Low Cost Extraction and Isothermal Amplification of DNA for Infectious Diarrhea Diagnosis

In order to counter the common perception that molecular diagnostics are too complicated to work in low resource settings, we have performed a difficult sample preparation and DNA amplification protocol using instrumentation designed to be operated without wall or battery power. In this work we have combined a nearly electricity-free nucleic acid extraction process with an electricity-free isothermal amplification assay to detect the presence of Clostridium difficile (C. difficile) DNA in the stool of infected patients. We used helicase-dependent isothermal amplification (HDA) to amplify the DNA in a low-cost, thermoplastic reaction chip heated with a pair of commercially available toe warmers, while using a simple Styrofoam insulator. DNA was extracted from known positive and negative stool samples. The DNA extraction protocol utilized an air pressure driven solid phase extraction device run using a standard bicycle pump. The simple heater setup required no electricity or battery and was capable of maintaining the temperature at 65°C±2°C for 55 min, suitable for repeatable HDA amplification. Experiments were performed to explore the adaptability of the system for use in a range of ambient conditions. When compared to a traditional centrifuge extraction protocol and a laboratory thermocycler, this disposable, no power platform achieved approximately the same lower limit of detection (1.25×10⁻² pg of C. difficile DNA) while requiring much less raw material and a fraction of the lab infrastructure and cost. This proof of concept study could greatly impact the accessibility of molecular assays for applications in global health.     

Oryza sativa COI Homologues Restore Jasmonate Signal Transduction in Arabidopsis coi1-1 Mutants

CORONATINE INSENSITIVE 1 (COI1) encodes an E3 ubiquitin ligase complex component that interacts with JAZ proteins and targets them for degradation in response to JA signaling. The Arabidopsis genome has a single copy of COI1, but the Oryza sativa genome has three closely related COI homologs. To examine the functions of the three OsCOIs, we used yeast two-hybrid assays to examine their interactions with JAZ proteins and found that OsCOIs interacted with OsJAZs and with JAZs, in a coronatine dependent manner. We also tested whether OsCOI1a and OsCOI1b could complement Arabidopsis coi1-1 mutants and found that overexpression of either gene in the coi1-1 mutant resulted in restoration of JA signal transduction and production of seeds, indicating successful complementation. Although OsCOI2 interacted with a few OsJAZs, we were not able to successfully complement the coi1-1 mutant with OsCOI2. Molecular modeling revealed that the three OsCOIs adopt 3D structures similar to COI1. Structural differences resulting from amino acid variations, especially among amino acid residues involved in the interaction with coronatine and JAZ proteins, were tested by mutation analysis. When His-391 in OsCOI2 was substituted with Tyr-391, OsCOI2 interacted with a wider range of JAZ proteins, including OsJAZ1, 2, 5∼9 and 11, and complemented coi1-1 mutants at a higher frequency than the other OsCOIs and COI1. These results indicate that the three OsCOIs are orthologues of COI1 and play key roles in JA signaling.     

Ethanol induces cell cycle arrest and triggers apoptosis via Sp1-dependent p75NTR expression in human neuroblastoma cells

Ethanol exposure has deleterious effects on the central nervous system. Although several mechanisms for ethanol-induced damage have been suggested, the precise mechanism underlying ethanol-induced neuronal cell death remains unclear. Recent studies indicate that the p75 neurotrophin receptor (p75NTR) has a critical role in the regulation of neuronal survival. This study was designed to examine the role of p75NTR in ethanol-induced apoptotic signaling in neuroblastoma cells. Ethanol caused highly increased level of p75NTR expression. The use of small interfering RNA to inhibit p75NTR expression markedly attenuated ethanol-induced cell cycle arrest and apoptosis. DNA binding activity of Sp1 was increased by ethanol, whereas inhibition of Sp1 activity by mithramycin, a Sp1 inhibitor, or short hairpin RNA suppressed ethanol-induced p75NTR expression. In addition, inhibitors of casein kinase 2 (CK2) and extracellular signal-regulated kinase (ERK) augmented ethanol-induced p75NTR expression. Our results also demonstrate that inhibition of ERK and CK2 caused a further increase in the activation of the p75NTR proximal promoter induced by ethanol. This increased activation was partially suppressed by the deletion of the Sp1 binding sites. These results suggest that Sp1-mediated p75NTR expression is regulated at least in part by ERK and CK2 pathways. The present study also showed that treatment with ethanol resulted in significant increases in the expression of p21, but not the levels of p53 and p53 target genes such as Bax, Puma, and Bcl-2. Furthermore, the inhibition of p75NTR expression or Sp1 activity suppressed ethanol-induced p21 expression, cell cycle arrest, and apoptosis. These data suggest that ethanol increases p75NTR expression, and CK2 and ERK signaling inversely regulate Sp1-mediated p75NTR expression in ethanol-treated neuroblastoma cells. Thus, our study provides more insight into the mechanisms underlying ethanol actions.     

Taboo-based Monte Carlo Search as a Method to Improve Sampling Efficiency

Abstract

Taboo-based Monte Carlo search which restricts the sampling of the region near an old configuration, is developed. In this procedure, Monte Carlo simulation and random search method are combined to improve the sampling efficiency. The feasibility of this method is tested on global optimization of a continuous model function, melting of the 256 Lennard-Jones particles at T? = 0.680 and ρ? = 0.850 and polypeptides (alanine dipeptide and Metenkephalin). From the comparison of results for the model function between our method and other methods, we find the increase of convergence rate and the high possibility of escaping from the local energy minima. The results of the Lennard-Jones solids and polypeptides show that the convergence property to reach the equilibrium state is better than that of others. It is also found that no significant bias in ensemble distribution is detected, though taboo-based Monte Carlo search does not sample the correct ensemble distribution owing to the restriction of the sampling of the region near an old configuration.     

Kinetic Monte Carlo simulation for the void defects formation in Czochralski silicon growth

The quality of silicon wafers used as substrates for microelectronic devices is measured in terms of the type, size and density of defects formed during crystal growth process. The native point defects such as vacancies and self-interstitials diffuse, react and aggregate to form intrinsic defects in the silicon wafers. We investigated the point defect behaviour using the kinetic lattice Monte Carlo (KLMC) model. The KLMC method has been applied extensively in various forms to the study of microdefects in silicon wafers. The purpose of this paper is to demonstrate the phenomena of void defect formation. The size and density of void defects are usually affected by system temperature, vacancy–vacancy reaction and vacancy–impurity reaction. In this paper, we study the temperature effect and the vacancy concentration effect. The simulation results with various temperatures are well matched with our experimental data, and the relationship between temperature and vacancy density describes well the phenomena of void defect formation. This is the first time such KLMC simulation results have been reported.     

Pollen morphology of some taxa of Vicia L. subgenus Vicia (Fabaceae) from Turkey

In this study, the pollen morphology of 11 taxa belonging to Atossa (Alef.) Asch. & Graebner, Hypechusa (Alef.) Asch. & Graebner, Peregrinae Kupicha, Wiggersia (Alef.) Maxted, Vicia L. and Narbonensis (Radzhi) Maxted sections of the genus Vicia L. subgenus Vicia (Fabeae, Fabaceae) naturally growing in Turkey has been studied using Light Microscopy (LM) and Scanning Electron Microscopy (SEM) to evaluate the taxonomic relevance of pollen characters. Twelve morphometric characters are analysed with one-way analysis of variance and Tukey’s honestly significant difference test for multiple comparisons. Of the taxa studied V. narbonensis var. narbonensis (sect. Narbonensis) has the largest pollen grains (P = 51.98 μm × E = 30.52 μm) and V. lathyroides (sect. Wiggersia) has the smallest pollen grains (P = 27.71 μm × E = 20.14 μm). The pollen grains are subprolate to perprolate (P/E = 1.16–2.11), but the prolate shape occurs in the majority of the taxa. The regular pollen grains of all taxa are trizonocolporate, isopolar, and released in monads. Ornamentation of the mesocolpium is psilate-perforate in V. lathyroides (sect. Wiggersia), reticulate-rugulate in V. narbonensis var. narbonensis (sect. Narbonensis), (micro)reticulate in V. sericocarpa var. sericocarpa (sect. Hypechusa), V. sativa subsp. sativa (sect. Vicia) and V. grandiflora var. grandiflora (sect. Vicia), and reticulate-perforate in the remaining taxa. The apocolpium and colpus area are psilate or perforate in all taxa except V. sericocarpa var. sericocarpa (sect. Hypechusa) and V. sativa subsp. sativa (sect. Vicia), which exhibit the obscurely reticulate-perforate pattern. Several palynological features have taxonomic importance in sectional level: polar axis, equatorial diameter, pollen shape (P/E ratio), colpus length, colpus width, size of pori, porus length/width ratio, lumina diameter, muri thickness and ornamentation. The results also indicate that pollen characters can be useful in distinguishing the examined taxa.