Use of DNA methylation for cancer detection and molecular classification

Conjugation of the methyl group at the fifth carbon of cytosines within the palindromic dinucleotide 5'-CpG-3' sequence (DNA methylation) is the best studied epigenetic mechanism, which acts together with other epigenetic entities: histone modification, chromatin remodeling and microRNAs to shape the chromatin structure of DNA according to its functional state. The cancer genome is frequently characterized by hypermethylation of specific genes concurrently with an overall decrease in the level of 5-methyl cytosine, the pathological implication of which to the cancerous state has been well established. While the latest genome-wide technologies have been applied to classify and interpret the epigenetic layer of gene regulation in the physiological and disease states, the epigenetic testing has also been seriously explored in clinical practice for early detection, refining tumor staging and predicting disease recurrence. This critique reviews the latest research findings on the use of DNA methylation in cancer diagnosis, prognosis and staging/classification.     

Time-Dependent Increase in Protein Phosphorylation Following One-Trial Enhancement in Hermissenda

Abstract: One-trial conditioning of the nudibranch mollusk Hermissenda produces short- and long-term changes in excitability (enhancement) of identified sensory neurons. To investigate the biochemical mechanisms underlying this example of plasticity, we have examined changes in protein phosphorylation at different times following the in vitro conditioning trial. Changes in the incorporation of ³²PO₄ into proteins were determined using two-dimensional polyacrylamide gel electrophoresis, autoradiography, and densitometry. Conditioning resulted in increases in levels of several phosphoproteins, five of which, ranging in apparent molecular mass from 22 to 55 kDa, were chosen for analysis. The increased phosphorylation of the 46- and 55-kDa phosphoproteins detected 2 h postconditioning was significantly greater than the level of phosphorylation detected in an unpaired control group, indicating that long-term enhancement is pairing specific. Statistically significant increases in phosphorylation as compared with the control group that received only light were detected immediately after conditioning (5 min) for the 55-, 46-, and 22-kDa phosphoproteins, at 1 h for the 55- and 46-kDa phosphoproteins, and at 2 h for the 55-, 46-, and 22-kDa phosphoproteins. The 46- and 55-kDa phosphoproteins are putative structural proteins, and the 22-kDa phosphoprotein is proposed to be a protein kinase C substrate previously identified in Hermissenda following multitrial classical conditioning. Time-dependent increases in protein phosphorylation may contribute to the induction and maintenance of different memory stages expressed in sensory neurons after one-trial conditioning.     

Studies on the Free Amino Acid Content in Anthers of Malesterile and Fertile Plants of Taigu Wheat,with Special Reference to Free Proline Content

Biochemical analyses were made on anthers and pistils at various developmental stages of both male-sterne and fertile plants of Taigu wheat. Analyses ineluded total free amino aeids and free proline. The following results were obtained: 1. There was no significant difference between the content of free proline in anthers of male-sterile and fertile plants at reduction division of mierospore mother cells. 2. In anthers with early uninucleate miorospores, the content of free proline of fertile plants was remarkably higher than that of male-sterile plants. It is interesting to note that at this stage the content of free proline in fertile plants rose to 1.65% of the dry weight of the anther, constituting 50% of the total free amino acids, and amounted to 7-fold of that in male-sterile plants. This result is in line with the results obtained with most cytoplasmic malesterile plants reported by other workers, although malesterility in Taigu wheat is controlled by the nueleus. 3. In pistils, at the stages eorresponding to the early uninneleate and the binueleate stages of the pollen, the free proline content of fertile plants was twice as much as that of the male-sterile plants. This differenee disappeared gradually after fertilization. 4. Tile content of total free amino aoids did not fluetuate as much as the free proline content. There was no differenee in anthers of both types of plants during reduction division of mierospore mother cells. In anthers with early uninueleate pollen grains, total free amino acid content of fertile plants exceeded that of male-sterile plant, the difference levelled off at latter stages. In pistils, before fertilization, the content of total free amino acids of the fertile phmts was slightly higher than that of the male-sterile plants. After fertilization t}fis difference was no nmre noticeable.     

Effect of Soybean Monoculture on the Bacterial Communities Associated with Cysts of Heterodera glycines

The soybean cyst nematode (SCN), Heterodera glycines, can cause significant reductions in soybean yield and quality in many parts of the world. Natural biological control may play an important role in regulating SCN population. In this study the bacterial communities associated with SCN cysts obtained from fields under different lengths of soybean monoculture were explored. Soil samples were collected in 2010 and 2011 from six fields that had been used for soybean monoculture for 2 to 41 yr. SCN population densities were determined and bacterial communities from SCN cysts were investigated by Biolog and PCR-DGGE methods. SCN population densities initially increased in the first 5 yr of soybean monoculture but then declined steeply as years of soybean monoculture increased. Catabolic diversity of bacterial communities associated with cysts tended to decline as number of years of monoculture increased. Some specific PCR-DGGE bands, mainly representing Streptomyces and Rhizobium, were obtained from the cysts collected from the long-term monoculture fields. Principal component analysis of Biolog and PCR-DGGE data revealed that bacterial communities associated with cysts could be divided into two groups: those from cysts obtained from shorter (< 8 yr) vs. longer (> 8 yr) monoculture. This research demonstrates that the composition of the bacterial communities obtained from SCN cysts changes with length of soybean monoculture; the suppressive impact of these bacterial communities to SCN is yet to be determined.     

Stable Li Metal Anode Enabled by Space Confinement and Uniform Curvature through Lithiophilic Nanotube Arrays

The application of lithium (Li) metal anodes in rechargeable batteries is primarily restricted by Li dendrite growth on the metal's surface, which leads to shortened cycle life and safety concerns. Herein, well‐spaced nanotubes with ultrauniform surface curvature are introduced as a Li metal anode structure. The ultrauniform nanotubular surface generates uniform local electric fields that evenly attract Li‐ions to the surface, thereby inducing even current density distribution. Moreover, the well‐defined nanotube spacing offers Li diffusion pathways to the electroactive areas as well as the confined spaces to host deposited Li. These structural attributes create a unique electrodeposition manner; i.e., Li metal homogenously deposits on the nanotubular wall, causing each Li nanotube to grow in circumference without obvious sign of dendritic formation. Thus, the full‐cell battery with the spaced Li nanotubes exhibits a high specific capacity of 132 mA h g^?1 at 1 C and an excellent coulombic efficiency of ≈99.85% over 400 cycles.     

Biochemical and photochemical changes in response to triacontanol in rice (Oryza sativa L.)

Triacontanol (TRIA) increased the contents of total chlorophyll (Chl), Chl a and Chl b by 25.1%, 26.1% and 22.4% respectively 4 h after treatment in rice seedlings. The minimal fluorescence (F₀), the maximal fluorescence (Fm) and Fv/Fm were also higher in TRIA-treated plants. In actinic light, other Chl fluorescence parameters were measured at different photon flux densities (PFD) to construct light response curves of the quantum yield of PSII electron transport (_PSII), light response curves of photochemical quenching (qp), and light response curves of non-photochemical quenching (qN), respectively. The _PSII and qp declined with the increasing PFD with a higher level present in TRIA-treated plants. The qN increased with the increasing PFD with a lower level present in TRIA-treated plants. Two-dimensional gel electrophoresis indicated a protein expression difference between TRIA-treated materials and the controls at the total-soluble-protein level. Rubisco was 30% higher in TRIA-treated plants than in controls. The quantity of other proteins was unchanged in response to TRIA. These data provide biochemical and photochemical evidence for the effects of TRIA on photosynthesis.     

Salicylate suppresses macrophage nitric-oxide synthase-2 and cyclo-oxygenase-2 expression by inhibiting CCAAT/enhancer-binding protein-beta binding via a common signaling pathway

We determined whether salicylate at pharmacological concentrations inhibits nitric-oxide synthase-2 (NOS-2) and cyclo-oxygenase-2 (COX-2) expressions in RAW 264.7 stimulated with lipopolysaccharide (LPS) and interferon-gamma (IFN-gamma). Cells were treated with sodium salicylate (10(-7)-10(-4) m) or vehicle for 30 min followed by LPS+IFN-gamma for up to 24 h. Salicylate suppressed NOS-2 and COX-2 protein levels and promoter activities stimulated by LPS+IFN-gamma for 4 h in a concentration-dependent manner but had no effect on NOS-2 expression stimulated by the combined agonists for 24 h. Results from promoter analysis indicate that the binding of CCAAT/enhancer-binding protein beta (C/EBPbeta) to its cognate site at -150/-142 on the NOS-2 promoter region was essential for NOS-2 expression at 4 h but not at 24 h. Salicylate reduced C/EBPbeta binding at 4 h and did not alter its binding at 24 h. NOS-2 and COX-2 protein levels and C/EBPbeta binding stimulated by LPS+IFN-gamma for 4 h were inhibited by a similar battery of signaling inhibitors, suggesting a common pathway for NOS-2 and COX-2 expression. Kinetic analysis indicates that NOS-2, similar to COX-2 expression, at 4 h was largely due to the action of LPS, which induced C/EBPbeta binding, whereas its expression at a longer time point was contributed by IFN-gamma. Our findings implicate two distinct pathways for NOS-2 expression induced by LPS+IFN-gamma. Salicylate at pharmacological concentrations is capable of suppressing the early phase of NOS-2 and COX-2 expression by blocking C/EBPbeta binding.     

Molecular Mechanism of Nicotine Degradation by a Newly Isolated Strain,Ochrobactrum sp. Strain SJY1

A newly isolated strain, SJY1, identified as Ochrobactrum sp., utilizes nicotine as a sole source of carbon, nitrogen, and energy. Strain SJY1 could efficiently degrade nicotine via a variant of the pyridine and pyrrolidine pathways (the VPP pathway), which highlights bacterial metabolic diversity in relation to nicotine degradation. A 97-kbp DNA fragment containing six nicotine degradation-related genes was obtained by gap closing from the genome sequence of strain SJY1. Three genes, designated vppB, vppD, and vppE, in the VPP pathway were cloned and heterologously expressed, and the related proteins were characterized. The vppB gene encodes a flavin-containing amine oxidase converting 6-hydroxynicotine to 6-hydroxy-N-methylmyosmine. Although VppB specifically catalyzes the dehydrogenation of 6-hydroxynicotine rather than nicotine, it shares higher amino acid sequence identity with nicotine oxidase (38%) from the pyrrolidine pathway than with its isoenzyme (6-hydroxy-l-nicotine oxidase, 24%) from the pyridine pathway. The vppD gene encodes an NADH-dependent flavin-containing monooxygenase, which catalyzes the hydroxylation of 6-hydroxy-3-succinoylpyridine to 2,5-dihydroxypyridine. VppD shows 62% amino acid sequence identity with the hydroxylase (HspB) from Pseudomonas putida strain S16, whereas the specific activity of VppD is ∼10-fold higher than that of HspB. VppE is responsible for the transformation of 2,5-dihydroxypyridine. Sequence alignment and phylogenetic analysis suggested that the VPP pathway, which evolved independently from nicotinic acid degradation, might have a closer relationship with the pyrrolidine pathway. The proteins and functional pathway identified here provide a sound basis for future studies aimed at a better understanding of molecular principles of nicotine degradation.     

Epitope Tags beside the N-Terminal Cytoplasmic Tail of Human BST-2 Alter Its Intracellular Trafficking and HIV-1 Restriction

BST-2 blocks the particle release of various enveloped viruses including HIV-1, and this antiviral activity is dependent on the topological arrangement of its four structural domains. Several functions of the cytoplasmic tail (CT) of BST-2 have been previously discussed, but the exact role of this domain remains to be clearly defined. In this study, we investigated the impact of truncation and commonly-used tags addition into the CT region of human BST-2 on its intracellular trafficking and signaling as well as its anti-HIV-1 function. The CT-truncated BST-2 exhibited potent inhibition on Vpu-defective HIV-1 and even wild-type HIV-1. However, the N-terminal HA-tagged CT-truncated BST-2 retained little antiviral activity and dramatically differed from its original protein in the cell surface level and intracellular localization. Further, we showed that the replacement of the CT domain with a hydrophobic tag altered BST-2 function possibly by preventing its normal vesicular trafficking. Notably, we demonstrated that a positive charged motif “KRXK” in the conjunctive region between the cytotail and the transmembrane domain which is conserved in primate BST-2 is important for the protein trafficking and the antiviral function. These results suggest that although the CT of BST-2 is not essential for its antiviral activity, the composition of residues in this region may play important roles in its normal trafficking which subsequently affected its function. These observations provide additional implications for the structure-function model of BST-2.