal one, and the physician's choice of treatment has been intended to be the best fit for the patient's needs. The necessary pooling/grouping of disease families and their assignment to a number of drugs or treatment methods has, consequently, led to an increase in the number of effective therapies. However, given the heterogeneity of most human diseases, and cancer specifically, it is currently impossible for the treating clinician to effectively predict a patient's response and outcome based on current technologies, much less the idiosyncratic resistances and adverse effects associated with the limited therapeutic options.

The molecular structure of the phosphate mineral kidwellite NaFe93+(PO4)6(OH)11⋅3H2O – a vibrational spectroscopic study

The mineral kidwellite, a hydrated hydroxy phosphate of ferric iron and sodium of approximate formula NaFe93+(PO4)6(OH)11⋅3H2O, has been studied using a combination of electron microscopy with EDX and vibrational spectroscopic techniques. Raman spectroscopy identifies an intense band at 978 cm−1 and 1014 cm−1. These bands are attributed to the PO43− ν1 symmetric stretching mode. The ν3 antisymmetric stretching modes are observed by a large number of Raman bands. The series of Raman bands at 1034, 1050, 1063, 1082, 1129, 1144 and 1188 cm−1 are attributed to the ν3 antisymmetric stretching bands of the PO43− and HOPO32− units. The observation of these multiple Raman bands in the symmetric and antisymmetric stretching region gives credence to the concept that both phosphate and hydrogen phosphate units exist in the structure of kidwellite. The series of Raman bands at 557, 570, 588, 602, 631, 644 and 653 cm−1are assigned to the PO43− ν2 bending modes. The series of Raman bands at 405, 444, 453, 467, 490 and 500 cm−1 are attributed to the PO43− and HOPO32− ν4 bending modes. The spectrum is quite broad but Raman bands may be resolved at 3122, 3231, 3356, 3466 and 3580 cm−1. These bands are assigned to water stretching vibrational modes. The number and position of these bands suggests that water is in different molecular environments with differing hydrogen bond distances. Infrared bands at 3511 and 3359 cm−1 are ascribed to the OH stretching vibration of the OH units. Very broad bands at 3022 and 3299 cm−1 are attributed to the OH stretching vibrations of water. Vibrational spectroscopy offers insights into the molecular structure of the phosphate mineral kidwellite.

Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics

Early full-term pregnancy is one of the most effective natural protections against breast cancer. To investigate this effect, we have characterized the global gene expression and epigenetic profiles of multiple cell types from normal breast tissue of nulliparous and parous women and carriers of BRCA1 or BRCA2 mutations. We found significant differences in CD44+ progenitor cells, where the levels of many stem cell-related genes and pathways, including the cell-cycle regulator p27, are lower in parous women without BRCA1/BRCA2 mutations. We also noted a significant reduction in the frequency of CD44+p27+ cells in parous women and showed, using explant cultures, that parity-related signaling pathways play a role in regulating the number of p27+ cells and their proliferation. Our results suggest that pathways controlling p27+ mammary epithelial cells and the numbers of these cells relate to breast cancer risk and can be explored for cancer risk assessment and prevention.

Control of morphology and nucleation density of iron oxide nanostructures by electric conditions on iron surfaces exposed to reactive oxygen plasmas

The possibility to control the morphology and nucleation density of quasi-one-dimensional, single-crystalline α -Fe2 O3 nanostructures by varying the electric potential of iron surfaces exposed to reactive oxygen plasmas is demonstrated experimentally. A systematic increase in the oxygen ion flux through rf biasing of otherwise floating substrates and then an additional increase of the ion/neutral density resulted in remarkable structural transformations of straight nanoneedles into nanowires with controlled tapering/aspect ratio and also in larger nucleation densities. Multiscale numerical simulations relate the microscopic ion flux topographies to the nanostructure nucleation and morphological evolution. This approach is applicable to other metal-oxide nanostructures.

Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma

Cancer can be defined as a deregulation or hyperactivity in the ongoing network of intracellular and extracellular signaling events. Reverse phase protein microarray technology may offer a new opportunity to measure and profile these signaling pathways, providing data on post-translational phosphorylation events not obtainable by gene microarray analysis. Treatment of ovarian epithelial carcinoma almost always takes place in a metastatic setting since unfortunately the disease is often not detected until later stages. Thus, in addition to elucidation of the molecular network within a tumor specimen, critical questions are to what extent do signaling changes occur upon metastasis and are there common pathway elements that arise in the metastatic microenvironment. For individualized combinatorial therapy, ideal therapeutic selection based on proteomic mapping of phosphorylation end points may require evaluation of the patient's metastatic tissue. Extending these findings to the bedside will require the development of optimized protocols and reference standards. We have developed a reference standard based on a mixture of phosphorylated peptides to begin to address this challenge.

Reactive oxygen plasma-enabled synthesis of nanostructured CdO : tailoring nanostructures through plasma–surface interactions

Plasma-assisted synthesis of nanostructures is one of the most precise and effective approaches used in nanodevice fabrication. Here we report on the innovative approach of synthesizing nanostructured cadmium oxide films on Cd substrates using a reactive oxygen plasma-based process. Under certain conditions, the surface morphology features arrays of crystalline CdO nano/micropyramids. These nanostructures grow via unconventional plasma-assisted oxidation of a cadmium foil exposed to inductively coupled plasmas with a narrow range of process parameters. The growth of the CdO pyramidal nanostructures takes place in the solid-liquid-solid phase, with the rates determined by the interaction of plasma-produced oxygen atoms and ions with the surface. It is shown that the size of the pyramidal structures can be effectively controlled by the fluxes of oxygen atoms and ions impinging on the cadmium surface. The unique role of the reactive plasma environment in the controlled synthesis of CdO nanopyramidal structures is discussed as well.

B-Raf mutation : a key player in molecular biology of cancer

B-Raf is one of the more commonly mutated proto-oncogenes implicated in the development of cancers. In this review, we consider the mechanisms and clinical impacts of B-Raf mutations in cancer and discuss the implications for the patient in melanoma, thyroid cancer and colorectal cancer, where B-Raf mutations are particularly common.

Reactive Oxygen Species and Reactive Nitrogen Species in Epigenetic Modifications

For the normal homeostasis of a cell, there must be a balance between radical oxygen species/radical nitrogen species (ROS/RNS) production and the neutralization of these species by antioxidant scavenging. In times of stress, this balance is not maintained, and the result is oxidative stress. This stress can affect many pathways in the body and result in pathological consequences. Recent evidence suggests that ROS/RNS can affect the epigenetic regulation of genes by affecting the function of histone and DNA modifying enzymes, thus affecting phenotypic changes within the cellular environment. In the following chapter, we provide a broad overview of how oxidative stress induced by ROS/RNS can affect epigenetics, and using lung disease as our model we link the connection between these processes.

Carcinoma ex pleomorphic adenoma : a comprehensive review of clinical, pathological and molecular data

Carcinoma ex pleomorphic adenoma (Ca ex PA) is a carcinoma arising from a primary or recurrent benign pleomorphic adenoma. It often poses a diagnostic challenge to clinicians and pathologists. This study intends to review the literature and highlight the current clinical and molecular perspectives about this entity. The most common clinical presentation of CA ex PA is of a firm mass in the parotid gland. The proportion of adenoma and carcinoma components determines the macroscopic features of this neoplasm. The entity is difficult to diagnose pre-operatively. Pathologic assessment is the gold standard for making the diagnosis. Treatment for Ca ex PA often involves an ablative surgical procedure which may be followed by radiotherapy. Overall, patients with Ca ex PA have a poor prognosis. Accurate diagnosis and aggressive surgical management of patients presenting with Ca ex PA can increase their survival rates. Molecular studies have revealed that the development of Ca ex PA follows a multi-step model of carcinogenesis, with the progressive loss of heterozygosity at chromosomal arms 8q, then 12q and finally 17p. There are specific candidate genes in these regions that are associated with particular stages in the progression of Ca ex PA. In addition, many genes which regulate tumour suppression, cell cycle control, growth factors and cell-cell adhesion play a role in the development and progression of Ca ex PA. It is hopeful that these molecular data can give clues for the diagnosis and management of the disease.

Signet-ring cell carcinoma of colorectum : current perspectives and molecular biology

PURPOSE Colorectal signet-ring cell carcinoma (SRCC) is rare, and very little detailed information on the molecular biology of the disease is available. METHODS The literature on the clinical, pathological and, in particular, the molecular biology of this rare entity was critically reviewed. The reviewed articles take into account a total of 1,817 cases of SRCC, but only 143 cases have molecular data available. The characteristics of two patients with colorectal SRCC were also discussed. RESULTS Colorectal SRCC mostly occurs in younger patients, is larger and has different site predilection compared with conventional colorectal adenocarcinoma. It can occur as one of the synchronous cancers in the colorectum. The cancer is usually diagnosed at advanced stages because of the late manifestation of symptoms, and aggressive treatment strategy is required. Limited reports in the literature have shown that the variant of colorectal cancer demonstrated a different pattern of genetic alterations of common growth kinase-related oncogenes (K-ras, BRAF), tumour suppressor genes (p53, p16), gene methylation and cell adhesion-related genes related to the Wingless signalling pathway (E-cadherin and beta-catenin) from conventional colorectal adenocarcinoma. Colorectal SRCC also showed high expression of mucin-related genes and genes related to the gastrointestinal system. There was also a higher prevalence of microsatellite instability-high tumours and low Cox-2 expression in colorectal SRCC as opposed to conventional adenocarcinoma. CONCLUSIONS Colorectal SRCC has unique molecular pathological features. The unique molecular profiles in SRCC may provide molecular-based improvements to patient management in colorectal SRCC.

Molecular basis for lysine specificity in the yeast ubiquitin-conjugating enzyme Cdc34

Ubiquitin (Ub)-conjugating enzymes (E2s) and ubiquitin ligases (E3s) catalyze the attachment of Ub to lysine residues in substrates and Ub during monoubiquitination and polyubiquitination. Lysine selection is important for the generation of diverse substrate-Ub structures, which provides versatility to this pathway in the targeting of proteins to different fates. The mechanisms of lysine selection remain poorly understood, with previous studies suggesting that the ubiquitination site(s) is selected by the E2/E3-mediated positioning of a lysine(s) toward the E2/E3 active site. By studying the polyubiquitination of Sic1 by the E2 protein Cdc34 and the RING E3 Skp1/Cul1/F-box (SCF) protein, we now demonstrate that in addition to E2/E3-mediated positioning, proximal amino acids surrounding the lysine residues in Sic1 and Ub are critical for ubiquitination. This mechanism is linked to key residues composing the catalytic core of Cdc34 and independent of SCF. Changes to these core residues altered the lysine preference of Cdc34 and specified whether this enzyme monoubiquitinated or polyubiquitinated Sic1. These new findings indicate that compatibility between amino acids surrounding acceptor lysine residues and key amino acids in the catalytic core of ubiquitin-conjugating enzymes is an important mechanism for lysine selection during ubiquitination.

Prediction of thermal expansion properties of carbon nanotubes using molecular dynamics simulations

The axial coefficients of thermal expansion (CTE) of various carbon nanotubes (CNTs), i.e., single-wall carbon nanotubes (SWCNTs), and some multi-wall carbon nanotubes (MWCNTs), were predicted using molecular dynamics (MDs) simulations. The effects of two parameters, i.e., temperature and the CNT diameter, on CTE were investigated extensively. For all SWCNTs and MWCNTs, the obtained results clearly revealed that within a wide low temperature range, their axial CTEs are negative. As the diameter of CNTs decreases, this temperature range for negative axial CTEs becomes narrow, and positive axial CTEs appear in high temperature range. It was found that the axial CTEs vary nonlinearly with the temperature, however, they decrease linearly as the CNT diameter increases. Moreover, within a wide temperature range, a set of empirical formulations was proposed for evaluating the axial CTEs of armchair and zigzag SWCNTs using the above two parameters. Finally, it was found that the absolute value of the negative axial CTE of any MWCNT is much smaller than those of its constituent SWCNTs, and the average value of the CTEs of its constituent SWCNTs. The present fundamental study is very important for understanding the thermal behaviors of CNTs in such as nanocomposite temperature sensors, or nanoelectronics devices using CNTs.

Calculation of the oxygen isotope discrimination factor for studying plant respiration

Measurement of discrimination against 18O during dark respiration in plants is currently accepted as the only reliable method of estimating the partitioning of electrons between the cytochrome and alternative pathways. In this paper, we review the theory of the technique and its application to a gas-phase system. We extend it to include sampling effects and show that the isotope discrimination factor, D, is calculated as –dln(1 + δ)/dlnO*, where δ is isotopic composition of the substrate oxygen and O*=[O2]/[N2] in a closed chamber containing tissue respiring in the dark. It is not necessary to integrate the expression but, if the integrated form is used, the resultant regression should not be constrained through the origin. This is important since any error in D will have significant effects on the estimation of the flux of electrons through the two pathways.

Field-effect transistors based on self-organized molecular nanostripes

Charge transport properties in organic semiconductors depend strongly on molecular order. Here we demonstrate field-effect transistors where drain current flows through a precisely defined array of nanostripes made of crystalline and highly ordered molecules. The molecular stripes are fabricated across the channel of the transistor by a stamp-assisted deposition of the molecular semiconductors from a solution. As the solvent evaporates, the capillary forces drive the solution to form menisci under the stamp protrusions. The solute precipitates only in the regions where the solution is confined by the menisci once the critical concentration is reached and self-organizes into molecularly ordered stripes 100-200 nm wide and a few monolayers high. The charge mobility measured along the stripes is 2 orders of magnitude larger than the values measured for spin-coated thin films.