PEG10 directly regulated by E2Fs might have a role in the development of hepatocellular carcinoma

AbstractPEG10 is an imprinted gene which is up-regulated in hepatocelluar carcinoma (HCC). However, the mechanism of PEG10 regulation remains to be elucidated. In this work the transcription factors E2F-1 and -4 were demonstrated to bind directly to the promoter of PEG10 and thereby regulate its expression. The expression profile of HCC tissues also suggested E2Fs were involved in PEG10 regulation. Further functional analysis showed that PEG10 was involved in the repression of apoptosis induced by serum deprivation and chemotherapeutic drugs. These findings link cancer genetics and epigenetics by showing that E2F acts directly upstream of an anti-apoptosis imprinted gene, PEG10

Comparison of MoS2, WS2, and Graphene Oxide for DNA Adsorption and Sensing

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Langmuir, © 2017 American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see Lu, C., Liu, Y., Ying, Y., & Liu, J. (2017). Comparison of MoS2, WS2, and Graphene Oxide for DNA Adsorption and Sensing. Langmuir, 33(2), 630–637. https://doi.org/10.1021/acs.langmuir.6b04502Interfacing DNA with two-dimensional (2D) materials has been intensely researched for various analytical and biomedical applications. Most of these studies have been performed on graphene oxide (GO) and two metal dichalcogenides, molybdenum disulfide (MoS2) and tungsten disulfide (WS2); all of them can all adsorb single-stranded DNA. However, they use different surface forces for adsorption based on their chemical structures. In this work, fluorescently labeled DNA oligonucleotides were used and their adsorption capacities and kinetics were studied as a function of ionic strength, DNA length, and sequence. Desorption of DNA from these surfaces was also measured. DNA is more easily desorbed from GO by various denaturing agents, whereas surfactants yield more desorption from MoS2 and WS2. Our results are consistent with the fact that DNA can be adsorbed by GO via pi-pi stacking and hydrogen bonding, and MoS, and WS2 mainly use van der Waals force for adsorption. Finally, fluorescent DNA probes were adsorbed by these 2D materials for detecting complementary DNA. For this assay, GO gave the highest sensitivity, whereas they all showed a similar detection limit. This study has enhanced our fundamental understanding of DNA adsorption by two important types of 2D materials and is useful for further rational optimization of their analytical and biomedical applications.Natural Sciences and Engineering Research Council of Canada (NSERC); Doctoral Fund for Priority Development Project from Ministry of Education of China [20120101130009

Covalent linking DNA to graphene oxide and its comparison with physisorbed probes for Hg2+ detection

The final publication is available at Elsevier via http://dx.doi.org/10.1016/j.bios.2015.12.043 © 2016. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Graphene oxide (GO) has attracted extensive research interest as a platform for DNA adsorption and biosensor development. While most researchers use simple physisorption of fluorescently labeled DNA, covalent sensors are less susceptible to non-specific probe displacement and minimize false positive results. In this work, three thymine-rich DNA probes of different lengths are modified on their 3'-end with an amino group for covalent conjugation to GO. They also each contain an internally labeled fluorophore so that Hg2+ binding can lead to a large distance increase between the fluorophore and the GO surface for fluorescence signaling. Hg2+-dependent fluorescence signaling from the covalent sensors are compared with that from the non-covalent sensors in terms of sensitivity, selectivity, signaling kinetics, and continuous monitoring. The covalent sensors are much more stable and resistant to nonspecific probe displacement, while still retaining high sensitivity and similar selectivity. The detection limits are 16.3 and 20.6 nM Hg2+, respectively, for the covalent and non-covalent sensors, and detection of spiked Hg2+ in Lake Ontario water is demonstrated. (C) 2015 Elsevier B.V. All rights reserved.Natural Sciences and Engineering Research Council of Canada (NSERC) [386326]; Doctoral Fund for Priority Development Project from the Ministry of Education of China [20120101130009

A RFID-Based Monitoring System for Characterization of Perching Behaviors of Individual Poultry

Perching is a natural behavior of poultry. However, it is difficult to distinguish individual birds in a large group in order to relate perching behavior to health condition or productivity. To enable such research, this study developed and validated a radio frequency identification (RFID)-based automated perching monitoring system (APMS) for characterizing individual perching behaviors of group-housed poultry. The APMS consisted of a RFID module, a load cell module, and a round wooden perch. The RFID module was comprised of a high-frequency RFID reader, three customized rectangular antennas, and multiple RFID transponders. The load cell module was comprised of a data acquisition system and two load cells supporting the two ends of the perch. Daily number of perch visits (PV) and perching duration (PD) of individual birds were used to delineate perching behavior. Three identical experimental pens, five hens per pen, were equipped with the monitoring system. Two RFID transponders were attached to each hen (one per leg) and a distinct color was marked on the bird‘s head for video or visual identification. Performance of the APMS was validated by comparing the system outputs with manual observation/labeling over an entire day. Sensitivity and specificity of the system were shown to improve from 97.77% and 99.88%, respectively, when using only the RFID module, to 99.83% and 99.93%, respectively, when incorporating weight information from the load cell module. This study revealed that the APMS has an excellent performance in measuring perching behaviors of individual birds in a group. The APMS offers great potentials for delineating differences in perching behavior among hens with different social status or health conditions in a group setting

Mobile robotics platform for strawberry temporal–spatial yield monitoring within precision indoor farming systems

Plant phenotyping and production management are emerging fields to facilitate Genetics, Environment, & Management (GEM) research and provide production guidance. Precision indoor farming systems (PIFS), vertical farms with artificial light (aka plant factories) in particular, have long been suitable production scenes due to the advantages of efficient land utilization and year-round cultivation. In this study, a mobile robotics platform (MRP) within a commercial plant factory has been developed to dynamically understand plant growth and provide data support for growth model construction and production management by periodical monitoring of individual strawberry plants and fruit. Yield monitoring, where yield = the total number of ripe strawberry fruit detected, is a critical task to provide information on plant phenotyping. The MRP consists of an autonomous mobile robot (AMR) and a multilayer perception robot (MPR), i.e., MRP = the MPR installed on top of the AMR. The AMR is capable of traveling along the aisles between plant growing rows. The MPR consists of a data acquisition module that can be raised to the height of any plant growing tier of each row by a lifting module. Adding AprilTag observations (captured by a monocular camera) into the inertial navigation system to form an ATI navigation system has enhanced the MRP navigation within the repetitive and narrow physical structure of a plant factory to capture and correlate the growth and position information of each individual strawberry plant. The MRP performed robustly at various traveling speeds with a positioning accuracy of 13.0 mm. The temporal–spatial yield monitoring within a whole plant factory can be achieved to guide farmers to harvest strawberries on schedule through the MRP’s periodical inspection. The yield monitoring performance was found to have an error rate of 6.26% when the plants were inspected at a constant MRP traveling speed of 0.2 m/s. The MRP’s functions are expected to be transferable and expandable to other crop production monitoring and cultural tasks

Comparison of Graphene Oxide and Reduced Graphene Oxide for DNA Adsorption and Sensing

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Langmuir, © 2016 American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see Lu, C., Huang, P.-J. J., Liu, B., Ying, Y., & Liu, J. (2016). Comparison of Graphene Oxide and Reduced Graphene Oxide for DNA Adsorption and Sensing. Langmuir, 32(41), 10776–10783. https://doi.org/10.1021/acs.langmuir.6b03032Fluorescently labeled DNA adsorbed on graphene oxide (GO) is a well-established sensing platform for detecting a diverse range of analytes. GO is a loosely defined material and its oxygen content may vary depending on the condition of preparation. Sometimes, a further reduction step is intentionally performed to decrease the oxygen content, and the resulting material is called reduced GO (rGO). In this study, DNA adsorption and desorption from GO and rGO is systematically compared. Under the same salt concentration, DNA adsorbs slightly faster with a 2.6-fold higher capacity on rGO. At the same time, DNA adsorbed on rGO is more resistant to desorption induced by temperature, pH, urea, and organic solvents. Various lengths and sequences of DNA probes have been tested. When its complementary DNA is added as a model target analyte, the rGO sample has a higher signal-to-background and signal-to-noise ratio, whereas the GO sample has a slightly higher absolute signal increase and faster signaling kinetics. DNAs adsorbed on GO or rGO are still susceptible to nonspecific, displacement by other DNA and proteins. Overall, although rGO adsorbs DNA more tightly, it allows efficient DNA sensing with an extremely low background fluorescence signal.Natural Sciences and Engineering Research Council of Canada (NSERC); Ministry of Education of China [20120101130009

Keto acid metabolites of branched-chain amino acids inhibit oxidative stress-induced necrosis and attenuate myocardial ischemia–reperfusion injury

Branched chain α-keto acids (BCKAs) are endogenous metabolites of branched-chain amino acids (BCAAs). BCAA and BCKA are significantly elevated in pathologically stressed heart and contribute to chronic pathological remodeling and dysfunction. However, their direct impact on acute cardiac injury is unknown. Here, we demonstrated that elevated BCKAs significantly attenuated ischemia-reperfusion (I/R) injury and preserved post I/R function in isolated mouse hearts. BCKAs protected cardiomyocytes from oxidative stress-induced cell death in vitro. Mechanistically, BCKA protected oxidative stress induced cell death by inhibiting necrosis without affecting apoptosis or autophagy. Furthermore, BCKAs, but not BCAAs, protected mitochondria and energy production from oxidative injury. Finally, administration of BCKAs during reperfusion was sufficient to significantly attenuate cardiac I/R injury. These findings uncover an unexpected role of BCAA metabolites in cardioprotection against acute ischemia/reperfusion injury, and demonstrate the potential use of BCKA treatment to preserve ischemic tissue during reperfusion

Subtractive Inhibition Assay for the Detection of E. coli O157:H7 Using Surface Plasmon Resonance

A surface plasmon resonance (SPR) immunosensor was developed for the detection of E. coli O157:H7 by means of a new subtractive inhibition assay. In the subtractive inhibition assay, E. coli O157:H7 cells and goat polyclonal antibodies for E. coli O157:H7 were incubated for a short of time, and then the E. coli O157:H7 cells which bound antibodies were removed by a stepwise centrifugation process. The remaining free unbound antibodies were detected through interaction with rabbit anti-goat IgG polyclonal antibodies immobilized on the sensor chip using a BIAcore 3000 biosensor. The results showed that the signal was inversely correlated with the concentration of E. coli O157:H7 cells in a range from 3.0 × 104 to 3.0 × 108 cfu/mL with a detection limit of 3.0 × 104 cfu/mL. Compared with direct SPR by immobilizing antibodies on the chip surface to capture the bacterial cells and ELISA for E. coli O157:H7 (detection limit: both 3.0 × 105 cfu/mL in this paper), the detection limit of subtractive inhibition assay method was reduced by one order of magnitude. The method simplifies bacterial cell detection to protein-protein interaction, which has the potential for providing a practical alternative for the monitoring of E. coli O157:H7 and other pathogens

Analysis of the effect of different withering methods on tea quality based on transcriptomics and metabolomics

Withering is very important to the quality of Wuyi rock tea. In this study, transcriptomics and metabolomics were used to analyze the effects of different withering methods on tea quality formation. The results showed that sunlight withering (SW) was most beneficial in increasing the gene expression of ubiquinone and other terpenoid-quinone biosynthesis (ko00130), pyruvate metabolism (ko00620), starch and sucrose metabolism (ko00500), and tryptophan metabolism (ko00380) pathways, and increasing the content of nucleotides and derivatives, terpenoids, organic acids and lipids, thus enhancing the mellowness, fresh and brisk taste and aroma of tea. Withering trough withering (WW) was most beneficial in increasing the gene expression of glutathione metabolism (ko00480), phenylpropanoid biosynthesis (ko00940) pathways, increasing the content of phenolic acids and flavonoids, thus enhancing tea bitterness. A comprehensive evaluation of the metabolite content and taste characteristics of tea leaves showed SW to be the best quality and charcoal fire withering (FW) to be the worst quality. This study provided an important basis for guiding the processing of Wuyi rock tea with different flavors