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Local recurrence is a common cause of treatment failure for patients with solid tumors. Tumor-specific intraoperative fluorescence imaging may improve staging and debulking efforts in cytoreductive surgery and, thereby improve prognosis. Here, we report in vivo assembly of the second near-infrared window (NIR-II) emitting downconversion nanoparticles (DCNPs) modified with DNA and targeting peptides to improve the image-guided surgery for metastatic ovarian cancer. The NIR-II imaging quality with DCNPs is superior to that of clinically approved ICG with good photostability and deep tissue penetration (8 mm). Stable tumor retention period experienced 6 h by in vivo assembly of nanoprobes can be used for precise tumor resection. Superior tumor-to-normal tissue ratio is successfully achieved to facilitate the abdominal ovarian metastases surgical delineation. Metastases with ≤1 mm can be completely excised under NIR-II bioimaging guidance. This novel technology provides a general new basis for the future design of nanomaterials for medical applications.

A small-molecule fluorophore FD-1080 with both excitation and emission in the NIR-II region has been successfully synthesized for in vivo imaging. A heptamethine structure is designed to shift the absorption and emission into NIR-II region. Sulphonic and cyclohexene groups are introduced to enhance its water solubility and stability. The quantum yield of FD-1080 is 0.31 %, and can be increased to 5.94 % after combining with fetal bovine serum (FBS). Significantly, 1064 nm NIR-II excitation was demonstrated with the high tissue penetration depth and superior imaging resolution compared to previously reported NIR excitation from 650 nm to 980 nm. FD-1080 is not only capable of realizing non-invasive high-resolution deep-tissue hindlimb vasculature and brain vessel bioimaging, but also quantifying the respiratory rate based on the dynamic imaging of respiratory craniocaudal motion of the liver for the awake and anaesthetized mouse., (© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

As a minimal or noninvasive therapeutic method for tumors, photodynamic therapy (PDT) induced by the external laser irradiations has attracted great attentions. However, the UV-visible responsive property with low tissue penetration and photothermal effect from the prolonged irradiation impedes their further applications. Herein, a near-infrared (NIR) rechargeable "optical battery" for irradiation-free PDT is fabricated by embedding upconversion materials, persistent luminescence materials, photosensitizer into biocompatible polydimethylsiloxane. After 5 s quickly charged by 980-nm NIR laser, the PDT "optical battery" can generate green persistent luminescence and produce cytotoxic singlet oxygen for continuous irradiation-free PDT (∼30 min) without external irradiation. Due to deep tissue penetration and discontinuous short exposure of NIR light charging source, the "optical battery" can still be charged to continuously generate singlet oxygen in deep tissue (∼4 mm) with low photothermal effect. The PDT implant can be easily optimized in size and shape aiming at different nidus sites and achieved different functions by adding other functional components (e.g. CaO 2 for oxygen envolving to overcome hypoxia tumor). The effective tumor proliferation inhibiting capability of this NIR rechargeable "optical battery" may give rise to next generation of intelligent stimuli-responsive nanomedicine and noninvasive photo bio-stimulation research for future clinical applications., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Following publication of the original article [1], a reader spotted that the article appears to have some misplaced/duplicated figures. In particular, Fig. 5a and Fig. 6a appear to be identical, and do not match what is written in the text. The authors apologized for this oversight and supplied the original pictures, which are reproduced below.

Understanding the interactions between graphene nanomaterials (GNMs) and antibiotics in aqueous solution is critical to both the engineering applications of GNMs and the assessment of their potential impact on the fate and transport of antibiotics in the aquatic environment. In this study, adsorption of one common antibiotic, tetracycline, by graphene oxide (GO) and reduced graphene oxide (RGO) was examined with multi-walled carbon nanotubes (MWCNTs) and graphite as comparison. The results showed that the tetracycline adsorption capacity by the four selected carbonaceous materials on the unit mass basis followed an order of GO>RGO>MWCNTs>graphite. Upon normalization by surface area, graphite, RGO and MWCNTs had almost the same high tetracycline adsorption affinity while GO exhibited the lowest. We proposed π-electron-property dependent interaction mechanisms to explain the observed different adsorption behaviors. Density functional theory (DFT) calculations suggested that the oxygen-containing functional groups on GO surface reduced its π-electron-donating ability, and thus decreased the π-based interactions between tetracycline and GO surface. Comparison of adsorption efficiency at different pH indicated that electrostatic interaction also played an important role in tetracycline-GO interactions. Site energy analysis confirmed a highly heterogeneous distribution of the binding sites and strong tetracycline binding affinity of GO surface., (Copyright © 2017. Published by Elsevier B.V.)

Tumor hypoxia is typically presented in the central region of solid tumors, which is mainly caused by an inadequate blood flow and oxygen supply. In the conventional treatment of hypoxic human tumors, not only the oxygen-dependent photodynamic therapy (PDT), but also antitumor drug-based chemotherapy, is considerably limited. The use of direct oxygen delivering approach with oxygen-dependent PDT or chemotherapy may potentiate the reactive oxygen species (ROS)-mediated cytotoxicity of the drug toward normal tissues. Herein, a synergetic one-for-all mesoporous cerium oxide upconversion biophotocatalyst is developed to achieve intratumorally endogenous H 2 O 2 -responsive self-sufficiency of O 2 and near-infrared light controlled PDT simultaneously for overcoming hypoxia cancer. Furthermore, the sufficient O 2 plays an important role in overcoming the chemotherapeutic drug-resistant cancer caused by hypoxia, therefore inducing tumor cell apoptosis significantly., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

To explore initial Maillard reaction pathways and mechanisms for maximal formation of meaty flavors in heated cysteine-xylose-glycine systems, model reactions with synthesized initial Maillard intermediates, Gly-Amadori, TTCA (2-threityl-thiazolidine-4-carboxylic acids) and Cys-Amadori, were investigated. Relative relativities were characterized by spectrophotometrically monitoring the development of colorless degradation intermediates and browning reaction products. Aroma compounds formed were determined by solid-phase microextraction combined with GC-MS and GC-olfactometry. Gly-Amadori showed the fastest reaction followed by Cys-Amadori then TTCA. Free glycine accelerated reaction of TTCA, whereas cysteine inhibited that of Gly-Amadori due to association forming relatively stable thiazolidines. Cys-Amadori/Gly had the highest reactivity in development of both meaty flavors and brown products. TTCA/Gly favored yielding meaty flavors, whereas Gly-Amadori/Cys favored generation of brown products. Conclusively, initial formation of TTCA and pathway involving TTCA with glycine were more applicable to efficiently produce processed-meat flavorings in a cysteine-xylose-glycine system., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Neo-formed compounds (NFCs) are commonly found in all kinds of foods due to the complex reaction between components during processing. Acrylamide, benzo(a)pyrene and heterocyclic aromatic amines are the main types of NFCs in foods enriched with carbohydrate, fats and proteins, respectively. They have exhibited diverse toxicity, such as neurotoxicity, genotoxicity, potentially carcinogenic and reproductive toxicity. In recent years, various phytochemicals have been found to be effective in alleviation of their related toxicities both in vitro and in vivo. This review provides evidences on the protection roles of phytochemicals against the diverse toxicity induced by three NFCs. Moreover, the prevention mechanisms of phytochemicals are summarized. Three potential aspects involving excellent antioxidant activity, DNA protection and enzyme induction contribute to the successful protection mechanism. Meanwhile, the limitations from existing knowledge have been illustrated and the possible perspectives for the further study have also been considered. The information from this review would be useful to provide an easier and better way to improve human health when considering the possibility of using foods enriched with phytochemicals for prevention of the toxicity of exogenous pollutants., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Effective delivery of imaging agents or therapeutics to the brain has remained elusive due to the poor blood-brain barrier (BBB) permeability, resulting in the apparent risks of inefficient diagnosis and therapeutic agents for brain disease. Herein, we report on the surface roughness mediated BBB transportation for the first time. The lanthanide-based core/shell/shell structured NaYF 4 :Yb,Er@NaGdF 4 :Yb@NaNdF 4 :Yb nanoplates with controllable surface roughness and multi-model bioimaging features were synthesized and used to evaluate the surface roughness dependent BBB permeability without any surface bio-functionalization. By controlling the kinetics of the shell coating process, the hexagon-disc, multi-petals and six-petals nanoplates with different surface roughness can be obtained. Comparing with the NPs with less Ra and receptor-conjugated NPs, the obtained six-petals nanoplates with highest roughness exhibit excellent performance in BBB transportation and tumor targeting, which lay solid foundation for the diagnosis and the therapy of brain tumor., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

The meat-like reactions of l-cysteine and d-(+)-xylose with or without glycine were investigated. LC-MS was used to quantitatively determine the initial stage intermediates including 2-threityl-thiazolidine-4-carboxylic acid, Cys-Amadori, and Gly-Amadori in the reaction mixtures. The results showed that the addition of glycine was only in positive correlation with the browning feature of cyseine-xylose reaction. When excessive glycine was added, a high browning rate would be achieved, but it did not benefit the formation of meaty compounds. For a complex meat-like reaction system containing cysteine, reducing sugars and glycine, to overcome the low rate of reaction, and particularly, to minimize the inhibitive effect of cysteine in the generation of meaty flavors, selection of an appropriate ratio between cysteine and glycine is important in an effort to make amounts of the intermediates of Cys-Amadori and Gly-Amadori approximately equally consist in the reaction mixture., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

The low-efficiency cellular uptake property of current nanoparticles greatly restricts their application in the biomedical field. Herein, we demonstrate that novel virus-like mesoporous silica nanoparticles can easily be synthesized, showing greatly superior cellular uptake property. The unique virus-like mesoporous silica nanoparticles with a spiky tubular rough surface have been successfully synthesized via a novel single-micelle epitaxial growth approach in a low-concentration-surfactant oil/water biphase system. The virus-like nanoparticles' rough surface morphology results mainly from the mesoporous silica nanotubes spontaneously grown via an epitaxial growth process. The obtained nanoparticles show uniform particle size and excellent monodispersity. The structural parameters of the nanoparticles can be well tuned with controllable core diameter (∼60-160 nm), tubular length (∼6-70 nm), and outer diameter (∼6-10 nm). Thanks to the biomimetic morphology, the virus-like nanoparticles show greatly superior cellular uptake property (invading living cells in large quantities within few minutes, <5 min), unique internalization pathways, and extended blood circulation duration ( t 1/2 = 2.16 h), which is much longer than that of conventional mesoporous silica nanoparticles (0.45 h). Furthermore, our epitaxial growth strategy can be applied to fabricate various virus-like mesoporous core-shell structures, paving the way toward designed synthesis of virus-like nanocomposites for biomedicine applications.

Acrylamide (AA) is a common food contaminant formed during food heat processing that has neurotoxic effects. We hypothesize that AA induces oxidative stress in astrocytes and microglia, leading to neurotoxicity. Oxidative status, translocation of Nrf2 and NF-κB, and related down-stream targets were measured in primary astrocytes and microglia obtained from BALB/c mice. The results showed that AA increased reactive oxygen species (ROS) formation and reduced glutathione levels, causing successive events associated with oxidative stress, including 4-hydroxynonenal and 8-hydroxy-2-deoxyguanosine adduct formation, in both cell types. Both Nrf2 and NF-κB pathways were activated, but Nrf2 and its downstream antioxidative genes acted at earlier stages in both cell types before NF-κB activation. After NF-κB activation, related cytokines, including IL-6, TNF-α, G-CSF, and IL-1β, were released and cell viability decreased. Greater ROS generation, faster glutathione reduction, and increased oxidative adduct formation were observed in microglia compared with astrocytes. Moreover, Nrf2/NF-κB and its downstream genes were up-regulated much faster and to greater degrees in microglia than astrocytes. These results clarify the roles of the Nrf2 and NF-κB pathways in AA-induced neurotoxicity. These cellular responses may provide new insights for the development of adverse outcome pathway approaches for risk assessments of AA., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Pork of black-pig in China is well known for its quality and preferred by consumers. However, there is a lack of research on its flavors. By solvent assisted flavor evaporation combined with GC-MS, 104 volatile compounds in the stewed pork broth of black-pig were identified with the dominant amounts of fatty acids, alcohols, and esters. By aroma extract dilution analysis-GC-O method, 27 odor-active compounds were characterized, including 2-methyl-3-furanthiol, 3-(methylthio)propanal, 2-furfurylthiol, γ-decalactone, nonanal, (E)-2-nonenal, and (E,E)-2,4-decadienal that had high FD factors. Compared to the common white-pig, the aroma compounds in both pork broths were almost the same, but the aroma profile of potent odorants for the black-pig pork broth showed less fatty and more roasted notes, which were partially attributed to the higher monounsaturated fatty acids and lower polyunsaturated fatty acids in meat. With aid of authentic chemicals and selected reaction monitoring mode of GC-MS/MS, 19 aroma compounds were quantitated., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Anthocyanins are one of the most widespread families of natural pigments in the plant kingdom. Their health beneficial effects have been documented in many in vivo and in vitro studies. This review summarizes the most recent literature regarding the health benefits of anthocyanins and their molecular mechanisms. It appears that several signaling pathways, including mitogen-activated protein kinase, nuclear factor κB, AMP-activated protein kinase, and Wnt/β-catenin, as well as some crucial cellular processes, such as cell cycle, apoptosis, autophagy, and biochemical metabolism, are involved in these beneficial effects and may provide potential therapeutic targets and strategies for the improvement of a wide range of diseases in future. In addition, specific anthocyanin metabolites contributing to the observed in vivo biological activities, structure-activity relationships as well as additive and synergistic efficacy of anthocyanins are also discussed.

Pre-existing hypoxia in tumors can result in an inadequate oxygen supply during photodynamic therapy (PDT), which in turn hampers photodynamic efficacy. To overcome this problem, we developed an orthogonal near-infrared upconversion controlled red blood cell (RBC) microcarriers to selectively deliver O 2 in hypoxia area. Moreover, this RBC microcarriers are able to overcome a series of complex biological barriers which include transporting across the inflamed endothelium, evading mononuclear phagocyte system, reducing reticuloendothelial system uptake. Based on these abilities, RBC microcarriers have efficient tumors accumulation and are capable of delivery a large amount of O 2 for PDT under near-infrared (NIR) irradiation to realize effective solid tumor eradication., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Acrylamide (AA), is a common food contaminant generated by heat processing. Astrocytes and microglia are the two major glial cell types in the brain that play pivotal but different roles in maintaining optimal brain function. The objective of this study is to investigate the neurotoxicity of AA, using a primary astrocytes/microglia co-culture model. Co-cultural cells obtained from Balb/c mice were cultured and treated with 0-1.0mM AA for 24-96h. Cell viability, reactive oxygen species (ROS) generation, oxidative end produces formation and glutathione (GSH) levels were measured. The expression of nuclear-E2-related factor 2(Nrf2), and nuclear factor kappa-beta (NF-κB) and selected down-stream genes were measured. Results showed that AA treatment led toa dose-dependent toxicity. Oxidative stress was induced as indicated by an increase of ROS, a decrease of GSH levels, and an increase in the formation of 4-hydroxynonenal-adduct and 8-hydroxy-2-deoxyguanosine-adduct. Both Nrf2 and NF-κB pathway contributed to the initiation of oxidative stress but the timing of two factors was different. Nrf2 and its related downstream genes were activated earlier than that in NF-κB pathway. In conclusion, AA-induced neurotoxicity attribute to oxidative stress via Nrf2 and NF-κB pathway. Moreover, the co-culture cell model was proven to be a viable model to study AA neurotoxicity., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Shanxi aged vinegar is one of the most famous Chinese traditional cereal vinegars produced by spontaneous solid-state fermentation. However, the aroma composition of Shanxi aged vinegar is still ambiguous. The Shanxi vinegars before and after aging were both analyzed by solvent-assisted flavor evaporation combined with gas chromatography-mass spectrometry (GC-MS) as well as gas chromatography-olfactometry (GC-O) in aroma extract dilution analysis. A total of 87 odor-active regions were found by GC-O, and 80 odor-active compounds were identified. By GC-MS/MS, in selected reaction monitoring mode, 30 important identifications were quantitated using authentic standards. In comparison, the aroma molecules for the vinegars before and after aging were almost the same; only their levels were altered, with mostly the esters and some compounds that produce pungent smells being lost and the levels of those from the Maillard reaction, especially the pyrazines (e.g., tetramethylpyrazine), being greatly increased. As for the aged vinegar, the compounds found to have high flavor dilution factors (>128) were 3-(methylthio)propanal, vanillin, 2,3-butanedione, tetramethylpyrazine, 3-methylbutanoic acid, γ-nonalactone, guaiacol, 3-(methylthio)propyl acetate, dimethyl trisulfide, phenylacetaldehyde, 2-ethyl-6-methylpyrazine, 2-acetylpyrazine, 2,3-dimethylpyrazine, furfural, and 3-hydroxy-2-butanone. However, the aroma compounds found at high concentrations (>25 μg/L) in the aged vinegar were acetic acid, followed by 2,3-butanedione, furfural, 3-hydroxy-2-butanone, tetramethylpyrazine, furfuryl alcohol, and 3-methylbutanoic acid.

Background: The different actions of abscisic acid (ABA) in the aboveground and belowground parts of plants suggest the existence of a distinct perception mechanism between these organs. Although characterization of the soluble ABA receptors PYR1/PYL/RCAR as well as core signaling components has greatly advanced our understanding of ABA perception, signal transduction, and responses, the environment-dependent organ-specific sensitivity of plants to ABA is less well understood., Results: By performing real-time quantitative PCR assays, we comprehensively compared transcriptional differences of core ABA signaling components in response to ABA or osmotic/dehydration stress between maize (Zea mays L.) roots and leaves. Our results demonstrated up-regulation of the transcript levels of ZmPYLs homologous to dimeric-type Arabidopsis ABA receptors by ABA in maize primary roots, whereas those of ZmPYLs homologous to monomeric-type Arabidopsis ABA receptors were down-regulated. However, this trend was reversed in the leaves of plants treated with ABA via the root medium. Although the mRNA levels of ZmPYL1-3 increased significantly in roots subjected to polyethylene glycol (PEG)-induced osmotic stress, ZmPYL4-11 transcripts were either maintained at a stable level or increased only slightly. In detached leaves subjected to dehydration, the transcripts of ZmPYL1-3 together with ZmPYL5, ZmPYL6, ZmPYL10 and ZmPYL11 were decreased, whereas those of ZmPYL4, ZmPYL7 and ZmPYL8 were significantly increased. Our results also showed that all of the evaluated transcripts of PP2Cs and SnRK2 were quickly up-regulated in roots by ABA or osmotic stress; conversely they were either up-regulated or maintained at a constant level in leaves, depending on the isoforms within each family., Conclusions: There is a distinct profile of PYR/PYL/RCAR ABA receptor gene expression between maize roots and leaves, suggesting that monomeric-type ABA receptors are mainly involved in the transmission of ABA signals in roots but that dimeric-type ABA receptors primarily carry out this function in leaves. Given that ZmPYL1 and ZmPYL4 exhibit similar transcript abundance under normal conditions, our findings may represent a novel mechanism for species-specific regulation of PYR/PYL/RCAR ABA receptor gene expression. A difference in the preference for core signaling components in the presence of exogenous ABA versus stress-induced endogenous ABA was observed in both leaves and roots. It appears that core ABA signaling components perform their osmotic/dehydration stress response functions in a stress intensity-, duration-, species-, organ-, and isoform-specific manner, leading to plasticity in response to adverse conditions and, thus, acclimation to life on land. These results deepen our understanding of the diverse biological effects of ABA between plant leaves and roots in response to abiotic stress at the stimulus-perception level.

Pu-erh ripened tea is produced through a unique microbial fermentation process from the sun-dried leaves of large-leaf tea species (Camellia sinensis (Linn.) var. assamica (Masters) Kitamura) in Yunnan province of China. In this study, the changes of amino acid profiles during fermentation of Pu-erh tea were investigated, based on the improved HPLC-UV method with PITC pre-column derivatization for the simultaneous determination of twenty free amino acids. Results showed that aspartic acid, glutamic acid, arginine, alanine, theanine and tyrosine were the major amino acids in tea samples. Fermentation significantly influenced on the amino acid profiles. The total free amino acid contents significantly decreased during fermentation (p<0.05). Meanwhile, low amount of acrylamide were detected. Its concentration increased after 7-days' fermentation and then decreased gradually. The results provided the useful information for the manipulation of fermentation process according to the changes of amino acids and acrylamide contents in Pu-erh ripened tea., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Background: Acrylamide (AA) is a potential carcinogen which widely exists in heat-processed foods. The addition of glycine (Gly) has been shown to reduce the formation of AA. The objective of this work was to investigate the kinetics of the inhibition of AA by Gly in both asparagine (Asn)/glucose (Glc) and Asn/Glc/Gly potato model systems during heating at 160 °C, 180 °C, and 200 °C., Results: The simplified two consecutive first-order kinetic model fitted well to the changes of AA in both systems. No significant difference in rate constant (kF) and apparent activation energy (EaF) was observed for AA formation between the two systems (P > 0.05). Whereas EaE and only kE at 200 °C for AA elimination in the Asn/Glc/Gly system was significantly higher than Asn/Glc system (P < 0.05). The elimination reaction between Gly and AA was confirmed by the identification of their major reaction product 2-((3-amino-3-oxopropyl)amino)acetic acid in the Asn/Glc/(15)  N-Gly system., Conclusion: The reduction of AA by Gly is predominantly attributed to the elimination reaction between Gly and AA., (© 2015 Society of Chemical Industry.)

There is an increasing need to synthesize biocompatible nanofibers with excellent mechanical and electrical performance for electrochemical and biomedical applications. Here we report a facile approach to prepare electroactive and flexible 3D nanostructured biomaterials with high performance based on bacterial cellulose (BC) nanofibers. Our approach can coat BC nanofibers with poly(3,4-ethylenedioxythiophene) (PEDOT) by in situ interfacial polymerization in a controllable manner. The PEDOT coating thickness is adjustable by the monomer concentration or reaction time during polymerization, producing nanofibers with a total diameter ranging from 30 to 200 nm. This fabrication process also provides a convenient method to tune different parameters such as the average pore size and electrical conductivity on the demands of actual applications. Our experiments have demonstrated that the 3D BC/PEDOT nanofibers exhibit high specific surface area, excellent mechanical properties, electroactive stability, and low cell cytotoxicity. With electrical stimulation, calcium imaging of PC12 neural cells on BC/PEDOT nanofibers has revealed a significant increase in the percentage of cells with higher action potentials, suggesting an enhanced capacitance effect of charge injection. As an attractive solution to the challenge of designing better electrode-cell interfaces, 3D BC/PEDOT nanofibers promise many important applications such as biosensing devices, smart drug delivery systems, and implantable electrodes for tissue engineering.

Acrylamide (AA) is one of the most important contaminants occurring in heated food products. Accumulating evidence indicates that AA-induced toxicity is associated with oxidative stress and long-term exposure to AA induced mitochondria collapse and finally leads to apoptosis. Whereas anthocyanins are natural antioxidants and have a strong ability to reduce oxidative damage in vivo. This study investigates the protection of a blueberry anthocyanin extract (BAE) against AA-induced mitochondrial oxidative stress in mice models. The activities of electron transport chain complexes, oxidative status, and the structure and function of mitochondria were measured. Results showed that pretreatment with BAE markedly inhibited reactive oxygen species (ROS) formation, and prevented the successive events associated with the mitochondrial damage and dysfunction, including recovered activities of electron transport chain, ATPase and superoxide dismutase, ameliorated depolarization of mitochondrial membrane potential and membrane lipid peroxidation, reduced release of cytochrome c and protection of mitochondria against swelling. In a word, mitochondria are a key target at the organelle level for the protective effect of BAE against AA toxicity. These results will be helpful to provide new clues for a better understanding of the AA toxicity intervention mechanism and for exploring effective dietary constituents for intervention of AA toxicity.

Berries are dietary plants with high antioxidant activity. The aim of this study is to investigate the protective effect of berries (strawberry, grape, and blueberry) against the acrylamide (AA)-induced general toxicity, genotoxicity, and reproductive toxicity in mice model, respectively. Mice were treated with 50 mg/kg b.w./day AA intraperitoneal injection for 5 d after feeding control diet or diet containing freeze-dried strawberry, grape, and blueberry powder. The results showed that AA induced a significant general toxicity, genotoxicity, and reproductive toxicity in mice. Compared with the control diet, the diets containing berries could reverse the AA-induced alterations in liver antioxidant enzymes activities (P < 0.05). Moreover, the AA-induced genotoxicity could be prevented by the diet containing berries. The DNA damage in the lymphocyte and liver cells and the micronucleus formation in bone marrow cell were significantly alleviated (P < 0.05). Meanwhile, the mice fed with diets containing berries showed a recovery in the sperm count, the sperm activity rate, sperm motility parameters, and the abnormal sperm rate (P < 0.05). Berry powders have remarkable intervention against the AA-induced general toxicity, genotoxicity, reproductive toxicity. Abundant phenolics, especially anthocyanins, may contribute to the intervention., (© 2015 Institute of Food Technologists®)

Background: The Smith-Waterman algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools for next-generation sequencing data. Though various fast Smith-Waterman implementations are developed, they are either designed as monolithic protein database searching tools, which do not return detailed alignment, or are embedded into other tools. These issues make reusing these efficient Smith-Waterman implementations impractical., Results: To facilitate easy integration of the fast Single-Instruction-Multiple-Data Smith-Waterman algorithm into third-party software, we wrote a C/C++ library, which extends Farrar's Striped Smith-Waterman (SSW) to return alignment information in addition to the optimal Smith-Waterman score. In this library we developed a new method to generate the full optimal alignment results and a suboptimal score in linear space at little cost of efficiency. This improvement makes the fast Single-Instruction-Multiple-Data Smith-Waterman become really useful in genomic applications. SSW is available both as a C/C++ software library, as well as a stand-alone alignment tool at: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library., Conclusions: The SSW library has been used in the primary read mapping tool MOSAIK, the split-read mapping program SCISSORS, the MEI detector TANGRAM, and the read-overlap graph generation program RZMBLR. The speeds of the mentioned software are improved significantly by replacing their ordinary Smith-Waterman or banded Smith-Waterman module with the SSW Library.

Understanding the degradation of anthocyanins (Acys) during microwave treatment is required for the application of this novel technology to fruit and vegetable processing. The pH 3.5 buffer solutions containing 50mg/l malvidin-3-glucoside (Mv-3-glu) and malvidin-3,5-diglucoside (Mv-3,5-diglu), respectively, were treated with microwaves at 700 W. In comparison, the samples were heated at 98±2 °C in a water bath. In total, nine degradation products were detected (using LC-UV/Vis-MS/MS) for each Acys after microwave treatment. Anthocyanone A, hydroxycoumarins and dihydroxy phenylacetaldehyde were characterised as the main degradation products of both Acys under microwave conditions, which were not detected in the thermal treatment. In addition, syringic acid, 2,4,6-trihydroxybenzaldehyde, coumarin glucosides and 2,6-dimethoxyphenol were found simultaneously under the microwave and thermal treatments. During the microwave treatment, hydrogen peroxide was formed and resulted in the Baeyer-Villiger-type oxidation of the Acys, which was the main degradation pathway. At the same time, the conventional thermal degradation pathway of Acys also occurred., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Acrylamide (AA) occurs in many cooked starchy foods and has caused widespread concern as a possible carcinogen. In the present study, we investigate the intervention of AA toxicity in MDA-MB-231 cells pretreated with cyanidin-3-glucoside (Cy-3-glu). Compared to the cells treated with AA, Cy-3-glu significantly inhibited AA-induced cytotoxicity, reduced reactive oxygen species (ROS) generation, recovered glutathione (GSH) depletion and decreased the activities of glutathione peroxidase (GPx) and glutathione S-transferase (GST). Moreover, the expression of GPx1, GSTP1 and gamma-glutamyl cysteine synthase (γ-GCS) were enhanced, and cytochrome P450 2E1 (CYP2E1) expression was inhibited by the pretreatment of Cy-3-glu. Cy-3-glu presents the protective role against oxidative stress induced by AA in MDA-MB-231 cells., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

The Tibetan Antelope (TA), which has lived at high altitude for millions of years, was selected as the model species of high hypoxia-tolerant adaptation. Here we constructed two cDNA libraries from lung and cardiac muscle tissues, obtained EST sequences from the libraries, and acquired extensive expression data related energy metabolism genes. Comparative analyses of synonymous (Ks) and nonsynonymous (Ka) substitution rates of nucleus-encoded mitochondrial unigenes among different species revealed that many antelope genes have undergone rapid evolution. Surfactant-associated protein A (SP-A) and surfactant-associated protein B (SP-B) genes in the AT lineage experienced accelerated evolution compared to goat and sheep, and these two genes are highly expressed in the lung tissue. This study suggests that many specific genes of lung and cardiac muscle tissues showed unique expression profiles and may undergo fast adaptive evolution in TA. These data provide useful information for studying on molecular adaptation to high-altitude in humans as well as other mammals., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Understanding the factors that contribute to the degradation of bioactive compounds during microwave treatment is meaningful for the practical application of this novel technology. The influence of microwave power, energy density, temperature, pH value, and initial concentration of anthocyanins (Acys) on the degradation behavior of malvidin-3-glucoside (Mv-3-glu) and malvidin-3,5-diglucoside (Mv-3,5-diglu) was investigated in this study. Results showed that the degradation of both Acys was accelerated with the increase of microwave power, energy density, temperature, pH value, and initial concentration of Acys. The degradation process of both Acys followed the first-order kinetics model (R² > 0.94), whereas the relationship between Acys degradation and energy density fitted to the logistic model well (R² > 0.98). In addition, Mv-3-glu was more susceptible to the microwave treatment than Mv-3,5-diglu. Compared with heating in a 98 ± 2 °C water bath, both Acys degraded more rapidly under microwave treatment at 100 °C, indicating the occurrence of microwave effect. The results provide a guide for the scientific application of microwave treatment.

ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository--a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse--a database of gene expression profiles and other bio-measurements and the ArrayExpress Atlas--a new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions. The Repository contains data from over 6000 experiments comprising approximately 200,000 assays, and the database doubles in size every 15 months. The majority of the data are array based, but other data types are included, most recently-ultra high-throughput sequencing transcriptomics and epigenetic data. The Warehouse and Atlas allow users to query for differentially expressed genes by gene names and properties, experimental conditions and sample properties, or a combination of both. In this update, we describe the ArrayExpress developments over the last two years.

The human UGT2B17 gene varies in copy number from zero to two per individual and also differs in mean number between populations from Africa, Europe, and East Asia. We show that such a high degree of geographical variation is unusual and investigate its evolutionary history. This required first reinterpreting the reference sequence in this region of the genome, which is misassembled from the two different alleles separated by an artifactual gap. A corrected assembly identifies the polymorphism as a 117 kb deletion arising by nonallelic homologous recombination between approximately 4.9 kb segmental duplications and allows the deletion breakpoint to be identified. We resequenced approximately 12 kb of DNA spanning the breakpoint in 91 humans from three HapMap and one extended HapMap populations and one chimpanzee. Diversity was unusually high and the time to the most recent common ancestor was estimated at approximately 2.4 or approximately 3.0 million years by two different methods, with evidence of balancing selection in Europe. In contrast, diversity was low in East Asia where a single haplotype predominated, suggesting positive selection for the deletion in this part of the world.