Rounds Of Propagation Research Articles

Species dynamics in natural bacterial communities over multiple rounds of propagation.

Our experimental work illustrates how microbial ecosystems can be shaped by selective pressures over long-term ecological time scales. Natural microbial ecosystems generally consist of various co-existing species, where community composition describes the frequency at which species or types are present. Overall functionality of the system is achieved by interacting species. Upon short-term selection, for instance by transfer to a novel environment, community composition and functionality may change in a process referred to as species sorting. Various factors, such as initial community composition and selective pressures from the environment, may influence this change. Mabisi is a traditional fermented food from Zambia that naturally contains a bacterial community of around twenty unique bacterial types. We used six comparable but different natural bacterial Mabisi communities, each split into five identical replicates, for 16 propagation cycles in a novel, common laboratory environment. Composition of the bacterial communities changed upon propagation. The influence of four main factors on community composition, i.e. initial composition (history), impact of the environment (adaptation), changes due to interaction between species and random processes (chance) in species dynamics, was tested using maximum likelihood ratios. Initial community composition seemed to determine the change in community composition, followed by random processes. Interestingly, we observed convergence at the level of ecosystem functionality, which was measured as profiles of metabolic output. This suggests different combinations of species or types can achieve similar eco-system functionality.

Abstract 1053: Highly characterized patient-derived PDX breast cancer collection for preclinical efficacy studies

Abstract We have acquired a world-class collection of highly characterized patient-derived breast cancer models (PDX) from Washington University, St. Louis, MO (1). We have established growth curves for 17 of these lines, 6 ER+, 2 HER2+ and 4 triple-negative (TNBC) models beyond what was originally published. Continued characterization of these models is ongoing in our lab to ensure the integrity of the models is being maintained over multiple rounds of propagation. Short tandem repeat (STR) analysis, sequencing, quantitative RTPCR and Western blots were run to confirm genotypic and phenotypic fidelity of many of these model. To further characterize these models, RNA samples have been run using NanoString PanCancer gene expression analysis with 770 genes from 13 cancer-associated pathways including: MAPK, STAT, PI3K, RAS, Cell Cycle, Apoptosis, Hedgehog, Wnt, DNA Damage Control, transcription regulation, chromatin modification and TGF-β. Results: These data sets show that we have maintained the integrity of the WHIM PDX models over several passages in mice and provided confidence in the use of these models for preclinical efficacy studies. Reference: 1. Li et al., Cell Reports 2013;4:1116-30. Citation Format: Michele Melton. Highly characterized patient-derived PDX breast cancer collection for preclinical efficacy studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1053.

Maximizing the Influence in Social Networks via Holistic Probability Maximization

Social media has become very popular nowadays by spreading plentiful human-centric data to a large number of audience. A rich body of literature has studied the influence maximization problem in social networks under certain propagation models. However, existing models suffer from the assumption of unlimited propagation time and some of them are nondeterministic. Influence maximization algorithms within those frameworks are often trading off between performance guarantee and computational cost. In this paper, we try to formulate the influence maximization problem in another way, where we limit the propagation time to a predefined propagation round and in each round maintain the probability to make the propagation process more tractable. We introduce a new diffusion model called a probability propagation model and formulate this optimization problem as a holistic probability maximization problem. We show that information diffusion estimation in the proposed framework is not NP-hard. Hence, any algorithm within it will be more efficient. However, the maximization problem is still NP-hard. After proving the submodularity in the proposed framework, we design a partial-updating greedy algorithm and its heuristic extension to solve the maximization problem. Extensive experiments on four synthetic data sets and four real-world data sets from Facebook, Wikipedia, arXiv, and Epinions demonstrate the effectiveness of the proposed algorithm.

Belated Analyses of Three Credit-Based Adaptive Polling Algorithms

We study the problem of credit-based adaptive polling in undirected arbitrary point-to-point asynchronous networks. Polling consists of two rounds, namely propagation (broadcast) and feedback (confirmation, response) rounds. By adaptive polling, a spanning tree of unknown topology is built dynamically during the propagation round, and feedback messages are free to choose their paths back to the initiator — a specific node who initiates the polling algorithm. The freedom in the feedback round relies on the use of credits in the propagation round. We re-visit three existing algorithms and analyse their average case communication bit complexities incurred by the credits in the propagation round, and these analyses match with the numerical results. We also give an optimal lower bound on the worst case bit message complexity for the case when the number of nodes in the network is unknown.

Calculating Floquet states of large quantum systems: A parallelization strategy and its cluster implementation

We present a numerical approach to calculate non-equilibrium eigenstates of a periodically time-modulated quantum system. The approach is based on the use of a chain of single-step propagating operators. Each operator is time-specific and constructed by combining the Magnus expansion of the time-dependent system Hamiltonian with the Chebyshev expansion of an operator exponent. The construction of the unitary Floquet operator, which evolves a system state over the full modulation period, is performed by propagating the identity matrix over the period. The independence of the evolution of basis vectors makes the propagation stage suitable for realization on a parallel cluster. Once the propagation stage is completed, a routine diagonalization of the Floquet matrix is performed. Finally, an additional propagation round, now involving the eigenvectors as the initial states, allows to resolve the time-dependence of the Floquet states and calculate their characteristics. We demonstrate the accuracy and scalability of the algorithm by applying it to calculate the Floquet states of two quantum models, namely (i) a synthesized random-matrix Hamiltonian and (ii) a many-body Bose–Hubbard dimer, both of the size up to 104 states.

Rice Dwarf Viruses with Dysfunctional Genomes Generated in Plants Are Filtered Out in Vector Insects: Implications for the Origin of the Virus

Rice dwarf virus (RDV), with 12 double-stranded RNA (dsRNA) genome segments (S1 to S12), replicates in and is transmitted by vector insects. The RDV-plant host-vector insect system allows us to examine the evolution, adaptation, and population genetics of a plant virus. We compared the effects of long-term maintenance of RDV on population structures in its two hosts. The maintenance of RDV in rice plants for several years resulted in gradual accumulation of nonsense mutations in S2 and S10, absence of expression of the encoded proteins, and complete loss of transmissibility. RDV maintained in cultured insect cells for 6 years retained an intact protein-encoding genome. Thus, the structural P2 protein encoded by S2 and the nonstructural Pns10 protein encoded by S10 of RDV are subject to different selective pressures in the two hosts, and mutations accumulating in the host plant are detrimental in vector insects. However, one round of propagation in insect cells or individuals purged the populations of RDV that had accumulated deleterious mutations in host plants, with exclusive survival of fully competent RDV. Our results suggest that during the course of evolution, an ancestral form of RDV, of insect virus origin, might have acquired the ability to replicate in a host plant, given its reproducible mutations in the host plant that abolish vector transmissibility and viability in nature.

Conservation of important plants from the Ionian Islands at the Balkan Botanic Garden of Kroussia, N Greece: using GIS to link the in situ collection data with plant propagation and ex situ cultivation

The Balkan Botanic Garden of Kroussia (BBGK) is dedicated to the ex situ conservation of native plants of Greece and the Balkans. The BBGK has formulated a conservation strategy for the collection of wild plant material for propagation, prioritizing mainly the endemic, rare, endangered, threatened and vulnerable plants of Europe found in different regions of Greece. Its aim is to contribute to the implementation of Target 8 of the Global and European Strategies for Plant Conservation at local, regional and international scales. In order to (i) define the ecological profile of the in situ requirements preferred and/or tolerated by each selected species, (ii) develop rapid and effective species-specific propagation protocols, and (iii) improve the cultivation of species of conservation concern in BBGK’s nurseries and ex situ conservation sections, geographical coordinates and in situ collection data obtained for each taxon were imported into a Geographic Information System environment (GIS). This information was then linked with several digital GIS thematic layers, including topographic, geological, edaphic, climatic, precipitation and temperature data derived from digital databases. Based on this approach, sexual and asexual propagation of plants from the Ionian Islands were conducted and rapid and effective baseline protocols were developed for 29 taxa (species and subspecies); four are presented here in detail and species-specific ex situ propagation and cultivation guidelines are given. Most of the taxa originating from the Ionian Islands were propagated by cuttings (55.2%) or seeds (34.5%), while the rest were propagated by root division at a rate from 1.7 to 2. The first round of propagation achieved a success rate ranging from 15 to 50% for 3 taxa, from 60 to 80% for 8 taxa and from more than 80 to 100% for 16 taxa, while the ex situ cultivation of the wild and propagated plant material has, so far, been successful. The application of GIS exemplified here presents a sensible and invaluable tool with a broad-scale potential in enhancing the prospects of the ex situ conservation of priority species collected from diverse environmental conditions in man-made habitats such as botanic gardens.

FAULT‐TOLERANT MULTI‐AGENT EXACT BELIEF PROPAGATION

Multiply sectioned Bayesian networks (MSBNs) support multi‐agent probabilistic inference in distributed large problem domains, where agents (subdomains) are organized by a tree structure (called hypertree). In earlier work, all belief updating methods on a hypertree are made of two rounds of propagation, each of which is implemented as a recursive process. Both processes need to be started from the same designated (root) hypernode. Agents perform local belief updating at most in a partial parallel manner. Such methods may not be suitable for practical multi‐agent environments because they are easy to crush for the problems happened in communication or local belief updating. In this paper, we present a fault‐tolerant belief updating method for multi‐agent probabilistic inference. In this method, multiple agents concurrently perform exact belief updating in a complete parallel. Temporary problems happened from time to time at some agents or some communication channels would not prevent agents from eventually converging to the correct beliefs. Permanently disconnected communication channels would not keep the properly connected portions of the system from appropriately finishing their belief updating within portions. Compared to the previous traversal‐based belief updating, the proposed approach is not only fault‐tolerant but also robust and scalable.

Selective Incorporation of Polyanionic Molecules into Hamster Prions

The central pathogenic event of prion disease is the conformational conversion of a host protein, PrPC, into a pathogenic isoform, PrPSc. We previously showed that the protein misfolding cyclic amplification (PMCA) technique can be used to form infectious prion molecules de novo from purified native PrPC molecules in an autocatalytic process requiring accessory polyanions (Deleault, N. R., Harris, B. T., Rees, J. R., and Supattapone, S. (2007) Proc. Natl. Acad. Sci. U. S. A. 104, 9741-9746). Here we investigated the molecular mechanism by which polyanionic molecules facilitate infectious prion formation in vitro. Ina PMCA reaction lacking PrPSc template seed, synthetic polyA RNA molecules induce hamster HaPrPC to adopt a protease-sensitive, detergent-insoluble conformation reactive against antibodies specific for PrPSc. During PMCA, labeled nucleic acids form nuclease-resistant complexes with HaPrP molecules. Strikingly, purified HaPrPC molecules subjected to PMCA selectively incorporate an approximately 1-2.5-kb subset of [32P]polyA RNA molecules from a heterogeneous mixture ranging in size from approximately 0.1 to >6 kb. Neuropathological analysis of scrapie-infected hamsters using the fluorescent dye acridine orange revealed that RNA molecules co-localize with large extracellular HaPrP aggregates. These findings suggest that polyanionic molecules such as RNA may become selectively incorporated into stable complexes with PrP molecules during the formation of native hamster prions.

Effect of DNA copy number on genetic stability of phage-displayed peptides.

A small model peptide, the FLAG epitope, was cloned into two filamentous phage display vectors, f88-4 and fd88-4, creating phages f88-FLAG and fd88-FLAG, respectively. Both vectors have a gene VIII display cassette (in addition to their normal phage gene VIII) and display the cloned peptide on a few percent of the virion's 3000-4000 pVIII (major coat protein) subunits. Vector f88-4 has a replication defect and attains low DNA copy number in infected cells, while vector fd88-4 has no replication defect and attains the normal, high DNA copy number characteristic of wild-type filamentous phage. Almost no loss of displayed peptide was observed during six rounds of propagation of low copy number f88-FLAG phage. In contrast, when high copy number fd88-FLAG phage was similarly propagated, variant clones that did not display the FLAG epitope accumulated gradually. The loss of displayed peptide from the high copy number vector is undoubtedly slow enough to be overcome by even weak affinity selection, and high copy number vectors have important advantages that make their use worth considering, at least when the displayed peptides are small.

Efficient generation and amplification of high-capacity adeno-associated virus/adenovirus hybrid vectors.

Effective gene therapy is dependent on safe gene delivery vehicles that can achieve efficient transduction and sustained transgene expression. We are developing a hybrid viral vector system that combines in a single particle the large cloning capacity and efficient cell cycle-independent nuclear gene delivery of adenovirus (Ad) vectors with the long-term transgene expression and lack of viral genes of adeno-associated virus (AAV) vectors. The strategy being pursued relies on coupling the AAV DNA replication mechanism to the Ad encapsidation process through packaging of AAV-dependent replicative intermediates provided with Ad packaging elements into Ad capsids. The generation of these high-capacity AAV/Ad hybrid vectors takes place in Ad early region 1 (E1)-expressing cells and requires an Ad vector with E1 deleted to complement in trans both AAV helper functions and Ad structural proteins. The dependence on a replicating helper Ad vector leads to the contamination of AAV/Ad hybrid vector preparations with a large excess of helper Ad particles. This renders the further propagation and ultimate use of these gene delivery vehicles very difficult. Here, we show that Cre/loxP-mediated genetic selection against the packaging of helper Ad DNA can reduce helper Ad vector contamination by 99.98% without compromising hybrid vector rescue. This allowed amplification of high-capacity AAV/Ad hybrid vectors to high titers in a single round of propagation.

ON THE COMPLEXITY OF SOME ADAPTIVE POLLING ALGORITHMS IN GENERAL NETWORKS

We study the problem of adaptive polling in undirected general networks. Polling, also known as broadcast-confirm, consists a propagation round and a feedback round. In adaptive polling, a spanning tree of unknown topology is built dynamically during the propagation round, and feedback messages are free to choose their paths in order to adapt to traffic and fault situations. We study three adaptive polling algorithms and analyze their worst-case communication bit complexities in the propagation round. Then, we prove a lower bound on the worst-case communication bit complexity of Ω(e+n log n) in the propagation round for all algorithms of the same kind as the three algorithms we study, where n is the number of nodes, and e the number of edges. We conclude that the cost introduced into the network due to the running of an adaptive polling algorithm is mild.

Phosphorylation at conserved carboxyl-terminal hydrophobic motif regulates the catalytic and regulatory domains of protein kinase C.

Mature protein kinase C is phosphorylated at a conserved carboxyl-terminal motif that contains a Ser (or Thr) bracketed by two hydrophobic residues; in protein kinase C betaII, this residue is Ser-660 (Keranen, L. M., Dutil, E. M., and Newton, A. C. (1995) Curr. Biol. 5, 1394-1403). This contribution examines how negative charge at this position regulates the function of protein kinase C. Specifically, Ser-660 in protein kinase C betaII was mutated to Ala or Glu and the enzyme's stability, membrane interaction, Ca2+ regulation, and kinetic parameters were compared with those of wild-type protein phosphorylated at residue 660. Negative charge at this position had no significant effect on the enzyme's diacylglycerol-stimulated membrane interaction nor the conformational change accompanying membrane binding. In contrast, phosphate caused a 10-fold increase in the enzyme's affinity for Ca2+ and a comparable increase in its affinity for phosphatidylserine, two interactions that are mediated by the C2 domain. Negative charge also increased the protein's thermal stability and decreased its Km for ATP and peptide substrate. These data indicate that phosphorylation at the extreme carboxyl terminus of protein kinase C structures the active site so that it binds ATP and substrate with higher affinity and structures determinants in the regulatory region enabling higher affinity binding of Ca2+. The motif surrounding Ser-660 in protein kinase C betaII is found in a number of other kinases, suggesting interactions promoted by phosphorylation of the carboxyl terminus may provide a general mechanism for stabilizing kinase structure.

Propagation characteristics of low-loss tubular waveguides

Tubular metal waveguides of circular cross-section supporting the H01-mode and operated at a frequency well above the cut-off value for the guide are known to be capable, in ideal circumstances, of providing a screened microwave channel having an attenuation of only a few decibels per mile. The paper is concerned with the practicability of this arrangement at a frequency of 35 Gc/s employing straight lengths of copper and aluminium tubes, 0.9?2.74 in inside diameter, manufactured and installed to commercial tolerances. Using pulses of 0.1 microsec duration at this frequency, it is demonstrated that with solid-drawn tubes of standard production attenuations about 30% above the theoretical value are readily obtainable, and the conditions of propagation are entirely stable. Arrangements for launching the wave both from the usual H01 rectangular-guide source and directly from a magnetron oscillator are discussed. Attention is drawn to the possible application of such a waveguide to trunk communication and to high-power transmission. Although progress has been made on the problem of propagation round bends in the guide, a really satisfactory solution has not yet been found, and further work on that aspect is in progress.