Defective Particles Research Articles

Nanocasting synthesis of mesoporous CeO2 particle abrasives from mesoporous SiO2 hard templates for enhanced chemical mechanical polishing performance

Mesoporous abrasive particles exhibit superior chemical mechanical polishing/planarization (CMP) performance, as compared with the corresponding bulk materials. Nevertheless, the lack of control over the shape and particle size or distribution extremely restricts the development of mesoporous abrasives and their potential applications. To overwhelm these drawbacks, pure and ytterbium-doped mesoporous ceria (mCeO2 and mCeYbO2) spheres with well-defined morphology and good uniformity were synthesized via a straightforward nanocasting strategy using high-quality mesoporous silica spheres as hard templates and metal nitrates as precursors. The resulting samples were characterized by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, selected area electron diffraction, X-ray photoelectron spectroscopy, Raman spectroscopy, UV–vis diffuse reflectance spectroscopy, photoluminescence spectroscopy, Zeta potential, and N2 adsorption-desorption measurements. The as-prepared mCeO2 and mCeYbO2 products exhibited enriched surface defects (trivalent Ce, vacancy oxygen, hydroxyls) and polycrystalline porous frameworks with a surface area of up to 160 m2/g and pore size of 4–7 nm. Benefiting from these synergistic attributes, the flexible and defective particle abrasives enabled significant improvements in both surface quality and removal efficiency during oxide-CMP, as compared to commercial CeO2. A possible CMP mechanism was proposed on the basis of the physical contact state, adsorption and adhesion behavior, as well as tribochemical interaction occurred at CeO2–SiO2 interfaces. This work demonstrates highly promising abrasive materials advancement combining architecture and defect engineering towards high-performance oxide-CMP.

Surface and Grain Boundary Coating for Stabilizing LiNi0.8Mn0.1Co0.1O2 Based Electrodes.

The widespread use of high-capacity Ni-rich layered oxides such as LiNi0.8Mn0.1Co0.1O2 (NMC811), in lithium-ion batteries is hindered due to practical capacity loss and reduced working voltage during operation. Aging leads to defective NMC811 particles, affecting electrochemical performance. Surface modification offers a promising approach to improve cycle life. Here, we introduce an amorphous lithium titanate (LTO) coating via atomic layer deposition (ALD), not only covering NMC811 surfaces but also penetrating cavities and grain boundaries. As NMC811 electrodes suffer from low structural stability during charge and discharge, We combined electrochemistry, operando X-ray diffraction (XRD), and dilatometry to understand structural changes and the coating protective effects. XRD reveals significant structural evolution during delithiation for uncoated NMC811. The highly reversible phase change in coated NMC811 highlights enhanced bulk structure stability. The LTO coating retards NMC811 degradation, boosting capacity retention from 86 % to 93 % after 140 cycles. This study underscores the importance of grain boundary engineering for Ni-rich layered oxide electrode stability and the interplay of chemical and mechanical factors in battery aging.

Influenza A defective viral genomes and non-infectious particles are increased by host PI3K inhibition via anti-cancer drug alpelisib.

RNA viruses produce abundant defective viral genomes during replication, setting the stage for interactions between viral genomes that alter the course of pathogenesis. Harnessing these interactions to develop antivirals has become a recent goal of intense research focus. Despite decades of research, the mechanisms that regulate the production and interactions of Influenza A defective viral genomes are still unclear. The role of the host is essentially unexplored; specifically, it remains unknown whether host metabolism can influence the formation of defective viral genomes and the particles that house them. To address this question, we manipulated host cell anabolic signaling activity and monitored the production of defective viral genomes and particles by A/H1N1 and A/H3N2 strains, using a combination of single-cell immunofluorescence quantification, third-generation long-read sequencing, and the cluster-forming assay, a method we developed to titer defective and fully-infectious particles simultaneously. Here we show that alpelisib (Piqray), a highly selective inhibitor of mammalian Class 1a phosphoinositide-3 kinase (PI3K) receptors, significantly changed the proportion of defective particles and viral genomes (specifically deletion-containing viral genomes) in a strain-specific manner, under conditions that minimize multiple cycles of replication. Alpelisib pre-treatment of cells led to an increase in defective particles in the A/H3N2 strain, while the A/H1N1 strain showed a decrease in total viral particles. In the same infections, we found that defective viral genomes of polymerase and antigenic segments increased in the A/H1N1 strain, while the total particles decreased suggesting defective interference. We also found that the average deletion size in polymerase complex viral genomes increased in both the A/H3N2 and A/H1N1 strains. The A/H1N1 strain, additionally showed a dose-dependent increase in total number of defective viral genomes. In sum, we provide evidence that host cell metabolism can increase the production of defective viral genomes and particles at an early stage of infection, shifting the makeup of the infection and potential interactions among virions. Given that Influenza A defective viral genomes can inhibit pathogenesis, our study presents a new line of investigation into metabolic states associated with less severe flu infection and the potential induction of these states with metabolic drugs.

BmHSP19.9 targeting P6.9 and VLF-1 to mediate the formation of defective progeny viruses in the silkworm antiviral variety 871C

The 871C silkworm strain exhibits a high level of resistance to Bombyx mori nucleopolyhedrovirus (BmNPV), making it a valuable variety for the sericulture industry. Understanding the underlying mechanism of its resistance holds great biological significance and economic value in addressing viral disease risks in sericulture. Initially, we infected the resistant strain 871C and its control strain 871 with BmNPV and conducted secondary infection experiments using the progeny occlusion bodies (OBs). As a result, a significant decrease in pathogenicity was observed. Electron microscopy analysis revealed that 871C produces progeny virions with defective DNA packaging, reducing virulence following BmNPV infection. Blood proteomic identification of the silkworm variety 871C and control 871 after BmNPV infection demonstrated the crucial role of the viral proteins P6.9 and VLF-1 in the production of defective viruses by impeding the proper encapsulation of viral DNA. Additionally, we discovered that BmHSP19.9 interacts with P6.9 and VLF-1 and that its expression is significantly upregulated after BmNPV infection. BmHSP19.9 exhibits strong antiviral activity, in part by preventing the entry of the proteins P6.9 and VLF-1 into the nucleus, thereby hindering viral nucleocapsid and viral DNA assembly. Our findings indicate that the antiviral silkworm strain 871C inhibits BmNPV proliferation by upregulating Bmhsp19.9 and impeding the nuclear localization of the viral proteins P6.9 and VLF-1, leading to the production of defective viral particles. This study offers a comprehensive analysis of the antiviral mechanism in silkworms from a viral perspective, providing a crucial theoretical foundation for future antiviral research and the breeding of resistant silkworm strains.

Defective HDL particles functionality in patients with ST-segment elevation acute myocardial infarction

Defective HDL particles functionality in patients with ST-segment elevation acute myocardial infarction

Advancing room temperature NO2 gas sensing performance through high-energy mechanical milling of Tin-dichalcogenides

Eco-friendly gas sensing devices with simple architecture, reduced cost, and high performance at room temperature are being sought to replace the traditional metallic oxide materials, aiming to address environmental concerns. Lamellae semiconducting materials have shown promising detection properties for this purpose. Here, we investigated the sensing response of SnS2, Sn(S0.5Se0.5)2, and SnSe2 tin-dichalcogenides prepared by high-energy mechanical milling. High RNO2/Rair response signals, from 102 to 106, for 2–100 ppm of NO2 were observed for temperatures between 30 °C and 300 °C. The materials were not sensitive to CO, while H2 detection could only be observed above 200 °C, implying high NO2 selectivity. Additionally, we investigated the influence of samples suspension in water and isopropanol on grain size and morphology. We found that isopropanol crystallizes amorphous selenium phase dispersed in the Sn-Se system and increase the agglomeration in the Sn(S0.5Se0.5)2 system. Deformed and defective particles were observed regardless the preparation methodology. This unique defect-rich morphology might increase surface reactivity for selective NO2 detection by physisorption, owing a high adsorption/desorption rate at room temperature.

Bipartite viral RNA genome heterodimerization influences genome packaging and virion thermostability.

Multi-segmented viruses often multimerize their genomic segments to ensure efficient and stoichiometric packaging of the correct genetic cargo. In the bipartite Nodaviridae family, genome heterodimerization is also observed and conserved among different species. However, the nucleotide composition and biological function for this heterodimer remain unclear. Using Flock House virus as a model system, we developed a next-generation sequencing approach ("XL-ClickSeq") to probe heterodimer site sequences. We identified an intermolecular base-pairing site which contributed to heterodimerization in both wild-type and defective virus particles. Mutagenic disruption of this heterodimer site exhibited significant deficiencies in genome packaging and encapsidation specificity to viral genomic RNAs. Furthermore, the disruption of this intermolecular interaction directly impacts the thermostability of the mature virions. These results demonstrate that the intermolecular RNA-RNA interactions within the encapsidated genome of an RNA virus have an important role on virus particle integrity and thus may impact its transmission to a new host.IMPORTANCEFlock House virus is a member of Nodaviridae family of viruses, which provides a well-studied model virus for non-enveloped RNA virus assembly, cell entry, and replication. The Flock House virus genome consists of two separate RNA molecules, which can form a heterodimer upon heating of virus particles. Although similar RNA dimerization is utilized by other viruses (such as retroviruses) as a packaging mechanism and is conserved among Nodaviruses, the role of heterodimerization in the Nodavirus replication cycle is unclear. In this research, we identified the RNA sequences contributing to Flock House virus genome heterodimerization and discovered that such RNA-RNA interaction plays an essential role in virus packaging efficiency and particle integrity. This provides significant insight into how the interaction of packaged viral RNA may have a broader impact on the structural and functional properties of virus particles.

In-Situ Derived Defective Ru Particles Anchored on Ru-Ni Layered Double Hydroxides for Enhanced Alkaline Hydrogen Evolution.

Developing active, stable, and cost-efficient electrocatalysts to replace platinum for the alkaline hydrogen evolution reaction (HER) is highly desirable yet represents a great challenge. Here, it is reported on a facile one-pot synthesis of RuxNi layered double hydroxides (RuxNi-LDHs) that exhibit remarkable HER activity and stability after an in-situ activation treatment, surpassing most state-of-the-art Ru-based catalysts as well as commercial Ru/C and Pt/C catalysts. The structural and chemical changes triggered by in-situ activation are systematically investigated, and the results clearly show that the pristine, less-active RuxNi-LDHs are transformed into a highly active catalyst characterized by raft-like, defect-rich Ru° particles decorated on the surface of RuxNi-LDHs. Density functional theory (DFT) calculations reveal that the defective Ru sites can effectively optimize the reaction pathway and lower the free energies of the elemental steps involved, leading to enhanced intrinsic activity. This work highlights the importance of the currently understudied strategy of defect engineering in boosting the HER activity of Ru-based catalysts and offers an effective approach involving in-situ electrochemical activation for the development of high-performance alkaline HER catalysts.

Vaccinia Virus Defective Particles Lacking the F17 Protein Do Not Inhibit Protein Synthesis: F17, a Double-Edged Sword for Protein Synthesis?

Vaccinia virus (Orthopoxvirus) F17 protein is a major virion structural phosphoprotein having a molecular weight of 11 kDa. Recently, it was shown that F17 synthesised in infected cells interacts with mTOR subunits to evade cell immunity and stimulate late viral protein synthesis. Several years back, we purified an 11 kDa protein that inhibited protein synthesis in reticulocyte lysate from virions, and that possesses all physico-chemical properties of F17 protein. To investigate this discrepancy, we used defective vaccinia virus particles devoid of the F17 protein (designated iF17- particles) to assess their ability to inhibit protein synthesis. To this aim, we purified iF17- particles from cells infected with a vaccinia virus mutant which expresses F17 only in the presence of IPTG. The SDS-PAGE protein profiles of iF17- particles or derived particles, obtained by solubilisation of the viral membrane, were similar to that of infectious iF17 particles. As expected, the profiles of full iF17- particles and those lacking the viral membrane were missing the 11 kDa F17 band. The iF17- particles did attach to cells and injected their viral DNA into the cytoplasm. Co-infection of the non-permissive BSC40 cells with a modified vaccinia Ankara (MVA) virus, expressing an mCherry protein, and iF17- particles, induced a strong mCherry fluorescence. Altogether, these experiments confirmed that the iF17- particles can inject their content into cells. We measured the rate of protein synthesis as a function of the multiplicity of infection (MOI), in the presence of puromycin as a label. We showed that iF17- particles did not inhibit protein synthesis at high MOI, by contrast to the infectious iF17 mutant. Furthermore, the measured efficiency to inhibit protein synthesis by the iF17 mutant virus generated in the presence of IPTG, was threefold to eightfold lower than that of the wild-type WR virus. The iF17 mutant contained about threefold less F17 protein than wild-type WR. Altogether these results strongly suggest that virion-associated F17 protein is essential to mediate a stoichiometric inhibition of protein synthesis, in contrast to the late synthesised F17. It is possible that this discrepancy is due to different phosphorylation states of the free and virion-associated F17 protein.

ANGPTL3 deficiency impairs lipoprotein production and produces adaptive changes in hepatic lipid metabolism

Angiopoietin-like protein 3 (ANGPTL3) is a hepatically secreted protein and therapeutic target for reducing plasma triglyceride-rich lipoproteins and low-density lipoprotein (LDL) cholesterol. Although ANGPTL3 modulates the metabolism of circulating lipoproteins, its role in triglyceride-rich lipoprotein assembly and secretion remains unknown. CRISPR-associated protein 9 (CRISPR/Cas9) was used to target ANGPTL3 in HepG2 cells (ANGPTL3−/−) whereupon we observed ∼50% reduction of apolipoprotein B100 (ApoB100) secretion, accompanied by an increase in ApoB100 early presecretory degradation via a predominantly lysosomal mechanism. Despite defective particle secretion in ANGPTL3−/− cells, targeted lipidomic analysis did not reveal neutral lipid accumulation in ANGPTL3−/− cells; rather ANGPTL3−/− cells demonstrated decreased secretion of newly synthesized triglycerides and increased fatty acid oxidation. Furthermore, RNA sequencing demonstrated significantly altered expression of key lipid metabolism genes, including targets of peroxisome proliferator-activated receptor α, consistent with decreased lipid anabolism and increased lipid catabolism. In contrast, CRISPR/Cas9 LDL receptor (LDLR) deletion in ANGPTL3−/− cells did not result in a secretion defect at baseline, but proteasomal inhibition strongly induced compensatory late presecretory degradation of ApoB100 and impaired its secretion. Additionally, these ANGPTL3−/−;LDLR−/− cells rescued the deficient LDL clearance of LDLR−/− cells. In summary, ANGPTL3 deficiency in the presence of functional LDLR leads to the production of fewer lipoprotein particles due to early presecretory defects in particle assembly that are associated with adaptive changes in intrahepatic lipid metabolism. In contrast, when LDLR is absent, ANGPTL3 deficiency is associated with late presecretory regulation of ApoB100 degradation without impaired secretion. Our findings therefore suggest an unanticipated intrahepatic role for ANGPTL3, whose function varies with LDLR status.

Marinomonas mediterranea synthesizes an R-type bacteriocin.

Prophages integrated into bacterial genomes can become cryptic or defective prophages, which may evolve to provide various traits to bacterial cells. Previous research on Marinomonas mediterranea MMB-1 demonstrated the production of defective particles. In this study, an analysis of the genomes of three different strains (MMB-1, MMB-2, and MMB-3) revealed the presence of a region named MEDPRO1, spanning approximately 52 kb, coding for a defective prophage in strains MMB-1 and MMB-2. This prophage seems to have been lost in strain MMB-3, possibly due to the presence of spacers recognizing this region in an I-F CRISPR array in this strain. However, all three strains produce remarkably similar defective particles. Using strain MMB-1 as a model, mass spectrometry analyses indicated that the structural proteins of the defective particles are encoded by a second defective prophage situated within the MEDPRO2 region, spanning approximately 13 kb. This finding was further validated through the deletion of this second defective prophage. Genomic region analyses and the detection of antimicrobial activity of the defective prophage against other Marinomonas species suggest that it is an R-type bacteriocin. Marinomonas mediterranea synthesizes antimicrobial proteins with lysine oxidase activity, and the synthesis of an R-type bacteriocin constitutes an additional mechanism in microbial competition for the colonization of habitats such as the surface of marine plants.IMPORTANCEThe interactions between bacterial strains inhabiting the same environment determine the final composition of the microbiome. In this study, it is shown that some extracellular defective phage particles previously observed in Marinomonas mediterranea are in fact R-type bacteriocins showing antimicrobial activity against other Marinomonas strains. The operon coding for the R-type bacteriocin has been identified.

Hyperbolic regularization-PointNet++: Automated three-dimensional soil particle roundness classification

Particle roundness significantly affects the macro-mechanics of granular soils. Nevertheless, current three-dimensional(3D) computational geometry (CG) -based methods for soil particle roundness classification exhibit inefficiency and struggle with defective particles. To overcome these limitations, this paper proposed a deep learning-based approach for intelligent soil particle classification to automatically assess roundness. We labeled 2400 soil particle point clouds into six classes: well rounded, rounded, subrounded, subangular, angular, and very angular. Using the labeled dataset, we trained the PointNet++ model with a novel hyperbolic regularizer, extracted hierarchical roundness features, and built a roundness classifier. The achieved automatic classification accuracy is 92.19%. Moreover, the classification results are similar to the 3D CG-Manual Charting method in terms of quantity, volume, surface area, and convex hull volume. Notably, our method overcomes the limitation of 3D CG's inability to classify soil particles with void defects. Moreover, it shows a classification speed of approximately 77 times faster than 3D CG.

Antagonism between viral infection and innate immunity at the single-cell level.

When infected with a virus, cells may secrete interferons (IFNs) that prompt nearby cells to prepare for upcoming infection. Reciprocally, viral proteins often interfere with IFN synthesis and IFN-induced signaling. We modeled the crosstalk between the propagating virus and the innate immune response using an agent-based stochastic approach. By analyzing immunofluorescence microscopy images we observed that the mutual antagonism between the respiratory syncytial virus (RSV) and infected A549 cells leads to dichotomous responses at the single-cell level and complex spatial patterns of cell signaling states. Our analysis indicates that RSV blocks innate responses at three levels: by inhibition of IRF3 activation, inhibition of IFN synthesis, and inhibition of STAT1/2 activation. In turn, proteins coded by IFN-stimulated (STAT1/2-activated) genes inhibit the synthesis of viral RNA and viral proteins. The striking consequence of these inhibitions is a lack of coincidence of viral proteins and IFN expression within single cells. The model enables investigation of the impact of immunostimulatory defective viral particles and signaling network perturbations that could potentially facilitate containment or clearance of the viral infection.

Investigation on close-coupled gas atomization for Fe-based amorphous powder production via simulation and industrial trials: Part II. Particle flight and cooling during secondary atomization

A two-way coupling Discrete Phase Model (DPM) is applied to calculate the secondary atomization process. The particle flight and cooling processes are studied under different process parameters. The results show that the average particle size (d50) depends on the gas-liquid interaction and decreases with increasing gas-to-melt ratio (GMR). The standard deviation of the particle size (d84/d50) increases as the melt mass flow rate increases, and both high and low atomization pressures result in a high d84/d50. The average cooling rate of particles can be improved by reducing the melt mass flow rate and increasing the atomization pressure. By increasing the gas temperature to 400 K, the d50 can be significantly reduced and the average cooling rate can be approximately increased two times, indicating that the hot gas atomization technique can effectively improve the yield of fine amorphous powders. However, excessive gas temperature not only has a limited effect on improving the cooling rate, but also significantly increases the d84/d50 and defective particles, suggesting that the gas temperature must be matched to the atomization process to achieve ideal effects. The powders produced at 2.0 MPa and 0.075 kg·s−1 exhibit good circularity with a d50 of 58.9 μm, which is in good agreement with the simulation analysis. Moreover, the powders with sizes less than 50 μm exhibit high amorphous fraction (96.6%) and outstanding soft magnetic properties. In this work, a flow-heat transfer-DPM coupling model is established to provide theoretical guidance for the production of high-performance Fe-based amorphous powders.

Enhanced nitrogen doping of fresh starch-derived carbon with regulation of cobalt to fabricate efficient bifunctional catalyst for rechargeable Zn-air batteries

Developing bifunctional catalysts to oxygen reduction (ORR) and oxygen evolution reactions (OER) is of vital to the practical application of rechargeable Zn-air batteries. Herein, an N-doped carbon-based catalyst (FeCo-NC-St) was prepared by using starch as a basic material which was transferred to defective carbon particles. The fresh starch-derived carbon is favor of the doping of nitrogen atoms to form more N-related ORR active sites. The existence of cobalt further positively regulates the OER activity of FeCo-NC-St. Resultantly, FeCo-NC-St shows 0.837 V of ORR E1/2 and 1.611 V of OER E10 which is slightly lower than the 0.850 V of ORR E1/2 for Pt/C but far better than the 1.723 V of OER E10 for the benchmark RuO2, revealing the superior bifunctional activities of FeCo-NC-St. Practically, the Zn-air battery with FeCo-NC-St outputs 1.505 V of open circuit voltage, 1.15–1.25 V of working voltage and 937.51 mW h g−1Zn of specific energy density at 10 mA cm−2. The Zn-air battery also exhibits remarkable rechargeability and long-term durability, demonstrating the promising potential to substitute the precious Pt/Ru-based catalysts in the practical applications.

Favipiravir Suppresses Zika Virus (ZIKV) through Activity as a Mutagen.

In a companion paper, we demonstrated that the nucleoside analogue favipiravir (FAV) suppressed Zika virus (ZIKV) replication in three human-derived cell lines-HeLa, SK-N-MC, and HUH-7. Our results revealed that FAV's effect was most pronounced in HeLa cells. In this work, we aimed to explain variation in FAV activity, investigating its mechanism of action and characterizing host cell factors relevant to tissue-specific differences in drug effect. Using viral genome sequencing, we show that FAV therapy was associated with an increase in the number of mutations and promoted the production of defective viral particles in all three cell lines. Our findings demonstrate that defective viral particles made up a larger portion of the viral population released from HeLa cells both at increasing FAV concentrations and at increasing exposure times. Taken together, our companion papers show that FAV acts via lethal mutagenesis against ZIKV and highlight the host cell's influence on the activation and antiviral activity of nucleoside analogues. Furthermore, the information gleaned from these companion papers can be applied to gain a more comprehensive understanding of the activity of nucleoside analogues and the impact of host cell factors against other viral infections for which we currently have no approved antiviral therapies.

Microstructural evolutions and mechanical characteristics of roll-bonding Mg/Al clad plate regulated by cold spraying micron particle interlayer

A new process of “cold spraying interlayer + roll-bonding” (CSIR) was put forward for the preparation of Mg/Al clad plates. First, the micron Ni and Al powders (including some Zn particles) were cold sprayed to form an ultrathin coating on Al or Mg substrate slabs. Then roll-bonding was performed at 400 °C. The influence of cold sprayed coating on slab surfaces, interfacial microstructures, texture evolutions, mechanical properties and the related mechanism were systematically investigated. The results show that the average shear strength of the as-rolled Mg/Al clad plate assisted by cold spraying Al and Ni micron powders interlayer on the substrate slabs was nearly twice (35.58 MPa) than that of conventional rolling under the same conditions (single pass, reduction ratio was 35%). For as-rolled Mg/Al clad plates, almost no reaction diffusion layers are generated, and the mechanical interlocking between cold sprayed coatings and substrate slabs is the main mechanism for improving the shear strength. The interface between the Al coating and the Ni coating is weakest of the as-rolled Mg/Al clad plates. As the reduction rate increases from 27.5% to 47.5%, the function of the mechanical interlocking of cold sprayed coatings will first increase and then weaken. After annealing at 400 °C for 1 h, the interface between the Al coating and the Mg substrate slab will form thick mixed brittle intermetallic compounds, including Al3Mg2, Mg17Al12, MgZn2 and AlMg4Zn11, and cause local gaps, holes, and cracks around the Zn-rich Ni coating. The fracture path after annealing starts from the vicinity of the defective Ni particles, and eventually enlarges along the mixed intermetallic compounds layer between the Al coating and the Mg substrate slab. The research indicates that the CSIR process has great potential in cooperating the metallurgical bonding with the mechanical interlocking of clad plates.

Assembly chaperone Nas6 selectively destabilizes 26S proteasomes with defective regulatory particle-core particle interfaces

The 26S proteasome is a 66-subunit-chambered protease present in all eukaryotes that maintains organismal health by degrading unneeded or defective proteins. Defects in proteasome function or assembly are known to contribute to the development of various cancers, neurodegeneration, and diabetes. During proteasome biogenesis, a family of evolutionarily conserved chaperones assembles a hexameric ring of AAA+ family ATPase subunits contained within the proteasomal regulatory particle (RP) and guide their docking onto the surface of the proteolytic core particle (CP). This RP-CP interaction couples the substrate capture and unfolding process to proteolysis. We previously reported a mutation in the proteasome that promoted dissociation of the RP and CP by one of these chaperones, Nas6. However, the nature of the signal for Nas6-dependent proteasome disassembly and the generality of this postassembly proteasome quality control function for Nas6 remain unknown. Here, we use structure-guided mutagenesis and invitro proteasome disassembly assays to demonstrate that Nas6 more broadly destabilizes 26S proteasomes with a defective RP-CP interface. We show that Nas6 can promote dissociation of mature proteasomes into RP and CP in cells harboring defects on either side of the RP-CP interface. This function is unique to Nas6 and independent from other known RP assembly chaperones. Further biochemical experiments suggest that Nas6 may exploit a weakened RP-CP interface to dissociate the RP from the CP. We propose that this postassembly role of Nas6 may fulfill a quality control function in cells by promoting the recycling of functional subcomplexes contained within defective proteasomes.

Computational Modeling of IN-CTD/TAR Complex to Elucidate Additional Strategies to Inhibit HIV-1 Replication.

HIV-1 integrase (IN) is a key enzyme that is essential for mediating the insertion of retroviral DNA into the host chromosome. IN also exhibits additional functions which are not fully elucidated, including its ability to bind to viral genomic RNA. Lack of binding of IN to RNA within the virions has been shown to be associated with production of morphologically defective virus particles. However, the exact structure of HIV-1 IN bound to RNA is not known. Based on the studies that C-terminal domain (CTD) of IN binds to TAR RNA region and based on the observation that TAR and the host factor INI1 binding to IN-CTD are identical, we computationally modelled the IN-CTD/TAR complex structure. Computational modeling of nucleic acid binding to proteins is a valuable method to understand the macromolecular interaction when experimental methods of solving the complex structures are not feasible. The current model of the IN-CTD/TAR complex may facilitate further understanding of this interaction and may lead to therapeutic targeting of IN-CTD/RNA interactions to inhibit HIV-1 replication.

Defective RNA Particles of Plant Viruses-Origin, Structure and Role in Pathogenesis.

The genomes of RNA viruses may be monopartite or multipartite, and sub-genomic particles such as defective RNAs (D RNAs) or satellite RNAs (satRNAs) can be associated with some of them. D RNAs are small, deletion mutants of a virus that have lost essential functions for independent replication, encapsidation and/or movement. D RNAs are common elements associated with human and animal viruses, and they have been described for numerous plant viruses so far. Over 30 years of studies on D RNAs allow for some general conclusions to be drawn. First, the essential condition for D RNA formation is prolonged passaging of the virus at a high cellular multiplicity of infection (MOI) in one host. Second, recombination plays crucial roles in D RNA formation. Moreover, during virus propagation, D RNAs evolve, and the composition of the particle depends on, e.g., host plant, virus isolate or number of passages. Defective RNAs are often engaged in transient interactions with full-length viruses-they can modulate accumulation, infection dynamics and virulence, and are widely used, i.e., as a tool for research on cis-acting elements crucial for viral replication. Nevertheless, many questions regarding the generation and role of D RNAs in pathogenesis remain open. In this review, we summarise the knowledge about D RNAs of plant viruses obtained so far.