scholarly journals The Effects of Statistical Multiplicity of Infection on Virus Quantification and Infectivity Assays

2018 ◽  
Author(s):  
Bhaven Mistry ◽  
Maria R. D’Orsogna ◽  
Tom Chou
Keyword(s):  
Viral Particle ◽  
Probabilistic Models ◽  
Host Cells ◽  
Luciferase Reporter ◽  
Parameter Estimates ◽  
Multiplicity Of Infection ◽  
Web Based ◽  
Large Numbers ◽  
Multiple Particles ◽  
Virus Quantification

Many biological assays are employed in virology to quantify parameters of interest. Two such classes of assays, virus quantification assays (VQA) and infectivity assays (IA), aim to estimate the number of viruses present in a solution, and the ability of a viral strain to successfully infect a host cell, respectively. VQAs operate at extremely dilute concentrations and results can be subject to stochastic variability in virus-cell interactions. At the other extreme, high viral particle concentrations are used in IAs, resulting in large numbers of viruses infecting each cell, enough for measurable change in total transcription activity. Furthermore, host cells can be infected at any concentration regime by multiple particles, resulting in a statistical multiplicity of infection (SMOI) and yielding potentially significant variability in the assay signal and parameter estimates. We develop probabilistic models for SMOI at low and high viral particle concentration limits and apply them to the plaque (VQA), endpoint dilution (VQA), and luciferase reporter (IA) assays. A web-based tool implementing our models and analysis is also developed and presented. We test our proposed new methods for inferring experimental parameters from data using numerical simulations and show improvement on existing procedures in all limits.

scholarly journals Resveratrol Inhibits Venezuelan Equine Encephalitis Virus Infection by Interfering with the AKT/GSK Pathway

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 346
Author(s):  
Caitlin W. Lehman ◽  
Kylene Kehn-Hall ◽  
Megha Aggarwal ◽  
Nicole R. Bracci ◽  
Han-Chi Pan ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Fluorescent Protein ◽  
Glycogen Synthase ◽  
Venezuelan Equine Encephalitis Virus ◽  
Encephalitis Virus ◽  
Host Cells ◽  
Dynamics Simulation ◽  
Luciferase Reporter ◽  
Venezuelan Equine Encephalitis ◽  
Equine Encephalitis Virus

The host proteins Protein Kinase B (AKT) and glycogen synthase kinase-3 (GSK-3) are associated with multiple neurodegenerative disorders. They are also important for the replication of Venezuelan equine encephalitis virus (VEEV), thereby making the AKT/GSK-3 pathway an attractive target for developing anti-VEEV therapeutics. Resveratrol, a natural phytochemical, has been shown to substantially inhibit the AKT pathway. Therefore, we attempted to explore whether it exerts any antiviral activity against VEEV. In this study, we utilized green fluorescent protein (GFP)- and luciferase-encoding recombinant VEEV to determine the cytotoxicity and antiviral efficacy via luciferase reporter assays, flow cytometry, and immunofluorescent assays. Our results indicate that resveratrol treatment is capable of inhibiting VEEV replication, resulting in increased viability of Vero and U87MG cells as well as reduced virion production and viral RNA contents within host cells for at least 48 h with a single treatment. Furthermore, the suppression of apoptotic signaling adaptors, caspase-3, caspase-7, and annexin V may also be implicated in resveratrol-mediated antiviral activity. We found that decreased phosphorylation of the AKT/GSK-3 pathway, mediated by resveratrol, can be triggered during the early stages of VEEV infection, suggesting that resveratrol disrupts the viral replication cycle and consequently promotes cell survival. Finally, molecular docking and dynamics simulation studies revealed that resveratrol can directly bind to VEEV glycoproteins, which may interfere with virus attachment and entry. In conclusion, our results suggest that resveratrol exerts inhibitory activity against VEEV infection and upon further modification could be a useful compound to study in neuroprotective research and veterinary sciences.

scholarly journals Foot-and-Mouth Disease (FMD) Virus 3C Protease Mutant L127P: Implications for FMD Vaccine Development

2017 ◽  
Vol 91 (22) ◽  
Author(s):  
Michael Puckette ◽  
Benjamin A. Clark ◽  
Justin D. Smith ◽  
Traci Turecek ◽  
Erica Martel ◽  
...  
Keyword(s):  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Host Cells ◽  
Luciferase Reporter ◽  
Bacterial Cells ◽  
Vaccine Production ◽  
3C Protease ◽  
Fmdv Serotypes ◽  
Mouth Disease Virus ◽  
Foot And Mouth

ABSTRACT The foot-and-mouth disease virus (FMDV) afflicts livestock in more than 80 countries, limiting food production and global trade. Production of foot-and-mouth disease (FMD) vaccines requires cytosolic expression of the FMDV 3C protease to cleave the P1 polyprotein into mature capsid proteins, but the FMDV 3C protease is toxic to host cells. To identify less-toxic isoforms of the FMDV 3C protease, we screened 3C mutants for increased transgene output in comparison to wild-type 3C using a Gaussia luciferase reporter system. The novel point mutation 3C(L127P) increased yields of recombinant FMDV subunit proteins in mammalian and bacterial cells expressing P1-3C transgenes and retained the ability to process P1 polyproteins from multiple FMDV serotypes. The 3C(L127P) mutant produced crystalline arrays of FMDV-like particles in mammalian and bacterial cells, potentially providing a practical method of rapid, inexpensive FMD vaccine production in bacteria. IMPORTANCE The mutant FMDV 3C protease L127P significantly increased yields of recombinant FMDV subunit antigens and produced virus-like particles in mammalian and bacterial cells. The L127P mutation represents a novel advancement for economical FMD vaccine production.

scholarly journals DHAV-1 Blocks the Signaling Pathway Upstream of Type I Interferon by Inhibiting the Interferon Regulatory Factor 7 Protein

2021 ◽  
Vol 12 ◽  
Author(s):  
Yalan Lai ◽  
Xiaoyan Xia ◽  
Anchun Cheng ◽  
Mingshu Wang ◽  
Xumin Ou ◽  
...  
Keyword(s):  
Immune Response ◽  
Innate Immunity ◽  
Viral Protein ◽  
Interferon Regulatory Factor ◽  
Host Cells ◽  
Luciferase Reporter ◽  
Type I ◽  
Dependent Manner ◽  
Regulatory Factor ◽  
Interferon Regulatory Factor 7

Duck hepatitis A virus (DHAV), which mainly infects 1- to 4-week-old ducklings, has a fatality rate of 95% and poses a huge economic threat to the duck industry. However, the mechanism by which DHAV-1 regulates the immune response of host cells is rarely reported. This study examined whether DHAV-1 contains a viral protein that can regulate the innate immunity of host cells and its specific regulatory mechanism, further exploring the mechanism by which DHAV-1 resists the host immune response. In the study, the dual-luciferase reporter gene system was used to screen the viral protein that regulates the host innate immunity and the target of this viral protein. The results indicate that the DHAV-1 3C protein inhibits the pathway upstream of interferon (IFN)-β by targeting the interferon regulatory factor 7 (IRF7) protein. In addition, we found that the 3C protein inhibits the nuclear translocation of the IRF7 protein. Further experiments showed that the 3C protein interacts with the IRF7 protein through its N-terminus and that the 3C protein degrades the IRF7 protein in a caspase 3-dependent manner, thereby inhibiting the IFN-β-mediated antiviral response to promote the replication of DHAV-1. The results of this study are expected to serve as a reference for elucidating the mechanisms of DHAV-1 infection and pathogenicity.

scholarly journals The Effects of Statistical Multiplicity of Infection on Virus Quantification and Infectivity Assays

2018 ◽  
Vol 114 (12) ◽  
pp. 2974-2985 ◽  
Author(s):  
Bhaven A. Mistry ◽  
Maria R. D’Orsogna ◽  
Tom Chou
Keyword(s):  
Multiplicity Of Infection ◽  
Virus Quantification

scholarly journals Basic astronomy as part of a general higher education in the developing world

2006 ◽  
Vol 2 (SPS5) ◽  
pp. 257-262
Author(s):  
John Baruch ◽  
Dan Hedges ◽  
James Machell ◽  
K. Norris ◽  
Chris Tallon
Keyword(s):  
General Education ◽  
Developing World ◽  
Current System ◽  
Education Programme ◽  
The Internet ◽  
Web Based ◽  
Astronomy Education ◽  
Large Numbers ◽  
Robotic Telescopes ◽  
Robotic Telescope

AbstractThis paper describes a new initiative in support of the aim of Commission 46 of the IAU to develop and improve astronomy education at all levels throughout the world. This paper discusses the ideal specification of a facility to support basic astronomy within education programmes which are delivered to students who have access to the Internet. The available robotic telescopes are discussed against this specification and it is argued that the Bradford Robotic Telescope, uniquely, can support many thousands of users in the area of basic astronomy education, and the resource is free.Access to the Internet is growing in the developing world and this is true in education programmes. This paper discusses the serious problems of delivering to large numbers of students a web based astronomy education programme supported by a robotic telescope as part of a general education. It examines the problems of this form of teaching for teachers who have little experience of working with IT and little knowledge of basic astronomy and proposes how such teachers can be supported.The current system (http://www.telescope.org/) delivers astronomy education in the language, culture and traditions of England. The paper discusses the need to extend this to other languages, cultures and traditions, although for trainee teachers and undergraduates, it is argued that the current system provides a unique and valuable resource.

PHENOTYPIC AND GENETIC PARAMETER ESTIMATES FOR GESTATION LENGTH, CALVING EASE AND BIRTH WEIGHT IN SIMMENTAL CATTLE

1988 ◽  
Vol 68 (1) ◽  
pp. 291-294 ◽  
Author(s):  
R. A. KEMP ◽  
J. W. WILTON ◽  
L. R. SCHAEFFER
Keyword(s):  
Birth Weight ◽  
Random Mating ◽  
Genetic Parameter ◽  
Parameter Estimates ◽  
Gestation Length ◽  
Calving Ease ◽  
Phenotypic Correlations ◽  
Large Numbers ◽  
Genetic And Phenotypic Correlations ◽  
Variance And Covariance Components

Variance components, heritabilities and genetic and phenotypic correlations were estimated using progeny records of 73 sires on the Young Sire Proving Program (YSPP) of the Canadian Simmental Association. The YSPP was based on random mating of 58 test and 15 reference sires to cows in cooperating herds. Data were collected on several traits but the ones of interest in this study were gestation length (GL), calving ease (CE) and birth weight (BW). Variance and covariance components were estimated using Henderson's method 3. Heritability estimates were 0.24, 0.06 and 0.19 for GL, CE and BW, respectively. Genetic and phenotypic correlations were negative between GL and CE and CE and BW. Correlations between GL and BW were moderate and positive. Selection programs, utilizing large numbers of progeny per sire, would be effective but should incorporate the correlations between these traits. Key words: Heritabilities, genetic and phenotypic correlations, selection

The ecology of Chytridium deltanum and other fungus parasites on Oocystis spp.

1971 ◽  
Vol 49 (1) ◽  
pp. 75-87 ◽  
Author(s):  
Margaret J. Masters
Keyword(s):  
Field Studies ◽  
Host Population ◽  
Host Cells ◽  
Aquatic Fungus ◽  
Potential Host ◽  
Large Numbers ◽  
Synchronous Development

Consideration of the population curves of Oocystis crassa and O. lacustris in Lake Manitoba during the summers of 1966 and 1967, and July 1968, indicated that the aquatic fungus Chytridium deltanum was able in two instances to attack growing populations of these algae. This strongly suggested that the fungus was a parasite. However, in July 1965, in Cadham Bay, the fungus bloomed as the host population stopped growing and began to decline. Probably the host cells were slightly senescent at that time and thus more susceptible to fungus attack. Consideration of the composition of the fungus population showed that during one epidemic at least, large numbers of zoospores were released every 7 to 9 days. This suggested a nearly synchronous development of the fungus population. It was also observed that zoospores, able to encyst and successfully infect one host, were sometimes unable to attack another potential host present at the same time. In 1966 and 1967 the fungus appeared a few days after the water had reached 25C. Comparison of culture data for the algae and field studies indicated that Chytridium deltanum most commonly grew on the algae at temperatures above the optimum for the algae.

scholarly journals Aminoglycosides Affect Intracellular Salmonella enterica Serovars Typhimurium and Virchow

2008 ◽  
Vol 52 (3) ◽  
pp. 920-926 ◽  
Author(s):  
Ofir Menashe ◽  
Elena Kaganskaya ◽  
Timor Baasov ◽  
Sima Yaron
Keyword(s):  
Salmonella Enterica ◽  
Eukaryotic Cell ◽  
Host Cells ◽  
Luciferase Reporter ◽  
Intracellular Bacteria ◽  
Bacterial Physiology ◽  
High Antibacterial Activity ◽  
Luciferase Reporter Plasmid ◽  
Acidity Level ◽  
Low Activity

ABSTRACT The high antibacterial activity and selectivity of aminoglycosides and their low activity against intracellular bacteria associated with eukaryotic cells make them the antibiotics of choice for the elimination of extracellular bacteria during intracellular studies. Given the evidence that aminoglycosides can penetrate the eukaryotic cell membrane, the goal of this study was to examine the influence of aminoglycosides on macrophage-associated Salmonella. Herein, we show that gentamicin, kanamycin, and tobramycin at concentrations between 15 to 150 μg ml−1 do not kill intracellular Salmonella but have other effects on the bacterial physiology. By using Salmonella enterica serovars Typhimurium and Virchow harboring luciferase reporter plasmid, we observed that the light produced by intracellular Salmonella declined immediately upon exposure to aminoglycosides, indicating that the bacteria were under stress. The extent of this effect was dependent on the macrophage host, on the identity of the aminoglycoside and its concentration, on the exposure time, and on the Salmonella serovar. Salmonella associated with Nramp1-negative macrophages, in which the phagosomal pH is higher, were more susceptible to aminoglycosides than Salmonella associated with Nramp1-expressing macrophages. These results verify that aminoglycosides affect intracellular bacteria and that the extent of this effect is dependent on the acidity level within the phagosome, suggesting that for the study of intracellular bacteria, the aminoglycoside concentration should be limited to two to five times the MIC for the bacterial strain studied. This precaution should guarantee the complete execution of extracellular bacteria with minimal effects on the intracellular bacteria and the host cells.

scholarly journals Structure-mining: screening structure models by automated fitting to the atomic pair distribution function over large numbers of models

2020 ◽  
Vol 76 (3) ◽  
pp. 395-409 ◽  
Author(s):  
Long Yang ◽  
Pavol Juhás ◽  
Maxwell W. Terban ◽  
Matthew G. Tucker ◽  
Simon J. L. Billinge
Keyword(s):  
Distribution Function ◽  
Pair Distribution Function ◽  
Complex Oxide ◽  
Web Based ◽  
New Approach ◽  
Atomic Pair Distribution Function ◽  
Large Numbers ◽  
Traditional Structure ◽  
Atomic Pair ◽  
Atomic Crystal

A new approach is presented to obtain candidate structures from atomic pair distribution function (PDF) data in a highly automated way. It fetches, from web-based structural databases, all the structures meeting the experimenter's search criteria and performs structure refinements on them without human intervention. It supports both X-ray and neutron PDFs. Tests on various material systems show the effectiveness and robustness of the algorithm in finding the correct atomic crystal structure. It works on crystalline and nanocrystalline materials including complex oxide nanoparticles and nanowires, low-symmetry and locally distorted structures, and complicated doped and magnetic materials. This approach could greatly reduce the traditional structure searching work and enable the possibility of high-throughput real-time auto-analysis PDF experiments in the future.

scholarly journals Simulation of Ecological and Evolutionary Interactions of Darwin's Finches—A Multimedia Learning Tool

HortScience ◽  
1997 ◽  
Vol 32 (6) ◽  
pp. 983b-983
Author(s):  
R.D. Quinn
Keyword(s):  
Population Size ◽  
Pilot Project ◽  
Early Summer ◽  
Initial Population ◽  
Introductory Biology ◽  
Web Based ◽  
Darwin's Finches ◽  
Darwin’S Finches ◽  
Large Numbers ◽  
Bill Morphology

Dr. Quinn is one of a team of six biology professors from six different CSU campuses collaborating on this pilot project. EvolvelT is a web-based method for students to learn the fundamentals of natural selection and speciation by simulating natural processes. The simulation will be modeled on the evolution of Darwin's Finches in the Galapagos Islands. Learners will manipulate variables such as initial population size, variability and heritability of bill morphology, and quantity and quality of seeds, and then observe changes with time in population size and bill morphology. The interactive model will allow variables to be changed and simulations to be repeated, producing results that can be graphed and statistically analyzed. The Integrated Technology Strategy (ITS) of the California State University System (CSU) is using the Internet to create new and more flexible learning opportunities. Recently the ITS brought together biologists from several CSU campuses to explore ways to use technology to improve learning in introductory biology laboratories for non-science students. These laboratories were chosen because they affect large numbers of students at all campuses. Development criteria include applicability across the CSU, improvement in learning quality, accessibility to large numbers of students, and measurable success. We selected evolution as a topic for web-based learning because it is a central concept of biology, and it is relatively difficult to teach in conventional introductory biology laboratories. Our development team will work with multimedia design specialists to insure that the web presentation promotes scientifically sound and efficient learning. We are collaborating via e-mail and occasional video conferences and face-to-face meetings. We will work on the actual teaching materials via a web page. The initial prototype will be ready by early summer 1997 and will be tested, modified, and released for beta testing by summer's end.

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