On some special classes of contact B0B_0-VPG graphs

A graph $G$ is a $B_0$-VPG graph if one can associate a path on a rectangular grid with each vertex such that two vertices are adjacent if and only if the corresponding paths intersect at at least one grid-point. A graph $G$ is a contact $B_0$-VPG graph if it is a $B_0$-VPG graph admitting a representation with no two paths crossing and no two paths sharing an edge of the grid. In this paper, we present a minimal forbidden induced subgraph characterisation of contact $B_0$-VPG graphs within four special graph classes: chordal graphs, tree-cographs, $P_4$-tidy graphs and $P_5$-free graphs. Moreover, we present a polynomial-time algorithm for recognising chordal contact $B_0$-VPG graphs.Comment: 34 pages, 15 figure

Purification and properties of a HeLa cell enzyme able to remove the 5'- terminal protein from poliovirus RNA

Using a rapid phenol extraction assay, an enzyme was purified from uninfected HeLa cells that can cleave the 5'-terminal protein (VPg) from poliovirus RNA. Both cytoplasmic and nuclear extracts had enzymes with similar behavior. A polypeptide of molecular weight 27,000 was the major one present in the purified preparation. Assuming that this protein is the enzyme, a very low turnover number was calculated for it. The purified enzyme would cleave the tyrosine-phosphate bond linking VPg to poliovirus RNA with minimal degradation of the RNA or of VPg. If the RNA was first treated with proteinase K to degrade VPg, leaving a small peptide on the RNA, this peptide could also be removed by the enzyme. If the RNA was degraded with T1 RNase, leaving VPg attached to a nonanucleotide, the enzyme still would cleave off VPg, although incompletely. If the RNA was degraded completely, leaving either pUp or pU attached to VPg, the enzyme would not remove the nucleotides from the protein. Thus, for the enzyme to be active requires some length of polynucleotide attached to the protein but only a short peptide need be present for the enzyme to act

VPg of murine norovirus binds translation initiation factors in infected cells

BACKGROUND: Norovirus genomic and subgenomic RNAs are covalently linked at the 5' nucleotide to a 15 kD protein called VPg. VPg of two human norovirus strains binds translation initiation factor eIF3 and other eIFs in vitro, suggesting VPg functions in initiation of protein synthesis on viral RNA. Human norovirus strains are not cultivable, and thus experimental evidence of interactions between VPg and eIFs in infected cells has been lacking. We used the cultivable murine norovirus MNV-1 as a model to study interactions between VPg and eIFs in infected cells. RESULTS: As shown previously for human norovirus VPg, MNV-1 VPg bound eIF3, eIF4GI, eIF4E, and S6 ribosomal protein in cell extracts by GST pull-down assay. Importantly, MNV-1 VPg co-precipitated eIF4GI and eIF4E from infected macrophages, providing evidence that VPg interacts with components of the translation machinery in norovirus infected cells. CONCLUSION: The interactions between MNV-1 VPg and eIFs completely mimic those reported for the human norovirus VPg, illustrating the utility of MNV-1 as a relevant molecular model to study mechanisms of human norovirus replication

Construction of a "mutagenesis cartridge" for poliovirus genome-linked viral protein: Isolation and characterization of viable and nonviable mutants

By following a strategy of genetic analysis of poliovirus, we have constructed a synthetic "mutagenesis cartridge" spanning the genome-linked viral protein coding region and flanking cleavage sites in an infectious cDNA clone of the type 1 (Mahoney) genome. The insertion of new restriction sites within the infectious clone has allowed us to replace the wild-type sequences with short complementary pairs of synthetic oligonucleotides containing various mutations. A set of mutations have been made that create methionine codons within the genome-linked viral protein region. The resulting viruses have growth characteristics similar to wild type. Experiments that led to an alteration of the tyrosine residue responsible for the linkage to RNA have resulted in nonviable virus. In one mutant, proteolytic processing assayed in vitro appeared unimpaired by the mutation. We suggest that the position of the tyrosine residue is important for genome-linked viral protein function(s)

Thermoelectric Properties of Electrostatically Tunable Antidot Lattices

We report on the fabrication and characterization of a device which allows the formation of an antidot lattice (ADL) using only electrostatic gating. The antidot potential and Fermi energy of the system can be tuned independently. Well defined commensurability features in magnetoresistance as well as magnetothermopower are obsereved. We show that the thermopower can be used to efficiently map out the potential landscape of the ADL.Comment: 4 pages, 3 figures; to appear in Appl. Phys. Let

Learning Synergies between Pushing and Grasping with Self-supervised Deep Reinforcement Learning

Skilled robotic manipulation benefits from complex synergies between non-prehensile (e.g. pushing) and prehensile (e.g. grasping) actions: pushing can help rearrange cluttered objects to make space for arms and fingers; likewise, grasping can help displace objects to make pushing movements more precise and collision-free. In this work, we demonstrate that it is possible to discover and learn these synergies from scratch through model-free deep reinforcement learning. Our method involves training two fully convolutional networks that map from visual observations to actions: one infers the utility of pushes for a dense pixel-wise sampling of end effector orientations and locations, while the other does the same for grasping. Both networks are trained jointly in a Q-learning framework and are entirely self-supervised by trial and error, where rewards are provided from successful grasps. In this way, our policy learns pushing motions that enable future grasps, while learning grasps that can leverage past pushes. During picking experiments in both simulation and real-world scenarios, we find that our system quickly learns complex behaviors amid challenging cases of clutter, and achieves better grasping success rates and picking efficiencies than baseline alternatives after only a few hours of training. We further demonstrate that our method is capable of generalizing to novel objects. Qualitative results (videos), code, pre-trained models, and simulation environments are available at http://vpg.cs.princeton.eduComment: To appear at the International Conference On Intelligent Robots and Systems (IROS) 2018. Project webpage: http://vpg.cs.princeton.edu Summary video: https://youtu.be/-OkyX7Zlhi

Transgenic resistance to PMTV and PVA provides novel insights to viral long-distance movement

The studies in this thesis describe forms of transgenic resistance to plant viruses and how they can be used for studying viral infection cycle. S. tuberosum cv. Saturna expressing the CP gene of Potato mop-top virus (PMTV) was grown in a field infested with the viruliferous vector of PMTV, S. subterranea. The incidence of PMTV-infected tubers was lower in the CP-transgenic potato than in non-transgenic potato. RNA dot-blot analysis revealed that in tubers infected with PMTV, all three RNAs were present. N. benthamiana plants expressing the CP gene of PMTV were inoculated by two different methods i) mechanical inoculation to leaves and ii) growing plants in soil infested with viruliferous S. subterranea. Results showed that the expression of the transgene-derived RNA (or CP) inhibits replication of homologous RNA 2 in transgenic N. benthamiana. Furthermore, the results showed that transgene-mediated resistance to PMTV differs in roots and leaves. Mechanical inoculation with PMTV on CP-transgenic N. benthamiana resulted in symptomless, systemic movement of RNA 1 and RNA 3, but not the CP-encoding RNA (RNA 2). These findings show that PMTV RNA 1 and RNA 3 can infect and move systemically in N. benthamiana without the CP and RNA 2. N. benthamiana transformed with the P1 and VPg cistron, respectively, of Potato virus A (PVA) displayed: i) resistance to PVA infection, ii) susceptibility, or iii) systemic infection followed by recovery from PVA infection of new leaves. Long-distance transport of PVA from lower, infected parts of recovered plants was compromised in the recovered tissue. This result suggests that PVA is moving as ribonucleoprotein complex other than virus particles. N. benthamiana transformed with a polycistronic transgene encoding the CI-NIa-CP cistrons of PVA was susceptible to PVA infection. VPg (the N-proximal part of NIa) is a well-known virulence factor of potyviruses and its possible role in suppression of RNA silencing was studied. PVA VPg was found to increase the severity of disease symptoms when expressed from a Potato virus X vector in N. benthamiana. However, PVA VPg did not show apparent RNA silencing suppression activity. The reason why the polycistronic transgene did not provide resistance could not be resolved

Transport Through an Electrostatically Defined Quantum Dot Lattice in a Two-Dimensional Electron Gas

Quantum dot lattices (QDLs) have the potential to allow for the tailoring of optical, magnetic and electronic properties of a user-defined artificial solid. We use a dual gated device structure to controllably tune the potential landscape in a GaAs/AlGaAs two-dimensional electron gas, thereby enabling the formation of a periodic QDL. The current-voltage characteristics, I(V), follow a power law, as expected for a QDL. In addition, a systematic study of the scaling behavior of I(V) allows us to probe the effects of background disorder on transport through the QDL. Our results are particularly important for semiconductor-based QDL architectures which aim to probe collective phenomena.Comment: 6 pages, 4 figure