Poly Depletion Research Articles

Translational arrest and mRNA decay are independent activities of alphaherpesvirus virion host shutoff proteins.

The herpes simplex virus 1 (HSV1) virion host shutoff (vhs) protein is an endoribonuclease that regulates the translational environment of the infected cell, by inducing the degradation of host mRNA via cellular exonuclease activity. To further understand the relationship between translational shutoff and mRNA decay, we have used ectopic expression to compare HSV1 vhs (vhsH) to its homologues from four other alphaherpesviruses - varicella zoster virus (vhsV), bovine herpesvirus 1 (vhsB), equine herpesvirus 1 (vhsE) and Marek's disease virus (vhsM). Only vhsH, vhsB and vhsE induced degradation of a reporter luciferase mRNA, with poly(A)+ in situ hybridization indicating a global depletion of cytoplasmic poly(A)+ RNA and a concomitant increase in nuclear poly(A)+ RNA and the polyA tail binding protein PABPC1 in cells expressing these variants. By contrast, vhsV and vhsM failed to induce reporter mRNA decay and poly(A)+ depletion, but rather, induced cytoplasmic G3BP1 and poly(A)+ mRNA- containing granules and phosphorylation of the stress response proteins eIF2α and protein kinase R. Intriguingly, regardless of their apparent endoribonuclease activity, all vhs homologues induced an equivalent general blockade to translation as measured by single-cell puromycin incorporation. Taken together, these data suggest that the activities of translational arrest and mRNA decay induced by vhs are separable and we propose that they represent sequential steps of the vhs host interaction pathway.

Targeting OGG1 and PARG radiosensitises head and neck cancer cells to high-LET protons through complex DNA damage persistence

Complex DNA damage (CDD), containing two or more DNA lesions within one or two DNA helical turns, is a signature of ionising radiation (IR) and contributes significantly to the therapeutic effect through cell killing. The levels and complexity of CDD increases with linear energy transfer (LET), however, the specific cellular response to this type of DNA damage and the critical proteins essential for repair of CDD is currently unclear. We performed an siRNA screen of ~240 DNA damage response proteins to identify those specifically involved in controlling cell survival in response to high-LET protons at the Bragg peak, compared to low-LET entrance dose protons which differ in the amount of CDD produced. From this, we subsequently validated that depletion of 8-oxoguanine DNA glycosylase (OGG1) and poly(ADP-ribose) glycohydrolase (PARG) in HeLa and head and neck cancer cells leads to significantly increased cellular radiosensitivity specifically following high-LET protons, whilst no effect was observed after low-LET protons and X-rays. We subsequently confirmed that OGG1 and PARG are both required for efficient CDD repair post-irradiation with high-LET protons. Importantly, these results were also recapitulated using specific inhibitors for OGG1 (TH5487) and PARG (PDD00017273). Our results suggest OGG1 and PARG play a fundamental role in the cellular response to CDD and indicate that targeting these enzymes could represent a promising therapeutic strategy for the treatment of head and neck cancers following high-LET radiation.

Epigallocatechin-3-gallate Induced HepG2 Cells Apoptosis through ROSmediated AKT /JNK and p53 Signaling Pathway.

Hepatocarcinoma is the third leading cause of cancer-related deaths around the world. Recently, some studies have reported that Epigallocatechin-3-gallate (EGCG) may have the anti-cancer potential. However, the affection and putative mechanisms of cytotoxicity induced by EGCG in HepG2 cells remain unknown. Based on the above, the present study evaluated the effect of EGCG on the cytotoxic and anti-cancer mechanisms of HepG2 cells. The effect of EGCG on the apoptosis of Hep-G2 cells and its mechanism were studied by cell counting kit-8, mitochondrial membrane potential assay with JC-1, Annexin V-FITC apoptosis detection, cell cycle, and apoptosis analysis, one step TUNEL apoptosis assay, caspase 3 activity assay, caspase 9 activity Assay, Reactive Oxygen Species assay, and Western blot. EGCG-induced HepG2 cell apoptosis was confirmed by accumulation of the sub-G1 cells population, translocation of phosphatidylserine, depletion of mitochondrial membrane potential, DNA fragmentation, caspase-3 activation, caspase-9 activation, and poly (ADP-ribose) polymerase cleavage. Furthermore, EGCG enhanced cytotoxic effects on HepG2 cells and triggered intracellular reactive oxygen species; the signaling pathways of AKT, JNK, and p53 were activated to advance cell apoptosis. The results reveal that EGCG may provide useful information on EGCG-induced HepG2 cell apoptosis and be an appropriate candidate for cancer chemotherapy.

The effect of gate geometric effect and polysilicon doping on the performance of scaled NMOS

Insufficiently high doping in polysilicon gates of metal oxide semiconductor field effect transistor (MOSFET) becomes unavoidable due to the demands for low-energy ion implantation and limited annealing conditions to achieve ultra-shallow source and drain junctions. This results in the poly-depletion effect for ultra-thin MOSFET, loss of current drive and shift in the threshold voltage. This problem gets intense when the device is further scaled down for the gate length and thickness of gate oxide. Hence, our current work focuses on the effect of gate geometrical effect and polysilicon gate doping on scaled n-channel MOSFET(NMOS) performance. The NMOS device was constructed using TCAD ATLAS tools from SILVACO software. Six different gate lengths of 0.6 μm, 0.4 μm, 0.2 μm, 60 nm, 40 nm and 20 nm were set, and the n-type doping concentration in the polysilicon gate was varied to 1× 1018, 1× 1020 and 1 × 1021 cm-3 respectively to see their effect on the NMOS I-V and C-V performances. The findings showed that as the gate length is scaled down, the drain current increases, and as the concentration of the polysilicon doping increases, the value of the threshold voltage, VTH decreases. Based on the simulation and data collected, it can be concluded that the optimum concentration of polysilicon doping that can reduce the poly-depletion effect is 1 × 1021 cm-3, and the optimum gate length that can be used to overcome the problem is 20 nm.

(Invited) Influence of Post Deposition Annealing on the Electrical Properties of Pt-Ti/HfO2/TiN/Sion/n-Si Capacitor for Flash Memory Applications

To address the cell-to-cell interference in conventional floating gate (FG) flash memory, a fully planar structure demands continuous scaling of poly silicon floating gate thickness. But the reduced FG thickness causes reliability issues due to ballistic current through inter-poly dielectric (IPD) and also decreases the gate coupling ratio (GCR). The introduction of metal FG in flash memory eliminates the problem of poly depletion and ballistic transport even with ultrathin floating gate (<10 nm) and excellent memory performance with 16 V P/E window for 1 nm metal floating gate. Numerous studies on flash memory devices reported that a hybrid FG, transition metal dichalcogenides and multilayer graphene as FG results in improved memory performance such as fast program speed, excellent data retention and endurance characteristics. According to ITRS scaling projections for FG NAND flash, GCR of 0.6-0.7 would be desirable for satisfactory operation. However, in order to obtain adequate GCR, high-k based IPD and/or tunnel barrier has been proposed as mandatory alternatives. The improvement in GCR owed to greater coupling between the control and floating gates as a result of increased dielectric constant. The incorporation of nitrogen into tunnel oxide of NVM through nitridation can enhance the reliability performance of tunnel oxide of charge storage NVM. In this paper, we report the fabrication of Pt-Ti/HfO2/TiN/SiON/n-Si capacitor for flash memory applications with gate coupling ratio (GCR) of 0.68 and 0.71 for as-deposited and annealed SiON respectively. The XRD, AFM, FTIR, FESEM and XPS characterizations have been performed for structural and morphological studies. Program/erase and retention characteristics reveal the largest memory window of approx. 11.2 V after post deposition annealing and excellent data retention at room temperature under ±10 V. The enhanced program/erase speed was due to the fact that annealed SiON tunnelling oxide provides stronger interface against Si dangling bond generation and the decrease in barrier height of both electrons and holes. These results indicate that the SiON tunnelling oxide can be engineered by post deposition annealing for the improvement of metal floating gate memory performance.

Improvement of cell reliability by floating gate implantation on 1Xnm NAND flash memory

Continuous scaling down NAND flash memory toward below 1Xnm node generation will result in serious floating gate (FG) poly depletion and significantly impact the cell reliability performance. In this study, the FG implantation before inter-poly-dielectric deposition was proposed. We have successfully explored the methods to minimize the FG implanted damage issue and hence the void-free control gate (CG) can be achieved after the CG poly-Si fill-in. After optimizing the FG implanted processes, the cell reliabilities on 1Xnm NAND flash device were verified. The FG poly depletion can be effectively reduced by the additional FG dopant, which results in the significant improvement on the natural threshold-voltage (Vt) distribution width, the program noise, and the program/erase Vt degradation. Moreover, there is no degradation on non-cycle data retention when adding the FG implantation, which suggests no extra FG dopant penetrated into tunnel oxide as the trap sites to enhance the trap-assisted tunneling leakage under high temperature baking.

Liesegang Mechanism with a Gradual Phase Transition.

We report a novel and generalized chemical model for the Liesegang mechanism that involves gradual phase transitions of macromolecules, unlike previous models that involved definite and discontinuous phase transitions. As a model system, an agarose gel medium doped with an initiator was contacted with a solution containing monomer 2-methoxyethyl acrylate (MEA), in which monomers diffused into the gel medium and initiated a polymerization reaction. As there is a monomer concentration gradient along the diffusion direction, the degree of polymerization and the corresponding degree of insolubility showed a similar spatial gradient in the reaction medium because molecular solubility gradually changes from soluble to insoluble with an increase in the degree of polymerization. Under this condition with such a spatial gradient in the degree of polymerization, multiple bands satisfying the spacing law were formed by repetitive precipitation and depletion of insoluble poly(2-methoxyethyl acrylate) (PMEA). In contrast to the Liesegang mechanism for salt formation reactions with definite transition points, such as the solubility product and nucleation threshold, our model involves a gradual transition with a nonzero transition width. The width of the transition point would be the governing parameter for the appearance and characteristics of periodic pattern formation. This model with a nonzero transition width is largely generalized and applicable to various processes involving any solubility transition and thus can be used as a generalized Liesegang model that can be applied to any system with both definite and gradual transitions.

Polyethylenimine-functionalized silver nanoparticle-based co-delivery of paclitaxel to induce HepG2 cell apoptosis.

Hepatocarcinoma is the third leading cause of cancer-related deaths around the world. Recently, a novel emerging nanosystem as anticancer therapeutic agents with intrinsic therapeutic properties has been widely used in various medical applications. In this study, surface decoration of functionalized silver nanoparticles (AgNPs) by polyethylenimine (PEI) and paclitaxel (PTX) was synthesized. The purpose of this study was to evaluate the effect of Ag@ PEI@PTX on cytotoxic and anticancer mechanism on HepG2 cells. The transmission electron microscope image and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay showed that Ag@PEI@PTX had satisfactory size distribution and high stability and selectivity between cancer and normal cells. Ag@PEI@PTX-induced HepG2 cell apoptosis was confirmed by accumulation of the sub-G1 cells population, translocation of phosphatidylserine, depletion of mitochondrial membrane potential, DNA fragmentation, caspase-3 activation, and poly(ADP-ribose) polymerase cleavage. Furthermore, Ag@PEI@PTX enhanced cytotoxic effects on HepG2 cells and triggered intracellular reactive oxygen species; the signaling pathways of AKT, p53, and MAPK were activated to advance cell apoptosis. In conclusion, the results reveal that Ag@ PEI@PTX may provide useful information on Ag@PEI@PTX-induced HepG2 cell apoptosis and as appropriate candidate for chemotherapy of cancer.

Depletion effect of polycrystalline-silicon gate electrode by phosphorus deactivation

A study of the polycrystalline silicon depletion effect generated from the subsequent thermal process is undertaken. Although phosphorus out-diffusion, which causes the polycrystalline silicon depletion effect, is increased with an increase in the thermal process temperature, the polysilicon depletion effect is stronger when inducing rapid thermal annealing in lower temperatures of 600–800°C than in 900°C. This indicates that the major reason for the polysilicon depletion effect is not the out-diffusion of phosphorus but the electrical deactivation of phosphorus, which is segregated at the grain boundary. Therefore, by increasing the size of polycrystalline silicon grain, we can efficiently reduce the polysilicon depletion effect and enhance the tolerance to deactivation.

The antimitotic potential of PARP inhibitors, an unexplored therapeutic alternative.

ADP-ribosylation or PARsylation is one of the most abundant modifications of proteins and DNA. Although the usual context for PARsylation involves the detection and repair of DNA damage in the cell, poly(ADP-ribose) polymerases are known to regulate a number of biological processes besides maintaining genome integrity. One of these processes is the assembly and maintenance of the mitotic spindle where the presence of PARP-1 and tankyrase 1 (TNKS1), two of the best-characterized members of the PARP superfamily, is of critical importance. Here, we recapitulate the biological implications of the absence of poly(ADP-ribose) polymerases and depletion of PARsylation occurrence in mitosis in order to better understand the antimitotic effects of PARP inhibitors. In this regard, we also present an overview of the existing and more relevant molecules, with a special attention to the historical development of their pharmacological properties and structures, as well as a brief summary of clinical trials involving PARP inhibitors.

Depletion of poly(A)-specific ribonuclease (PARN) inhibits proliferation of human gastric cancer cells by blocking cell cycle progression

Regulation of mRNA decay plays a crucial role in the post-transcriptional control of cell growth, survival, differentiation, death and senescence. Deadenylation is a rate-limiting step in the silence and degradation of the bulk of highly regulated mRNAs. However, the physiological functions of various deadenylases have not been fully deciphered. In this research, we found that poly(A)-specific ribonuclease (PARN) was upregulated in gastric tumor tissues and gastric cancer cell lines MKN28 and AGS. The cellular function of PARN was investigated by stably knocking down the endogenous PARN in the MKN28 and AGS cells. Our results showed that PARN-depletion significantly inhibited the proliferation of the two types of gastric cancer cells and promoted cell death, but did not significantly affect cell motility and invasion. The depletion of PARN arrested the gastric cancer cells at the G0/G1 phase by upregulating the expression levels of p53 and p21 but not p27. The mRNA stability of p53 was unaffected by PARN-knockdown in both types of cells. A significant stabilizing effect of PARN-depletion on p21 mRNA was observed in the AGS cells but not in the MKN28 cells. We further showed that the p21 3′-UTR triggered the action of PARN in the AGS cells. The dissimilar observations between the MKN28 and AGS cells as well as various stress conditions suggested that the action of PARN strongly relied on protein expression profiles of the cells, which led to heterogeneity in the stability of PARN-targeted mRNAs.

Influenza a virus host shutoff disables antiviral stress-induced translation arrest.

Influenza A virus (IAV) polymerase complexes function in the nucleus of infected cells, generating mRNAs that bear 5′ caps and poly(A) tails, and which are exported to the cytoplasm and translated by host machinery. Host antiviral defences include mechanisms that detect the stress of virus infection and arrest cap-dependent mRNA translation, which normally results in the formation of cytoplasmic aggregates of translationally stalled mRNA-protein complexes known as stress granules (SGs). It remains unclear how IAV ensures preferential translation of viral gene products while evading stress-induced translation arrest. Here, we demonstrate that at early stages of infection both viral and host mRNAs are sensitive to drug-induced translation arrest and SG formation. By contrast, at later stages of infection, IAV becomes partially resistant to stress-induced translation arrest, thereby maintaining ongoing translation of viral gene products. To this end, the virus deploys multiple proteins that block stress-induced SG formation: 1) non-structural protein 1 (NS1) inactivates the antiviral double-stranded RNA (dsRNA)-activated kinase PKR, thereby preventing eIF2α phosphorylation and SG formation; 2) nucleoprotein (NP) inhibits SG formation without affecting eIF2α phosphorylation; 3) host-shutoff protein polymerase-acidic protein-X (PA-X) strongly inhibits SG formation concomitant with dramatic depletion of cytoplasmic poly(A) RNA and nuclear accumulation of poly(A)-binding protein. Recombinant viruses with disrupted PA-X host shutoff function fail to effectively inhibit stress-induced SG formation. The existence of three distinct mechanisms of IAV-mediated SG blockade reveals the magnitude of the threat of stress-induced translation arrest during viral replication.

Temperature dependent model for threshold voltage and subthreshold slope of strained-Si channel MOSFETs with a polysilicon gate

We present a temperature dependent model for the threshold voltage Vt and subthreshold slope S of strained-Si channel MOSFETs and validate it with reported experimental data for a wide range of temperature, channel doping concentration, oxide thickness and strain value. Such model includes the effect of lattice strain on material, temperature dependent effective mass of carriers, interface-trapped charge density and bandgap narrowing due to heavy channel doping. Also considered are polydepletion effects, carrier localization effect in the ultra-thin channel and quantum-mechanical effects. Our investigation reveals that the threshold voltage reduces linearly with increasing temperature whereas the subthreshold slope increases. In addition Vt is found to be sensitive to strain while S is weakly dependent on strain. Moreover, the channel doping concentration influences both Vt and S, and also the rate of change of Vt with temperature. Furthermore, S decreases for a lightly doped channel particularly at lower temperatures.

BSIM6: Analog and RF Compact Model for Bulk MOSFET

BSIM6 is the latest industry-standard bulk MOSFET model from the BSIM group developed specially for accurate analog and RF circuit designs. The popular real-device effects have been brought from BSIM4. The model shows excellent source-drain symmetry during both dc and small signal analysis, thus giving excellent results during analog and RF circuit simulations, e.g., harmonic balance simulation. The model is fully scalable with geometry, biases, and temperature. The model has a physical charge-based capacitance model including polydepletion and quantum-mechanical effect thereby giving accurate results in small signal and transient simulations. The BSIM6 model has been extensively validated with industry data from 40-nm technology node.

Depletion of Nuclear Poly(A) Binding Protein PABPN1 Produces a Compensatory Response by Cytoplasmic PABP4 and PABP5 in Cultured Human Cells

BackgroundIn vertebrates, poly(A) binding protein (PABP) is known to exist in five different isoforms. PABPs are primarily cytosolic with the exception of the nuclear PABP (PABPN1), which is located in the nucleus. Within the nucleus, PABPN1 is believed to bind to the poly(A) tail of nascent mRNA and along with cleavage and polyadenylation specificity factor (CPSF) define the length of the newly synthesized poly(A) tail.Methodology/Principal FindingsThe cellular role of PABP1 has been extensively studied over the years; however, the function of other PABPs remains poorly defined. In order to understand the role of PABPN1 in cellular mRNA metabolism and it’s interrelation with other PABPs, we depleted PABPN1 using RNAi in HeLa and HEK293 cells. Our results show that PABPN1 depletion did not have any effect on the poly(A) tail length, nuclear export of mRNA, mRNA translation, and transcription. Rather, PABPN1 depletion resulted in a compensatory response as observed by increased level of PABP5 and nuclear accumulation of PABP4. In addition, PABP4 was associated with the poly(A) tract of pre-mRNA and CPSF in PABPN1 depleted cells. Nevertheless, PABPN1 depletion significantly affected cell survival as evidenced by an increase in apoptosis markers: phosphorylated p53 and PUMA and as judged by the expression of ER stress marker GRP78.ConclusionOur results suggest that although function of PABPN1 may be compensated by nuclear translocation of PABP4 and perhaps by increase in the cytoplasmic abundance of PABP5, these were not sufficient to prevent apoptosis of cells. Thus PABPN1 may have a novel anti apoptotic role in mammalian cells.

Natural Inhibitors of Poly(ADP-ribose) Polymerase-1

Poly(ADP-ribose) polymerases (PARPs) are enzymes that catalyze the transfer of ADP-ribose units from β-nicotinamide adenine dinucleotide (NAD(+)) to acceptor proteins. PARP-1 is responsible for more than 90 % of protein poly-ADP-ribosylation in the brain and may play a role as a molecular switch for cell survival and death. The functional roles of PARP-1 are largely mediated by its activation after binding to damaged DNA. Upon binding, PARP-1 activity increases rapidly and cleaves NAD(+) into ADP-ribose and nicotinamide. Increased activity of PARP-1 can promote DNA repair and its interaction with several transcription factors, whereas hyperactivation of PARP-1 can result in poly(ADP-ribose) accumulation and depletion of NAD(+) and ATP which may lead to caspase independent apoptotic or necrotic cell death, respectively. Excessive PARP-1 activity has been implicated in the pathogenesis of numerous clinical conditions such as stroke, myocardial infarction, inflammation, diabetes, and neurodegenerative disorders. Therefore, it is not surprising that the search for PARP-1 inhibitors with specific therapeutic uses (e.g., brain ischemia, cancer) has been an active area of research. Beyond medicinal uses, naturally occurring PARP-1 inhibitors may also offer a unique preventative means at attenuating chronic inflammatory diseases through dietary supplementation. This possibility has prompted research for specific, naturally occurring inhibitors of PARP-1. Though fewer investigations focus on identifying endogenous inhibitors/modulators of PARP-1 activity in vivo, these activities are very important for better understanding the complex regulation of this enzyme and the potential long-term benefits of supplementation with PARP-1 inhibitors. With this in mind, the focus of this article will be on providing a state-of-the-science review on endogenous and naturally occurring compounds that inhibit PARP-1.

Impact of Gate Poly Depletion on Evaluation of Channel Temperature in Silicon-on-Insulator Metal–Oxide–Semiconductor Field-Effect Transistors with Four-Point Gate Resistance Measurement Method

Self-heating effects (SHEs) in silicon-on-insulator (SOI) metal–oxide–semiconductor field-effect transistors (MOSFETs) is evaluated and an accurate measurement method for device temperature is developed using the four-point gate resistance measurement method. Although the method of using a polysilicon gate as a temperature sensor was proposed more than 20 years ago, the accuracy of the technique has not been checked. In this work, it is demonstrated that the channel temperature estimated by the conventional method is not accurate under some special conditions. The measurements of gate resistance under various biases revealed that the depletion of the polysilicon gate had a significant impact on gate resistance. We propose a method of accurately evaluating channel temperature, where the effect of poly depletion is successfully subtracted. At an input power of 5 mW the increase in channel temperature is approximately 30 K, corresponding to a thermal resistance of 6.0 K W-1 m-1.

Impact of Gate Poly Depletion on Evaluation of Channel Temperature in Silicon-on-Insulator Metal–Oxide–Semiconductor Field-Effect Transistors with Four-Point Gate Resistance Measurement Method

Impact of Gate Poly Depletion on Evaluation of Channel Temperature in Silicon-on-Insulator Metal–Oxide–Semiconductor Field-Effect Transistors with Four-Point Gate Resistance Measurement Method

Study of gate depletion effect in strained Si NMOSFET with polycrystalline silicon germanium gate

Based on the analysis of Poly-Si1-xGex gate work function and by solving Poisson equation, the models of vertical electric field and potential distribution in strained Si NMOSFET with Poly-Si1-xGex gate are obtained; threshold voltage model and the gate depletion thickness and it's normalization model are established in strained Si NMOSFET based on the above results, with the gate depletion effect of Poly-Si1-xGex taken into account. Then the influences of device geometrical and physical parameters of device especially the Ge fraction on Poly-Si1-xGex gate depletion thickness are investigated. Furthermore, the effect of gate depletion thickness on threshold voltage is analyzed. It shows that the poly depletion thickness decreases with the increases of Ge fraction and gate doping concentration, while it increases with the increase of substrate doping concentration. Furthermore, the threshold voltage increases with the increase of gate depletion thickness. The results can provide theoretical references to the design of strained Si devices.

Depletion of cellular poly (A) binding protein prevents protein synthesis and leads to apoptosis in HeLa cells

The cytoplasmic poly (A) binding protein (PABP) is important in mRNA translation and stability. In yeast, depletion of PABP leads to translation arrest. Similarly, the PABP gene in Drosophila is important for proper development. It is however uncertain, whether mammalian PABP is essential for mRNA translation. Here we showed the effect of PABP depletion on mRNA metabolism in HeLa cells by using a small interfering RNA. Our results suggest that depletion of PABP prevents protein synthesis and consequently leads to cell death through apoptosis. Interestingly, no detectable effect of PABP depletion on transcription, transport and stability of mRNA was observed.