Ligand Effect in 1-Octanethiol Passivation of InP/ZnSe/ZnS Quantum Dots-Evidence of Incomplete Surface Passivation during Synthesis.

The lack of anionic carboxylate ligands on the surface of InP/ZnSe/ZnS quantum dots (QDs), where zinc carboxylate ligands can be converted to carboxylic acid or carboxylate ligands via proton transfer by 1-octanethiol, is demonstrated. The as-synthesized QDs initially have an under-coordinated vacancy surface, which is passivated by solvent ligands such as ethanol and acetone. Upon exposure of 1-octanethiol to the QD surface, 1-octanethiol effectively induces the surface binding of anionic carboxylate ligands (derived from zinc carboxylate ligands) by proton transfer, which consequently exchanges ethanol and acetone ligands that bind on the incomplete QD surface. These systematic chemical analyses, such as thermogravimetric analysis-mass spectrometry and proton nuclear magnetic resonance spectroscopy, directly show the interplay of surface ligands, and it associates with QD light-emitting diodes (QD-LEDs). It is believed that this better understanding can lead to industrially feasible QD-LEDs.

Activation of galactose utilization by the addition of glucose for the fermentation of agar hydrolysate using Lactobacillus brevis ATCC 14869.

OBJECTIVE: To investigate the application of carbon catabolite repression (CCR) relaxed Lactobacillus brevis ATCC 14869 in the utilization of agar hydrolysate to produce bioethanol and lactic acid through fermentation. RESULTS: As a single carbon source, galactose was not metabolized by L. brevis. However, L. brevis consumed galactose simultaneous to glucose and ceased cell growth after depletion of glucose. For complete use of galactose from agar hydrolysis, glucose need to be periodically replenished into the growth medium. Overall, L. brevis successfully used agar hydrolysate and produced 17.2 g/L of ethanol and 31.9 g/L of lactic acid. The maximum specific cell growth rate on galactose and glucose mixture was the same with the glucose-only medium at 0.12 h-1. The molar product yields from glucose for lactic acid and ethanol were 1.02 and 0.95 respectively, equal to values obtained from the simultaneous utilization of glucose and galactose. CONCLUSION: In contribution to the ongoing efforts to utilize marine biomass, the relaxed CCR in Lactobacillus brevis ATCC 14869 was herein exploited to produce bioethanol and lactic acid from red seaweed hydrolysates.

Serum-stable quantum dot-protein hybrid nanocapsules for optical bio-imaging.

We introduce shell cross-linked protein/quantum dot (QD) hybrid nanocapsules as a serum-stable systemic delivery nanocarrier for tumor-targeted in vivo bio-imaging applications. Highly luminescent, heavy-metal-free Cu0.3InS2/ZnS (CIS/ZnS) core-shell QDs are synthesized and mixed with amine-reactive six-armed poly(ethylene glycol) (PEG) in dichloromethane. Emulsification in an aqueous solution containing human serum albumin (HSA) results in shell cross-linked nanocapsules incorporating CIS/ZnS QDs, exhibiting high luminescence and excellent dispersion stability in a serum-containing medium. Folic acid is introduced as a tumor-targeting ligand. The feasibility of tumor-targeted in vivo bio-imaging is demonstrated by measuring the fluorescence intensity of several major organs and tumor tissue after an intravenous tail vein injection of the nanocapsules into nude mice. The cytotoxicity of the QD-loaded HSA-PEG nanocapsules is also examined in several types of cells. Our results show that the cellular uptake of the QDs is critical for cytotoxicity. Moreover, a significantly lower level of cell death is observed in the CIS/ZnS QDs compared to nanocapsules loaded with cadmium-based QDs. This study suggests that the systemic tumor targeting of heavy-metal-free QDs using shell cross-linked HSA-PEG hybrid nanocapsules is a promising route for in vivo tumor diagnosis with reduced non-specific toxicity.

Transcriptome sequencing of the Antarctic vascular plant Deschampsia antarctica Desv. under abiotic stress.

Antarctic hairgrass (Deschampsia antarctica Desv.) is the only natural grass species in the maritime Antarctic. It has been studied as an extremophile that has successfully adapted to marginal land with the harshest environment for terrestrial plants. However, limited genetic research has focused on this species due to the lack of genomic resources. Here, we present the first de novo assembly of its transcriptome by massive parallel sequencing and its expression profile using D. antarctica grown under various stress conditions. Total sequence reads generated by pyrosequencing were assembled into 60,765 unigenes (28,177 contigs and 32,588 singletons). A total of 29,173 unique protein-coding genes were identified based on sequence similarities to known proteins. The combined results from all three stress conditions indicated differential expression of 3,110 genes. Quantitative reverse transcription polymerase chain reaction showed that several well-known stress-responsive genes encoding late embryogenesis abundant protein, dehydrin 1, and ice recrystallization inhibition protein were induced dramatically and that genes encoding U-box-domain-containing protein, electron transfer flavoprotein-ubiquinone, and F-box-containing protein were induced by abiotic stressors in a manner conserved with other plant species. We identified more than 2,000 simple sequence repeats that can be developed as functional molecular markers. This dataset is the most comprehensive transcriptome resource currently available for D. antarctica and is therefore expected to be an important foundation for future genetic studies of grasses and extremophiles.

miRGator v2.0: an integrated system for functional investigation of microRNAs.

miRGator is an integrated database of microRNA (miRNA)-associated gene expression, target prediction, disease association and genomic annotation, which aims to facilitate functional investigation of miRNAs. The recent version of miRGator v2.0 contains information about (i) human miRNA expression profiles under various experimental conditions, (ii) paired expression profiles of both mRNAs and miRNAs, (iii) gene expression profiles under miRNA-perturbation (e.g. miRNA knockout and overexpression), (iv) known/predicted miRNA targets and (v) miRNA-disease associations. In total, >8000 miRNA expression profiles, ∼300 miRNA-perturbed gene expression profiles and ∼2000 mRNA expression profiles are compiled with manually curated annotations on disease, tissue type and perturbation. By integrating these data sets, a series of novel associations (miRNA-miRNA, miRNA-disease and miRNA-target) is extracted via shared features. For example, differentially expressed genes (DEGs) after miRNA knockout were systematically compared against miRNA targets. Likewise, differentially expressed miRNAs (DEmiRs) were compared with disease-associated miRNAs. Additionally, miRNA expression and disease-phenotype profiles revealed miRNA pairs whose expression was regulated in parallel in various experimental and disease conditions. Complex associations are readily accessible using an interactive network visualization interface. The miRGator v2.0 serves as a reference database to investigate miRNA expression and function (http://miRGator.kobic.re.kr).

Enhanced Electroluminescence via a Nanohybrid Material Consisting of Aromatic Ligand-Modified InP Quantum Dots and an Electron-Blocking Polymer as the Single Active Layer in Quantum Dot-LEDs.

Electron overcharge causes rapid luminescence quenching in the quantum dot (QD) emission layer in QD light-emitting diodes (QD-LEDs), resulting in low device performance. In this paper we describe the application of different aromatic thiol ligands and their influence on device performance as well as their behavior in combination with an electron blocking material (EBM). The three different ligands, 1-octanethiol (OcSH), thiophenol (TP), and phenylbutan-1-thiol (PBSH), were introduced on to InP/ZnSe/ZnS QDs referred to as QD-OcSH, QD-TP, and QD-PBSH. PBSH is in particular applied as a ligand to improve QD solubility and to enhance the charge transport properties synergistically with EBM probably via π-π interaction. We synthesized poly-[N,N-bis[4-(carbazolyl)phenyl]-4-vinylaniline] (PBCTA) and utilized it as an EBM to alleviate excess electrons in the active layer in QD-LEDs. The comparison of the three QD systems in an inverted device structure without the application of PBCTA as an EBM shows the highest efficiency for QD-PBSH. Moreover, when PBCTA is introduced as an EBM in the active layer in combination with QD-PBSH in a conventional device structure, the current efficiency shows a twofold increase compared to the reference device without EBM. These results strongly confirm the role of PBCTA as an EBM that effectively alleviates excess electrons in the active layer, leading to higher device efficiency.

Maternal exposure to polystyrene nanoplastics causes brain abnormalities in progeny.

As global plastic production continues to grow, microplastics released from a massive quantity of plastic wastes have become a critical environmental concern. These microplastic particles are found in a wide range of living organisms in a diverse array of ecosystems. In this study, we investigated the biological effects of polystyrene nanoplastic (PSNP) on development of the central nervous system using cultured neural stem cells (NSCs) and mice exposed to PSNP during developmental stages. Our study demonstrates that maternal administration of PSNP during gestation and lactating periods altered the functioning of NSCs, neural cell compositions, and brain histology in progeny. Similarly, PSNP-induced molecular and functional defects were also observed in cultured NSCs in vitro. Finally, we show that the abnormal brain development caused by exposure to high concentrations of PSNP results in neurophysiological and cognitive deficits in a gender-specific manner. Our data demonstrate the possibility that exposure to high amounts of PSNP may increase the risk of neurodevelopmental defects.

Metal Sulfide Nanoparticle Synthesis with Ionic Liquids - State of the Art and Future Perspectives.

Metal sulfides are among the most promising materials for a wide variety of technologically relevant applications ranging from energy to environment and beyond. Incidentally, ionic liquids (ILs) have been among the top research subjects for the same applications and also for inorganic materials synthesis. As a result, the exploitation of the peculiar properties of ILs for metal sulfide synthesis could provide attractive new avenues for the generation of new, highly specific metal sulfides for numerous applications. This article therefore describes current developments in metal sulfide nanoparticle synthesis as exemplified by a number of highlight examples. Moreover, the article demonstrates how ILs have been used in metal sulfide synthesis and discusses the benefits of using ILs over more traditional approaches. Finally, the article demonstrates some technological challenges and how ILs could be used to further advance the production and specific property engineering of metal sulfide nanomaterials, again based on a number of selected examples.

Effects of Ultra-high doserate FLASH Irradiation on the Tumor Microenvironment in Lewis Lung Carcinoma: Role of Myosin Light Chain.

PURPOSE: To investigate whether the vascular collapse in tumors by conventional dose rate (CONV) irradiation (IR) would also occur by the ultra-high dose rate FLASH IR. METHODS AND MATERIALS: Lewis lung carcinoma (LLC) cells were subcutaneously implanted in mice. This was followed by CONV or FLASH IR at 15 Gy. Tumors were harvested at 6 or 48 hours after IR and stained for CD31, phosphorylated myosin light chain (p-MLC), γH2AX (a surrogate marker for DNA double strand break), intracellular reactive oxygen species (ROS), or immune cells such as myeloid and CD8α T cells. Cell lines were irradiated with CONV IR for Western blot analyses. ML-7 was intraperitoneally administered daily to LLC-bearing mice for 7 days before 15 Gy CONV IR. Tumors were similarly harvested and analyzed. RESULTS: By immunostaining, we observed that CONV IR at 6 hours resulted in constricted vessel morphology, increased expression of p-MLC, and much higher numbers of γH2AX-positive cells in tumors, which were not observed with FLASH IR. Mechanistically, MLC activation by ROS is unlikely, because FLASH IR produced significantly more ROS than CONV IR in tumors. In vitro studies demonstrated that ML-7, an inhibitor of MLC kinase, abrogated IR-induced γH2AX formation and disappearance kinetics. Lastly, we observed that CONV IR when combined with ML-7 produced some effects similar to FLASH IR, including reduction in the vasculature collapse, fewer γH2AX-positive cells, and increased immune cell influx to the tumors. CONCLUSIONS: FLASH IR produced novel changes in the tumor microenvironment that were not observed with CONV IR. We believe that MLC activation in tumors may be responsible for some of the microenvironmental changes differentially regulated between CONV and FLASH IR.

In silico identification of gene amplification targets for improvement of lycopene production.

The identification of genes to be deleted or amplified is an essential step in metabolic engineering for strain improvement toward the enhanced production of desired bioproducts. In the past, several methods based on flux analysis of genome-scale metabolic models have been developed for identifying gene targets for deletion. Genome-wide identification of gene targets for amplification, on the other hand, has been rather difficult. Here, we report a strategy called flux scanning based on enforced objective flux (FSEOF) to identify gene amplification targets. FSEOF scans all the metabolic fluxes in the metabolic model and selects fluxes that increase when the flux toward product formation is enforced as an additional constraint during flux analysis. This strategy was successfully employed for the identification of gene amplification targets for the enhanced production of the red-colored antioxidant lycopene. Additional metabolic engineering based on gene knockout simulation resulted in further synergistic enhancement of lycopene production. Thus, FSEOF can be used as a general strategy for selecting genome-wide gene amplification targets in silico.

Variable Tumor Microenvironment-on-a-chip with Temporal Angiogenic Switching System by Diffusion Control.

Organ-on-a-chip has the potential to replace preclinical trials which have been problematic for decades due to unaffordable cost and time. The performance of in vitro tumor-on-a-chip depends on how accurately the system represents analogous tumor-microenvironment (TME) and TME associated phenomena. In this study, we have focused on angiogenesis, one of the most significant features of TME for tumor growth and metastasis. Angiogenesis in TME is triggered through cascaded interactions among TME associated neighboring cells including immune cells, tumor cells, and fibroblast cells [1]. Therefore, temporally-controlled TME-on-a-chip is desired for an accurate representation of angiogenesis. However, conventional microfluidic devices cannot temporarily manipulate the condition of interacting cells and secreted signal molecules. Here, we proposed a hydrogel-based variable TME-on-a-chip with diffusion switch channels. The channels between hydrogel walls enable temporal diffusion control by controlling inflow. The diffusion control was observed in diffusion experiment with a fluorescent dye. Furthermore, experiment of HUVEC's migration toward diffused VEGF also confirmed that TME-on-a-chip is capable of reproducing an angiogenic switch triggering through temporal diffusion control. Due to a simple fabrication procedure, the design of the microfluidic device can be easily modified to represent more complex variable TME models.

CD64-targeted HO-1 RNA interference enhances chemosensitivity in orthotopic model of acute myeloid leukemia and patient-derived bone marrow cells.

Acute myeloid leukemia is the most frequent and life-threatening blood cancer. The main treatment is chemotherapy, sometimes followed by stem cell transplant. Resistance to chemotherapy and hepatotoxicity of the CD33-targeted therapy require an alternative therapeutic strategy. Here, we report CD64-targeted RNA interference as a novel AML therapy, which was delivered by a recombinant fusion protein of CD64-binding antibody and nona-arginine (sR9). The sR9-mediated heme oxygenase-1 siRNA (siHO-1) delivery efficiently enhanced apoptotic response to daunorubicin of AML cells and AML-targeted HO-1 silencing improved chemotherapy and prolonged survival in orthotopic myeloid leukemia model. CD64 expression was verified and HO-1-silencing-mediated chemo-sensitization was also validated in leukemic blast cells originated from AML M4/M5 patient's bone marrow. Collectively, CD64-targeted RNA interference could be a promising strategy for AML therapy and AML-targeted HO-1 suppression is expected to improve the chemotherapeutic effect in future clinical trials.

Why have serine/threonine/tyrosine kinases been evolutionarily selected in eukaryotic signaling cascades?

The signal transduction systems of eukaryotes are different from those of prokaryotes with respect to their structures and mechanisms. The main signal transduction system of prokaryotes called the two-component system (TCS) is a one-step phosphorelay system composed of a histidine kinase (HK) while the central signal transduction system of eukaryotes called the mitogen-activated protein kinase (MAPK) cascade system (MCS) is a multi-step phosphorelay system composed of serine/threonine/tyrosine kinases (STYKs). The two signal transduction systems are also different in their transphosphorylation mechanisms. HK in the TCS transfers its own phosphate group to the response regulator protein while STYKs in the MCS phosphorylate other proteins using ATP. We were intrigued by the different dynamics resulting from such differences and wondered why STYKs instead of HKs have been evolutionarily selected in eukaryotic signaling cascades. In this paper, we compared the dynamical characteristics of two mathematical models which reflect such differences between the TCS and the MCS, and found that STYKs are more appropriate for cascade structures in eukaryotic signal transduction than HK with respect to the duration and settling time of response signals.

Volatile profiles and involvement step of moisture in bulk oils during oxidation by action of deuterium oxide (D2O).

Volatile formation is an inevitable result of lipid oxidation, which impact the quality of lipid rich foods. In this study, moisture role on the formation of volatiles were evaluated using deuterium oxide (D2O) and possible steps of moisture involvement were suggested. Moisture content in corn oil with deuterium free water (H2O) was significantly (p < 0.05) higher than that in corn oil with D2O. The contents of some volatiles including pentane, hexanal, 2-hexenal, and t-2-heptenal in corn oil with D2O were higher than those in corn oil with H2O for the first 8 days. Volatiles containing deuterium appeared in the order of pentane, t-2-pentenal, and t-2-heptenal during oxidation. Deuterium incorporated volatiles could be formed after the ß-scission of lipid hydroperoxides. Therefore, moisture plays important roles in the formation of volatiles as well as the locations of oxidation in bulk oils.

Surfactant-free solubilization and systemic delivery of anti-cancer drug using low molecular weight methylcellulose.

Docetaxel, an advanced taxoid, has been widely used as an anti-mitotic agent, but further augmentation of its properties is still required, including improvement in low aqueous solubility. Herein, we report the development of bio-eliminable low molecular weight methylcellulose-based surfactant-free injectable formulation for the delivery of docetaxel. Crude methylcellulose, a hydrophobically modified cellulose derivative, was hydrolyzed by an enzymatic degradation method to obtain low molecular weight methylcellulose (LMwMC). Docetaxel was successfully loaded in micelles with small particle sizes high drug loading and sustained release profile. The in vivo anti-cancer effects of intravenously injected nanoparticle systems in B16F10 melanoma xenograft mice were evaluated and demonstrated a significantly enhanced therapeutic effect with the docetaxel-LMwMC micellar aggregates compared to a commercially available docetaxel, Taxotere®. Surfactant-free solubilization of docetaxel could be a promising delivery method for effective insoluble drug delivery for anti-tumor efficacy.

Coupled positive feedbacks provoke slow induction plus fast switching in apoptosis.

Apoptosis is a form of a programmed cell death for multicellular organisms to remove unwanted or damaged cells. This critical choice of cellular fate is an all-or-none process, but its dynamics remains unraveled. The switch-like apoptotic decision has to be reliable, and once a pro-apoptotic fate is determined it requires fast and irreversible execution. One of the key regulators in apoptosis is caspase-3. Interestingly, activated caspase-3 quickly executes apoptosis, but it takes considerable time to activate it. Here, we have analyzed this "slow induction plus fast switching" mechanism of caspase-3 through mathematical modeling and computational simulation. First, we have shown that two positive feedbacks, composed of caspase-8 and XIAP, are essential for the "slow induction plus fast switching" behavior of caspase-3. Second, we have found that XIAP in the feedback loops primarily regulates induction time of caspase-3. In many cancer cells activation of caspase-3 is suppressed. Our results suggest that reinforcement of the positive feedback by XIAP, which relieves XIAP-mediated caspase-3 inhibition, might favor a pro-apoptotic cellular fate.

Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants.

One of the well-established approaches for the quantitative characterization of large-scale underdetermined metabolic network is constraint-based flux analysis, which quantifies intracellular metabolic fluxes to characterize the metabolic status. The system is typically underdetermined, and thus usually is solved by linear programming with the measured external fluxes as constraints. Thus, the intracellular flux distribution calculated may not represent the true values. (13)C-constrained flux analysis allows more accurate determination of internal fluxes, but is currently limited to relatively small metabolic networks due to the requirement of complicated mathematical formulation and limited parameters available. Here, we report a strategy of employing such partial information obtained from the (13)C-labeling experiments as additional constraints during the constraint-based flux analysis. A new methodology employing artificial metabolites and converging ratio determinants (CRDs) was developed for improving constraint-based flux analysis. The CRDs were determined based on the metabolic flux ratios obtained from (13)C-labeling experiments, and were incorporated into the mass balance equations for the artificial metabolites. These new mass balance equations were used as additional constraints during the constraint-based flux analysis with genome-scale E. coli metabolic model, which allowed more accurate determination of intracellular metabolic fluxes.

Unraveling the functional interaction structure of a biomolecular network through alternate perturbation of initial conditions.

Various approaches attempting to infer the functional interaction structure of a hidden biomolecular network from experimental time-series measurements have been developed; however, due to both experimental limitations and methodological complexities, a large majority of these approaches have been unsuccessful. In particular, with respect to the elucidation of such networks, there are (i) a dimensionality problem: too many network nodes with too few available sampling points, (ii) a computational complexity problem: exponential complexity if a priori information is unavailable for regulatory nodes, and (iii) an experimental measurement problem: no guidelines for an appropriate experimental design for distinguishing direct and indirect influences among network nodes. Here, we sought to develop a new methodology capable of identifying the correct functional interaction structure with only a few sampling points through relatively simple computations. We also attempted to provide guidelines for an experimental design capable of supporting this methodology by taking proper measurements of the direct influences among the network nodes. In the present study, we considered an experiment where measurements were taken at two sampling time points with alternate perturbation (up-regulation or down-regulation) of initial conditions while keeping the same initial conditions for unperturbed network nodes, and propose a new method of identifying the functional interaction structure from such measurements. The proposed method is able to avoid the dimensionality problem caused by the practically limited number of sampling time points, and does not suffer from the computational complexity problem, as it only uses a simple algebra based on the Mean Value Theorem (see Supplementary mathematical descriptions) without any other complicated computation. In addition, we provide a detailed guideline for an experimental design that can take proper measurements of the direct influences among the network nodes through perturbation of initial conditions. The proposed method is particularly useful for cases investigating the local interaction structure around a specific network node of interest. An example, based on simulated data, is provided to illustrate the proposed method.

Activation of professional antigen presenting cells by acharan sulfate isolated from giant African snail, Achatina fulica.

Acharan sulfate isolated from the giant African snail, Achatina fulica, has been reported to have antitumor activity in vivo. In an effort to determine the mechanisms of its antitumor activity, we examined the effects of acharan sulfate on professional antigen presenting cells (APCs). Acharan sulfate increased the phagocytic activity, the production of cytokines such as TNF-alpha and IL-1beta, and the release of nitric oxide on a macrophage cell line, Raw 264.7 cells. In addition, acharan sulfate induced phenotypic and functional maturation of immature dendritic cells (DCs). Immature DCs cultured with acharan sulfate expressed higher levels of class II MHC molecules and major co-stimulatory molecules such as B7-1, B7-2, and CD40. Functional maturation of immature DCs cultured in the presence of acharan sulfate was confirmed by the increased allostimulatory capacity and IL-12 production. These results suggest that the antitumor activity of acharan sulfate is partly due to the activation of professional antigen presenting cells.

Inferring biomolecular regulatory networks from phase portraits of time-series expression profiles.

Reverse engineering of biomolecular regulatory networks such as gene regulatory networks, protein interaction networks, and metabolic networks has received an increasing attention as more high-throughput time-series measurements become available. In spite of various approaches developed from this motivation, it still remains as a challenging subject to develop a new reverse engineering scheme that can effectively uncover the functional interaction structure of a biomolecular network from given time-series expression profiles (TSEPs). We propose a new reverse engineering scheme that makes use of phase portraits constructed by projection of every two TSEPs into respective phase planes. We introduce two measures of a slope index (SI) and a winding index (WI) to quantify the interaction properties embedded in the phase portrait. Based on the SI and WI, we can reconstruct the functional interaction network in a very efficient and systematic way with better inference results compared to previous approaches. By using the SI, we can also estimate the time-lag accompanied with the interaction between molecular components of a network.