Test of the Jarzynski and Crooks fluctuation relations in an electronic system

Recent progress on micro- and nanometer-scale manipulation has opened the possibility to probe systems small enough that thermal fluctuations of energy and coordinate variables can be significant compared with their mean behavior. We present an experimental study of nonequilibrium thermodynamics in a classical two-state system, namely, a metallic single-electron box. We have measured with high statistical accuracy the distribution of dissipated energy as single electrons are transferred between the box electrodes. The obtained distributions obey Jarzynski and Crooks fluctuation relations. A comprehensive microscopic theory exists for the system, enabling the experimental distributions to be reproduced without fitting parameters.

First Report of Rice stripe virus of Proso Millet in Korea

Rice stripe virus (RSV; genus Tenuivirus) is a serious threat to rice production in Korea (2). In 1965, a disease outbreak was observed on rice in South Korea, with plants showing yellow stripe symptoms (2). Reoccurrence of RSV in rice was observed again in 1980 in Gyeonggi and Chungcheong. In 2001, RSV was estimated to be infecting approximately 4,663 ha of rice in the provinces of Gyeonggi and Gangwha and approximately 5,000 ha of riceland in the provinces of Buan and, Seocheon (3). Proso millet (Panicum miliaceum L.) is grown as a cereal grain crop and used mainly for human food in South Korea (1). In June 2009, proso millet plants that displayed yellow stripe symptoms were collected at Sinjeon-Myeon, Gangjin-Gun, and Jeollanam-do provinces, where an outbreak of RSV in rice was reported. Diseased plants tested positive to RSV with an ELISA Kit (KisanBio, Seoul, Korea). Total RNA was extracted from leaf tissue with an RNeasy Plant Mini Kit (Qiagen Inc., Valencia, CA). RSV coat protein specific-primers were produced (5' TGTGGAACATAGTCCCACAGTAAGT 3'(upstream), 5' CTAAGCCGCAACCATTCCTCCAGT 3'(downstream). Reverse transcription-PCR confirmed the presence of a 494-bp product as predicted for the presence of RSV. The coat protein of RSV isolates collected from proso millet, rice, and foxtail millet in the same area was also sequenced. Results confirmed that phylogenetic relationships were of high homology: 98.9% between RSV isolates from rice and foxtail millet, 99.2% between isolates from rice (GenBank Accession No. JN245626) and proso millet (GenBank Accession No. JN245627); 99.6% between rice and foxtail millet (GenBank Accession No. JN245628); and 99.6% between foxtail millet and proso millet. In addition, sequence comparisons showed 96 to 99% identity with known RSV sequences available in GenBank (Accession No. X53563) (4). To our knowledge, this is the first report of RSV of proso millet in South Korea. The finding of this disease confirms further spread of the virus within the northern part of South Korea and the need for research to develop more effective management options to reduce the impact of RSV in proso millet. References: (1) Y. Y. Choi et al. Biosci. Biotechnol. Biochem. 69:31, 2005. (2) B. C. Lee et al. Res. Plant Dis. 10:30, 2004. (3) B. C. Lee et al. Res. Plant Dis. 14:210, 2008. (4) Y. Zhu. J. Gen. Virol. 72:763, 1991.

Curcumin suppresses Streptococcus mutans adherence to human tooth surfaces and extracellular matrix proteins

Streptococcus mutans is the key causative agent of caries and infective endocarditis. The first step in biofilm development and the consequent initiation of further disease is bacterial adherence to host cell surfaces. Therefore, the aim of this study was to evaluate the inhibitory effect of curcumin on S. mutans adherence to extracellular matrices and tooth surfaces. The effect of curcumin on the ability of S. mutans to adhere to glass surfaces coated with collagen and fibronectin was tested in order to determine whether the decrease of the bacterial adhesion by curcumin is achieved by hindering the bacteria in adhering to collagen and/or fibronectin. Also, human teeth inoculated with S. mutans were treated with curcumin in vitro in order to assess the relevance of the anti-adhesive effect to oral conditions in vivo. The minimum inhibitory concentration (MIC) at which curcumin completely inhibited bacterial growth was 128 μg/mL. The addition of curcumin below the MIC diminished bacterial adherence onto both collagen- and fibronectin-coated glass surfaces and human tooth surfaces. It appears that the anti-adhesive effect of curcumin against S. mutans is mediated through collagen and fibronectin. These results support the widespread use of curcumin as a food-based antimicrobial agent.

Interlayer tunneling in counterflow experiments on the excitonic condensate in quantum Hall bilayers

The effect of tunneling on the transport properties of quantum Hall double layers in the regime of the excitonic condensate at a total filling factor one is studied in counterflow experiments. If the tunnel current I is smaller than a critical I{C}, tunneling is large and is effectively shorting the two layers. For I>I{C} tunneling becomes negligible. Surprisingly, the transition between the two tunneling regimes has only a minor impact on the features of the filling-factor one state as observed in magnetotransport, but at currents exceeding I{C} the resistance along the layers increases rapidly.

Asarone inhibits adipogenesis and stimulates lipolysis in 3T3-L1 adipocytes

Asarone is a molecule found in certain plants such as Acorus calamus, the root of which is used in traditional medicine to treat diabetes. We determined the molecular mechanism underlying the anti-diabetic activity of asarone. Treatment of asarone significantly inhibited the differentiation of 3T3-L1 preadipocytes through suppression of expression of the transcription factors, CCAAT/enhancer binding protein-alpha and peroxisome proliferator activated receptor-gamma, which activate adipogenesis. Intracellular triglyceride levels were reduced by asarone in a dose-dependent manner and asarone treatment stimulated the phosphorylation of hormone-sensitive lipase. Together, the present findings indicate that asarone inhibits adipogenesis by down-regulation of PPARgamma and C/EBPalpha and reduces lipid accumulation by stimulation of lipolysis through an increase in hormone-sensitive lipase activity.

MicroRNAs that respond to histone deacetylase inhibitor SAHA and p53 in HCT116 human colon carcinoma cells

MicroRNAs (miRNAs) are important post-transcriptional regulators involved in many biological processes. We investigated the expression profiles of miRNAs affected by the histone deacetylase inhibitor, suberoylanilide hydroxamic acid (SAHA), and p53 in the human colon cancer cell line, HCT116 (wt-p53) and its derivative, HCT116 (null-p53). In a microarray assay, 144 of 275 human miRNAs showed several-fold changes in transcription. Most of these miRNAs were strongly affected by SAHA, and their expression profiles varied depending on the presence of p53. Thirty-one miRNAs showing the greatest expression changes were selected for target prediction, and genes related to apoptosis (102), cell cycle (38), and differentiation (102) were predicted. Each miRNA had many target genes, and several genes also were targeted by many miRNAs. Putative p53 upstream binding sites for the miRNAs were determined, and most sites scored >85%, suggesting a high probability of binding. In conclusion, we identified several miRNAs whose expression was affected by both SAHA and p53. Many of the miRNAs showed dramatic changes and were predicted to target many mRNAs. Further studies will be needed to verify these predictions.

Carbon nanotube reservoirs for self-healing materials

A novel nanoreservoir made of carbon nanotubes (CNTs) is proposed for realizing tougher and automated self-healing materials. The advantages of the approach are that CNTs have the potential to play the role of reinforcing elements prior to and after sealing a crack and that the number of voids is reduced after the material and the CNTs themselves are healed. The focus of this paper is on investigating the feasibility of using CNTs as a nanoreservoir by analyzing the dynamics of a fluid flowing out of a ruptured single-walled CNT (SWNT), where the fluid resembles an organic healing agent. With this in mind the escaping mechanism of organic molecules stored inside a cracked SWNT was investigated through a molecular dynamics study. The study shows that, when a SWNT wall suffers the formation of a crack, a certain amount of organic molecules, stored inside the SWNT, escape into space in a few picoseconds. This phenomenon is found to depend on the temperature and on the size of the cracks. The results of this study indicate that CNTs have the potential to be successfully used to realize the next generation of stronger, lighter and self-healing materials.

Suberoylanilide hydroxamic acid (SAHA) changes microRNA expression profiles in A549 human non-small cell lung cancer cells

Suberoylanilide hydroxamic acid (SAHA) is a histone deacetylase inhibitor (HDACI) with antitumor effects that is being explored as a therapeutic drug. However, it has been reported that non-small cell lung cancer (NSCLC) is resistant to HDACIs. MicroRNAs (miRNAs) are a key class of small, non-coding RNA molecules that modulate post-transcriptional regulation of gene expression in multi-cellular organisms. miRNA expression patterns are involved in deregulation of gene expression in human lung cancer. Here we identified miRNA expression profile changes in response to SAHA treatment in the human lung carcinoma cell line A549. We also examined potential mRNA targets of SAHA-responsive miRNAs by using a target prediction program. Using microarray analysis, we found 64 miRNAs with >2-fold expression changes in SAHA-treated A549 cells. Among them, two unique miRNAs were altered in 2.5 microM SAHA-treated cells, 31 unique miRNAs were altered in 5.0 microM SAHA-treated cells and 31 miRNAs were altered with both doses. These miRNAs are predicted to have several target genes related to angiogenesis, apoptosis, chromatin modification, cell proliferation and differentiation. In conclusion, we have identified a unique set of miRNAs and their expression profiles that are influenced significantly by SAHA in the A549 NSCLC cell line model, which might provide useful information for understanding the anticancer mechanism of SAHA.

Characterization of fish sauce aroma-impact compounds using GC-MS, SPME-Osme-GCO, and Stevens' power law exponents

The objectives of this study were to characterize volatile compounds and to determine the characteristic aromas associated with impact compounds in 4 fish sauces using solid-phase micro-extraction, gas chromatography-mass spectrometry, Osme, and gas chromatography olfactometry (SPME-Osme-GCO) coupled with Stevens' Power Law. Compounds were separated using GCMS and GCO and were identified with the mass spectral database, aroma perceived at the sniffing port, retention indices, and verification of compounds by authentic standards in the GCMS and GCO. Aromas that were isolated and present in all 4 fish sauce samples at all concentrations included fishy (trimethylamine), pungent and dirty socks (combination of butanoic, pentanoic, hexanoic, and heptanoic acids), cooked rice and buttery popcorn (2,6-dimethyl pyrazine), and sweet and cotton candy (benzaldehyde). All fish sauces contained the same aromas as determined by GCO and GCMS (verified using authentic standard compounds), but the odor intensity associated with each compound or group of compounds was variable for different fish sauce samples. Stevens' Power Law exponents were also determined using this analytical technique, but exponents were not consistent for the same compounds that were found in all fish sauces. Stevens' Power Law exponents ranged from 0.14 to 0.37, 0.24 to 0.34, 0.09 to 0.21, and 0.10 to 0.35 for dirty socks, fishy, buttery popcorn, and sweet aromas, respectively. This demonstrates that there is variability in Stevens' Power Law exponents for odorants within fish sauce samples.

Autoinducer-2 activity of gram-negative foodborne pathogenic bacteria and its influence on biofilm formation

This study evaluated whether autoinducer-2 (AI-2) activity would be associated with biofilm formation by Salmonella and Escherichia coli O157:H7 strains on food contact surfaces. In study I, a Salmonella Typhimurium DT104 strain and an E. coli O157:H7 strain, both AI-2 positive, were individually inoculated into 50 mL of Luria-Bertani (LB) or LB + 0.5% glucose (LBG) broth, without or with stainless steel or polypropylene (Salmonella) coupons. At 0, 14 (Salmonella), 24, 48, and 72 h of storage (25 degrees C), cells in suspension and detached cells from the coupons, obtained by vortexing, were enumerated on tryptic soy agar. In study II, a Salmonella Thompson AI-2-positive strain and an AI-2-negative strain, and an E. coli O157:H7 AI-2-positive strain and an AI-2-negative strain were inoculated into LB broth with stainless steel coupons. Cells were enumerated as in study I. In both studies, AI-2 activity was determined in cell-free supernatants. Cell numbers of S. Typhimurium DT104 on biofilms were higher (P < 0.05) in LB than those in LBG, while the E. coli O157:H7 strain showed no difference (P>or= 0.05) in biofilm cell counts between LB and LBG after storage for 72 h. Both S. Typhimurium DT104 and E. coli O157:H7 strains produced higher (P < 0.05) AI-2 activity in LBG than LB cell suspensions. Cell counts of AI-2-positive and-negative S. Thompson and E. coli O157:H7 strains were not different (P>or= 0.05) within suspensions or coupons (study II). The results indicated that, under the conditions of this study, AI-2 activity of the pathogen strains tested may not have a major influence on biofilm formation on food contact surfaces, which was similar between AI-2-positive and -negative strains.

Genome-wide screening and identification of novel proteolytic cleavage targets of caspase-8 and -10 in vitro

Apoptosis executed by the mammalian caspase family plays a fundamental role in cellular homeostasis. Deregulation of this process is associated with several human diseases. The multimerization of ligand-induced death receptors results in the recruitment of the death inducing signaling complex and autocatalytic activation of initiator caspases, including caspase-8 and -10. However, it is still unclear how initiator caspases trigger and control the early apoptotic signaling pathways, partly because the downstream proteolytic cleavage targets of the initiator caspases are not completely known. Although it is known that a number of proteins are cleaved by various members of the caspase family, the identification of specific cleavage substrates of the initiator caspases 8 and 10, has been hindered by a lack of systematic and broadly applicable strategies for substrate identification. In the present study we constructed a mouse cDNA library and used it to perform a systematic, genome-wide screen for novel in vitro substrates of caspase-8 and -10. From this, we successfully identified six putative caspase substrates, including five novel proteins (ABCF1, AKAP1, CPE, DOPEY1 and GOPC1) that may be targeted specifically by the initiator caspases 8 and 10 during the early stages of apoptosis. These findings may provide useful information for elucidating the apoptotic signaling pathways downstream of the death receptors.

Antimicrobial activity of epsilon-polylysine against Escherichia coli O157:H7, Salmonella Typhimurium, and Listeria monocytogenes in various food extracts

This study compared the antimicrobial effects of epsilon-polylysine (epsilon-PL) against Escherichia coli O157:H7, Salmonella Typhimurium, and Listeria monocytogenes in 6 food extracts and in broth. The food extracts (10% (w/w) in distilled water) evaluated were fat-free and whole fat milk, beef, bologna, rice, and vegetables (50:50 ratio of broccoli and cauliflower). epsilon-PL was tested at 0.005% and 0.02% (w/v) against E. coli O157:H7 and L. monocytogenes, and 0.02% and 0.04% (w/v) against S. Typhimurium. The substrates were inoculated (5 log CFU/mL) and periodically analyzed for surviving populations during storage at 12 degrees C for 6 d. In general, all 3 pathogens reached 7 to 9 log CFU/mL within 2 d in control substrates (no epsilon-PL). Immediate bactericidal effects (P < 0.05) following exposure to epsilon-PL were obtained in the rice (all pathogens) and vegetable (E. coli O157:H7 and S. Typhimurium) extracts. During storage, antimicrobial effects of epsilon-PL were more pronounced in the food extracts than in the broth medium. The greatest antimicrobial activity for all 3 pathogens was obtained in the rice and vegetable extracts, where counts were reduced (P < 0.05) to below the detection limit (0.0 log CFU/mL) by one or both epsilon-PL concentrations tested. In the other food extracts (fat-free milk, whole fat milk, beef, and bologna), both epsilon-PL concentrations tested generally resulted in lower (P < 0.05) pathogen levels at the end of storage compared to initial counts, with better bactericidal effects exerted by the higher of the 2 epsilon-PL concentrations. Additional research is needed to explore the potential antimicrobial effects of epsilon-PL in real food systems.

Probing the microscopic structure of bound states in quantum point contacts

Using an approach that allows us to probe the electronic structure of strongly pinched-off quantum point contacts (QPCs), we provide evidence for the formation of self-consistently realized bound states (BSs) in these structures. Our approach exploits the resonant interaction between closely coupled QPCs, and demonstrates that the BSs may give rise to a robust confinement of single spins, which show clear Zeeman splitting in a magnetic field.

CEBPG regulates ERCC5/XPG expression in human bronchial epithelial cells and this regulation is modified by E2F1/YY1 interactions

Marked inter-individual variation in lung cancer risk cannot be accounted for solely by cigarette smoke and other environmental exposures. Evidence suggests that variation in bronchial epithelial cell expression of key DNA repair genes plays a role. Variation in these genes correlates with variation in expression of CEBPG and E2F1 transcription factors. Here, we investigated the mechanistic basis for correlation of the DNA repair gene ERCC5 (previously known as XPG) with CEBPG and E2F1. CEBPG expression vector transfected into H23 or H460 cell lines up-regulated endogenous ERCC5 and also luciferase from a reporter construct containing 589 bp of ERCC5 5' regulatory region. A recognition site for CEBPG and a region containing sites for YY1 on the sense strand and E2F1 on the anti-sense strand participated in CEBPG up-regulation of ERCC5. CEBPG, E2F1 and YY1 binding to their respective sites were confirmed by electrophoretic mobility shift assay. Thus, we conclude that CEBPG regulates ERCC5 expression and this regulation is modified by E2F1/YY1 interactions. Several polymorphisms have been identified in these regions and, based on the data presented here, it is reasonable to hypothesize that they may contribute to risk for bronchogenic carcinoma.

Oxidation of corn oil during frying of soy-flour-added flour dough

Oxidation of corn oil during frying of soy-flour-added dough was studied. Flour dough containing soy flour at 0%, 10%, 20%, and 30% was fried in corn oil at 180 degrees C for 2.5 min, and a total of 60 fryings were performed every 30 min. The oxidation of oil was determined by contents of free fatty acids (FFA), conjugated dienoic acids (CDA), polar compounds, and p-anisidine values (PAV). Tocopherols and phospholipids (PLs) in the oil were determined by HPLC. Tocopherols were present in corn oil at 1000 ppm before frying and increased after the first frying of dough containing soy flour due to tocopherol transfer from soy-flour-added dough to the oil during frying. However, as the oil repeated frying, tocopherol contents decreased and its degradation rate was higher in the oil that fried soy-flour-added dough than in the oil that fried the dough without soy flour. PL was not detected in corn oil before and after frying. As the oil repeated frying, FFA, CDA, and polar compounds contents, and PAV of frying oil increased due to the oil oxidation. The values were higher in the oil which fried soy-flour-added dough than in the oil fried the dough without soy flour, indicating the acceleration of oil oxidation by soy flour added to dough. Increase in the oil oxidation by soy flour added to the dough was highly correlated with fast decomposition of tocopherol in the oil.