NDT-C11 as a viable novel detergent for single particle cryo-EM.

Single particle cryo electron microscopy (cryo-EM) is now the major method for the determination of integral membrane protein structure. For the success of a given project the type of membrane mimetic used for extraction from the native cell membrane, purification to homogeneity and finally cryo-grid vitrification is crucial. Although small molecule amphiphiles - detergents - are the most widely used membrane mimetic, specific tailoring of detergent structure for single particle cryo-EM is rare and the demand for effective detergents not satisfied. Here, we compare the popular detergent lauryl maltose-neopentyl glycol (LMNG) with the novel detergent neopentyl glycol-derived triglucoside-C11 (NDT-C11) in its behavior as free detergent and when bound to two types of multisubunit membrane protein complexes - cyanobacterial photosystem I (PSI) and mammalian F-ATP synthase. We conclude that NDT-C11 has high potential to become a very useful detergent for single particle cryo-EM of integral membrane proteins.

Overlapping and unique toxic effects of three alternative antifouling biocides (Diuron, Irgarol 1051®, Sea-Nine 211®) on non-target marine fish.

The use of alternative biocides has increased due to their economic and ecological relevance. Although data regarding the toxicity of commercial alternative biocides in marine organisms are accumulating, little is known about their toxic pathways or mechanisms. To compare the toxic effects of commercial alternative biocides on non-target pelagic fish (flounder) embryos, we investigated the adverse effects of developmental malformation and transcriptional changes. Three biocides including Diuron, Irgarol 1051® and Sea-Nine 211® produced a largely overlapping suite of developmental malformations, including tail-fin fold defects and dorsal body axis curvature. In our test, the potencies of these biocides were ranked in the following order with respect to malformation and mortalities: Sea-Nine 211®â€¯> Irgarol 1051®â€¯> Diuron. Consistent with the toxicity rankings, the expression of genes related to heart formation was greater in embryonic flounder exposed to Sea-Nine 211® than in those exposed to Irgarol 1051® or Diuron, while expression of genes related to fin malformation was greater in the Irgarol 1051® exposure group. In analyses of differential gene expression (DEG) profiles (fold change of genes with a cutoff P < 0.05) by high-throughput sequencing (RNA-seq), genes associated with nervous system development, transmembrane transport activity, and muscle cell development were significantly changed commonly. Embryos exposed to Diuron showed changes related to cellular protein localization, whereas genes associated with immune system processes were up-regulated significantly in embryos exposed to Irgarol 1051®. Genes related to actin filament organization and embryonic morphogenesis were up-regulated in embryos exposed to Sea-Nine 211®. Overall, our study provides a better understanding of the overlapping and unique developmental toxic effects of three commercial booster biocides through transcriptomic analyses in a non-target species, embryonic flounder.

Web-drive based source measure unit for automated evaluations of ionic liquid-gated MoS2 transistors.

For reliable characterization of two-dimensional semiconducting devices and continuous monitoring in toxic environments, construction of an electrical characterization-based massive database using a portable source measure unit (SMU) with a WiFi connection is desirable. The web-drive based SMU using a microcontroller developed here exhibits superior voltage source performance (∼1 mV) and voltage/current measurement (∼0.15 mV/∼1 nA) capabilities, with automatic construction of a measurement database for online storage using web-drive based software, which can be applied for reliable electrical characterization. Electrical characterization of ionic liquid-gated MoS2 transistors was achieved with the designed SMU and showed results comparable with those obtained using a commercial semiconductor characterization system. Ionic liquid-gated transistors only require a small gate bias (∼1.5 V) for on-state operation because of the high gate capacitance originating from the thin dielectric layer constructed of an electrical double layer, which makes the device a promising candidate for low power consumption applications. Finally, several electrical parameters of the ionic liquid-gated transistor were extracted from the datasets and uploaded to the web-drive.

Adverse effects and immune dysfunction in response to oral administration of weathered Iranian heavy crude oil in the rockfish Sebastes schlegeli.

To demonstrate the effects of weathered crude oil residue on the immune systems of resident fish, we measured the changes in toxic chemical concentrations, apoptosis, phagocytosis, metabolism, immune-related gene expression, and cell cycle arrest in livers or kidneys for up to 96 h after the weathered Iranian heavy crude oil (WIHCO) exposure by oral gavage in juvenile rockfish Sebastes schlegeli. Parent polyaromatic hydrocarbons (PAHs) in livers increased up to 5590 ng/g after 6 h exposure and then declined rapidly within 24 h. Hepato-detoxification and immune-related gene expression were also significantly increased (P < 0.05) after 6 h exposure and then declined rapidly within 24 h. However, biliary PAH metabolites and EROD activity remained elevated throughout the test period. Flow cytometry analysis also indicated sustained apoptosis and cell cycle arrests with reduced phagocytic activity for 96 h. Taken together, these results demonstrate rapid declination of the parent PAHs, whereas PAH metabolites remained much longer in tissues with prolonged suppression of immunity in molecular and cellular level, suggesting that weathered crude oil residue is likely linked to the high incidence of immune dysfunction in residential rockfish in oil spill area.

Comparative analysis of distinctive transcriptome profiles with biochemical evidence in bisphenol S- and benzo[a]pyrene-exposed liver tissues of the olive flounder Paralichthys olivaceus.

Flounder is a promising model species for environmental monitoring of coastal regions. To assess the usefulness of liver transcriptome profiling, juvenile olive flounder Paralichthys olivaceus were exposed to two pollutants, bisphenol S (BPS) and benzo[a]pyrene (BaP), which have different chemical characteristics and have distinct modes of metabolic action in teleost. Six hours after intraperitoneal injection with BPS (50 mg/kg bw) or BaP (20 mg/kg bw), liver transcriptomes were analyzed using the Illumina Hiseq 3000 platform. Interestingly, the transcriptome was highly sensitive and was distinctively expressed in response to each chemical. The primary effect of BPS was significantly increased transcription of egg process and vitellogenesis related genes, including vitellogenins (vtg1, vtg2), zona pellucida sperm-binding proteins (zp3, zp4), and estrogen receptors (erα, erß), with increases in plasma 17ß-estradiol (E2) and vitellogenin (VTG) concentrations. Following BaP treatment, detoxification- and biotransformation-related genes such as cyp1a1 and UDP-glucuronosyltransferase (ugt1a1) were significantly increased, with an increase in EROD activity. In both transcriptomes, mRNA expression of genes involved in antioxidant defense systems was increased, while genes involved in innate immunity were decreased upon BPS or BaP exposure with a decrease in complement activity. This study provides useful insight into the chemical-specific hepatic transcriptional response of P. olivaceus and suggests a basis for further studies examining biomarker application of liver transcriptomes for environmental pollution.

Few-Layer WSe2 Schottky Junction-Based Photovoltaic Devices through Site-Selective Dual Doping.

Ultrathin sheets of two-dimensional (2D) materials like transition metal dichalcogenides have attracted strong attention as components of high-performance light-harvesting devices. Here, we report the implementation of Schottky junction-based photovoltaic devices through site-selective surface doping of few-layer WSe2 in lateral contact configuration. Specifically, whereas the drain region is covered by a strong molecular p-type dopant (NDP-9) to achieve an Ohmic contact, the source region is coated with an Al2O3 layer, which causes local n-type doping and correspondingly an increase of the Schottky barrier at the contact. By scanning photocurrent microscopy using green laser light, it could be confirmed that photocurent generation is restricted to the region around the source contact. The local photoinduced charge separation is associated with a photoresponsivity of up to 20 mA W-1 and an external quantum efficiency of up to 1.3%. The demonstrated device concept should be easily transferrable to other van der Waals 2D materials.

4-Hydroxy-7-methyl-3-phenylcoumarin Suppresses Aflatoxin Biosynthesis via Downregulation of aflK Expressing Versicolorin B Synthase in Aspergillus flavus.

Naturally occurring coumarins possess antibacterial and antifungal properties. In this study, these natural and synthetic coumarins were used to evaluate their antifungal activities against Aspergillus flavus, which produces aflatoxins. In addition to control antifungal activities, antiaflatoxigenic properties were also determined using a high-performance liquid chromatography in conjunction with fluorescence detection. In this study, 38 compounds tested and 4-hydroxy-7-methyl-3-phenyl coumarin showed potent antifungal and antiaflatoxigenic activities against A. flavus. Inhibitory mode of antiaflatoxigenic action by 4-hydroxy-7-methyl-3-phenyl coumarin was based on the downregulation of aflD, aflK, aflQ, and aflR in aflatoxin biosynthesis. In the cases of coumarins, antifungal and aflatoxigenic activities are highly related to the lack of diene moieties in the structures. In structurally related compounds, 2,3-dihydrobenzofuran exhibited antifungal and antiaflatoxigenic activities against A. flavus. The inhibitory mode of antiaflatoxigenic action by 2,3-dihydrobenzofuran was based on the inhibition of the transcription factor (aflS) in the aflatoxin biosynthesis pathway. These potent inhibitions of 2,3-dihydrobenzofuran and 4-hydroxy-7-methyl-3-phenyl coumarin on the Aspergillus growth and production of aflatoxins contribute to the development of new controlling agents to mitigate aflatoxin contamination.

Antifungal and Antiaflatoxigenic Methylenedioxy-Containing Compounds and Piperine-Like Synthetic Compounds.

Twelve methylenedioxy-containing compounds including piperine and 10 piperine-like synthetic compounds were assessed to determine their antifungal and antiaflatoxigenic activities against Aspergillus flavus ATCC 22546 in terms of their structure-activity relationships. Piperonal and 1,3-benzodioxole had inhibitory effects against A. flavus mycelial growth and aflatoxin B1 production up to a concentration of 1000 µg/mL. Ten piperine-like synthetic compounds were synthesized that differed in terms of the carbon length in the hydrocarbon backbone and the presence of the methylenedioxy moiety. In particular, 1-(2-methylpiperidin-1-yl)-3-phenylprop-2-en-1-one had potent antifungal and antiaflatoxigenic effects against A. flavus up to a concentration of 1 µg/mL. This synthetic compound was remarkable because the positive control thiabendazole had no inhibitory effect at this concentration. Reverse transcription-PCR analysis showed that five genes involved in aflatoxin biosynthesis pathways were down-regulated in A. flavus, i.e., aflD, aflK, aflQ, aflR, and aflS; therefore, the synthetic compound inhibited aflatoxin production by down-regulating these genes.

SELDI-TOF MS-based discovery of a biomarker in Cucumis sativus seeds exposed to CuO nanoparticles.

Metal oxide nanoparticles (NPs) can inhibit plant seed germination and root elongation via the release of metal ions. In the present study, two acute phytotoxicity tests, seed germination and root elongation tests, were conducted on cucumber seeds (Cucumis sativus) treated with bulk copper oxide (CuO) and CuO NPs. Two concentrations of bulk CuO and CuO NPs, 200 and 600ppm, were used to test the inhibition rate of root germination; both concentrations of bulk CuO weakly inhibited seed germination, whereas CuO NPs significantly inhibited germination, showing a low germination rate of 23.3% at 600ppm. Root elongation tests demonstrated that CuO NPs were much stronger inhibitors than bulk CuO. SELDI-TOF MS analysis showed that 34 proteins were differentially expressed in cucumber seeds after exposure to CuO NPs, with the expression patterns of at least 9 proteins highly differing from those in seeds treated with bulk CuO and in control plants. Therefore, these 9 proteins were used to identify CuO NP-specific biomarkers in cucumber plants exposed to CuO NPs. A 5977-m/z protein was the most distinguishable biomarker for determining phytotoxicity by CuO NPs. Principal component analysis (PCA) of the SELDI-TOF MS results showed variability in the modes of inhibitory action on cucumber seeds and roots. To our knowledge, this is the first study to demonstrate that the phytotoxic effect of metal oxide NPs on plants is not caused by the same mode of action as other toxins.

Transcriptional targeting of gene expression in breast cancer by the promoters of protein regulator of cytokinesis 1 and ribonuclease reductase 2.

For cancer gene therapy, cancer-specific over- expression of a therapeutic gene is required to reduce side effects derived from expression of the gene in normal cells. To develop such an expression vector, we searched for genes over-expressed and/or specifically expressed in cancer cells using bioinformatics and have selected genes coding for protein regulator of cytokinesis 1 (PRC1) and ribonuclease reductase 2 (RRM2) as candidates. Their cancer-specific expressions were confirmed in both breast cancer cell lines and patient tissues. We compared each promoter's cancer-specific activity in the breast normal and cancer cell lines using the luciferase gene as a reporter and confirmed cancer-specific expression of both PRC1 and RRM2 promoters. To test activities of these promoters in viral vectors, the promoters were also cloned into an adeno-associated viral (AAV) vector containing green fluorescence protein (GFP) as the reporter. The GFP expression levels by these promoters were various depending on cell lines tested and, in MDA-MB-231 cells, GFP activities derived from the PRC1 and RRM2 promoters were as strong as that from the cytomegalovirus (CMV) promoter. Our result showed that a vector containing the PRC1 or RRM2 promoter could be used for breast cancer specific overexpression in gene therapy.