scholarly journals Coalescence modeling of intrainfection Bacillus anthracis populations allows estimation of infection parameters in wild populations

2020 ◽  
Vol 117 (8) ◽  
pp. 4273-4280 ◽  
Author(s):  
W. Ryan Easterday ◽  
José Miguel Ponciano ◽  
Juan Pablo Gomez ◽  
Matthew N. Van Ert ◽  
Ted Hadfield ◽  
...  
Keyword(s):  
Experimental Data ◽  
Bacillus Anthracis ◽  
Model Organism ◽  
Laboratory Animals ◽  
Effective Population ◽  
New Host ◽  
Natural Systems ◽  
Colony Forming Units ◽  
Infection Parameters ◽  
Founding Populations

Bacillus anthracis, the etiological agent of anthrax, is a well-established model organism. For B. anthracis and most other infectious diseases, knowledge regarding transmission and infection parameters in natural systems, in large part, comprises data gathered from closely controlled laboratory experiments. Fatal, natural anthrax infections transmit the bacterium through new host−pathogen contacts at carcass sites, which can occur years after death of the previous host. For the period between contact and death, all of our knowledge is based upon experimental data from domestic livestock and laboratory animals. Here we use a noninvasive method to explore the dynamics of anthrax infections, by evaluating the terminal diversity of B. anthracis in anthrax carcasses. We present an application of population genetics theory, specifically, coalescence modeling, to intrainfection populations of B. anthracis to derive estimates for the duration of the acute phase of the infection and effective population size converted to the number of colony-forming units establishing infection in wild plains zebra (Equus quagga). Founding populations are small, a few colony-forming units, and infections are rapid, lasting roughly between 1 d and 3 d in the wild. Our results closely reflect experimental data, showing that small founding populations progress acutely, killing the host within days. We believe this method is amendable to other bacterial diseases from wild, domestic, and human systems.

scholarly journals Surveys of larval sealworm (Pseudoterranova decipiens) infection in various fish species sampled from Nova Scotian waters between 1988 and 1996, with an assessment of examination procedures

2001 ◽  
Vol 3 ◽  
pp. 57 ◽  
Author(s):  
G McClelland ◽  
DJ Martell
Keyword(s):  
Gadus Morhua ◽  
Gulf Of Maine ◽  
New Host ◽  
Pseudoterranova Decipiens ◽  
Infection Parameters ◽  
Routine Inspection ◽  
Frozen Fish ◽  
Nova Scotian ◽  
New Host Records ◽  
Benthic Consumers

Between November 1988 and October 1996, >10,000 fish from the Breton Shelf, Sable Island Bank and the northeastern Gulf of Maine were examined for larval anisakines. Larval sealworm, Pseudoterranova decipiens, occurred in 30 of 39 species surveyed, including 8 new host records, Enchelyopus cimbrius, Lycodes reticulatus, Eumesogrammus praecisus, Lumpenus lumpretaeformis, Lumpenus maculatus, Cryptacanthodes maculatus, Artediellus atlanticus and Triglops murrayi. The parasite was most prevalent and abundant in mature demersal piscivores and benthic consumers. Sealworm densities (nr kg-1 host wt.), however, were greatest in small benthophagous fish including mature E. cimbrius, A. atlanticus, T. murrayi and Aspidophoroides monopterygius, and juvenile Hippoglossoides platessoides. ANOVA revealed that geographical disparities in sealworm prevalence and abundance were highly significant in 14 of 20 species tested, although significant disparities between samples from each of the three areas were evident only in H. platessoides. Almost invariably, infection parameters were greatest in fish from Sable Island Bank. ANOVA also indicated that sealworm prevalence and/or abundance increased significantly in Sable Island Bank populations of Gadus morhua, H. platessoides, and seven other species between 1985-1986 and 1989-1990. Routine examinations, in which host flesh was sliced and candled, proved as efficacious as digestion in warm (35° C) pepsin-HCl for detection of larval sealworm in the flesh of large frozen fish. Procedures employing fresh (iced) samples, digestion at ambient temperature and microscopy are recommended, however, for surveys of small benthic consumers. Many of the sealworm infecting the latter hosts are tiny (2 to 10 mm in length) nematodes, which escape detection by routine inspection, and may not survive in warm pepsin-HCl solution.

scholarly journals Exploring the effect of biological delays in kinetic models of influenza within a host or cell culture

2021 ◽  
Author(s):  
Benjamin P Holder ◽  
Catherine A. A. Beauchemin
Keyword(s):  
Differential Equation ◽  
Experimental Data ◽  
Influenza Infection ◽  
Biologically Relevant ◽  
Differential Equation Models ◽  
Viral Yield ◽  
Infection Parameters ◽  
Delay Differential

Background For a typical influenza infection in vivo, viral titers over time are characterized by 1–2 days of exponential growth followed by an exponential decay. This simple dynamic can be reproduced by a broad range of mathematical models which makes model selection and the extraction of biologically-relevant infection parameters from experimental data difficult. Results We analyze in vitro experimental data from the literature, specifically that of single-cycle viral yield experiments, to narrow the range of realistic models of infection. In particular, we demonstrate the viability of using a normal or lognormal distribution for the time a cell spends in a given infection state (e.g., the time spent by a newly infected cell in the latent state before it begins to produce virus), while exposing the shortcomings of ordinary differential equation models which implicitly utilize exponential distributions and delay-differential equation models with fixed-length delays. Conclusions By fitting published viral titer data from challenge experiments in human volunteers, we show that alternative models can lead to different estimates of the key infection parameters.

scholarly journals Nonhuman primates’ tissue banks: resources for all model organism research

2021 ◽  
Author(s):  
Claire Witham ◽  
Sara Wells
Keyword(s):  
Nonhuman Primates ◽  
Ex Vivo ◽  
Model Organism ◽  
Translation Studies ◽  
Model Organisms ◽  
Laboratory Animals ◽  
Tissue Banks ◽  
Post Mortem ◽  
Wide Range ◽  
Research Programmes

AbstractBiobanks containing tissue and other biological samples from many model organisms provide easy and faster access to ex vivo resources for a wide-range of research programmes. For all laboratory animals, collecting and preserving tissue at post-mortem is an effective way of maximising the benefits of individual animals and potentially reducing the numbers required for experimentation in the future. For primate tissues, biobanks represent the scarcest of these resources but quite possibly those most valuable for preclinical and translation studies.

Bacteriological examination of a modern animal house containing small laboratory animals

1979 ◽  
Vol 13 (1) ◽  
pp. 21-27 ◽  
Author(s):  
Martin Wierup
Keyword(s):  
Staphylococcus Epidermidis ◽  
Bacterial Species ◽  
Laboratory Animals ◽  
Bacteriological Examination ◽  
Small Laboratory ◽  
Bacterial Counts ◽  
Colony Forming Units ◽  
Animal House ◽  
Conventional Unit ◽  
Bacteriological Contamination

Floors and other areas totalling 1800 m2, comprising conventional and specified-pathogen-free (SPF) units, were screened bacteriologically 6 times in a year. The contamination indices observed were lower within than outside the units, and lower in the SPF than in the conventional unit. Bacterial counts in rooms containing animals in the conventional and SPF units were very similar. In all of the areas investigated within the units, most of the samples revealed <2 colony forming units per cm2. In contrast, high degrees of bacteriological contamination were detected in the changing rooms after showering or washing before entry. Staphylococcus epidermidis was the dominant bacterial species isolated. The bacteriological spectrum did not vary between the areas surveyed.

scholarly journals Laser capture microdissection in combination with mass spectrometry: Approach to characterization of tissue-specific proteomes of Eudiplozoon nipponicum (Monogenea, Polyopisthocotylea)

2020 ◽  
Author(s):  
Pavel Roudnický ◽  
David Potěšil ◽  
Zbyněk Zdráhal ◽  
Milan Gelnar ◽  
Martin Kašný
Keyword(s):  
Mass Spectrometry ◽  
Laser Capture Microdissection ◽  
Bacterial Infections ◽  
Protein Localization ◽  
Model Organism ◽  
Surrounding Tissue ◽  
Laboratory Animals ◽  
Tissue Specific ◽  
Laser Capture ◽  
Eudiplozoon Nipponicum

AbstractEudiplozoon nipponicum (Goto, 1891) is a hematophagous monogenean ectoparasite which inhabits the gills of the common carp (Cyprinus carpio). Heavy infestation can lead to anemia and in conjunction with secondary bacterial infections cause poor health and eventual death of the host.This study is based on an innovative approach to protein localization which has never been used in parasitology before. Using laser capture microdissection, we dissected particular areas of the parasite body without contaminating the samples by surrounding tissue, and in combination with analysis by mass spectrometry obtained tissue-specific proteomes of tegument, intestine, and parenchyma of our model organism, E. nipponicum. We successfully verified the presence of certain functional proteins (e.g. cathepsin L) in tissues where their presence was expected (intestine) and confirmed that there were no traces of these proteins in other tissues (tegument and parenchyma). Additionally, we identified a total of 2,059 proteins, including 72 peptidases and 33 peptidase inhibitors. As expected, the greatest variety was found in the intestine and the lowest variety in the parenchyma.Our results are significant on two levels. Firstly, we demonstrated how one can localize all proteins in one analysis and without using laboratory animals (antibodies for immunolocalization of single proteins). Secondly, this study offers the first complex proteomic data on not only the E. nipponicum but within the whole class of Monogenea, which was from this point of view until recently neglected.

scholarly journals Experimental production of actinomycetoma in BALB/c mice

1980 ◽  
Vol 29 (3) ◽  
pp. 1141-1145
Author(s):  
H Zlotnik ◽  
H R Buckley
Keyword(s):  
Skin Lesions ◽  
Chemotherapeutic Agents ◽  
Tumor Formation ◽  
Laboratory Animals ◽  
Suitable Model ◽  
Experimental Production ◽  
Therapeutic Trials ◽  
Colony Forming Units ◽  
Superficial Skin ◽  
Subcutaneous Inoculation

Chronic actinomycetoma associated with grain production was induced in BALB/c mice by subcutaneous inoculation of live Nocardia brasiliensis in Freund incomplete adjuvant into the hind footpads. Similar inoculation of N. asteroides and N. caviae resulted in local tumor formation which healed spontaneously after 5 months, the disease disseminating into the peritoneum, where masses or organisms could be detected. Grains were recovered from superficial skin lesions of N. caviae, but not from the N. asteroides-infected mice. Mycetoma lesions, appearing as early as 1 month after inoculation of 1.2 X 10(7) colony-forming units of N. brasiliensis per ml or as late as 3 months with inoculation of 1.0 X 10(5) colony-forming units per ml, became persistent and were readily detectable even 6 months after inoculation. No spontaneous healing occurred, and grains were recovered at different stages of the disease. Saline suspensions of N. brasiliensis also produced typical mycetoma lesions, although the incubation period was ca. 6 months. Adjuvant addition appeared to accelerate the onset of the disease. Experimental production of actinomycetoma in laboratory animals allows the study of many unanswered aspects of the disease and also provides a suitable model for therapeutic trials in the search for new and more effective chemotherapeutic agents.

scholarly journals Variation of the Performance of Machine-Learning Based Image Classifier in Automated Detection of Itch-Induced Scratch

2020 ◽  
Author(s):  
Chuan Liu ◽  
Sheng-Xiang Yan ◽  
Xiao-Bo Wu ◽  
Zhi-Jun Zhang ◽  
Wei Li
Keyword(s):  
Machine Learning ◽  
Experimental Data ◽  
Laboratory Animal ◽  
Automated Detection ◽  
Laboratory Animals ◽  
Primary Role ◽  
Data Recording ◽  
Non Invasive ◽  
Overall Performance ◽  
First Time

A 'little brother' of pain, itch is an unpleasant sensation that creates a specific urge to scratch. To date, various machine-learning based image classifiers (MBICs) have been proposed for quantitative analysis of itch-induced scratch behaviour of laboratory animals in an automated, non-invasive, inexpensive and real-time manner. In spite of MBICs' advantages, the overall performances (accuracy, sensitivity and specificity) of current MBIC approaches remains inconsistent, with their values varying from ~50% to ~99%, for which the reasons underlying have yet to be investigated further, both computationally and experimentally. To look into the variation of the performance of MBICs in automated detection of itch-induced scratch, this article focuses on the experimental data recording step, and reports here for the first time that MBICs' overall performance is inextricably linked to the sharpness of experimentally recorded video of laboratory animal scratch behaviour. This article furthermore demonstrates for the first time that a linearly correlated relationship exists between video sharpness and overall performance (accuracy and specificity, but not sensitivity) of MBICs, and highlight the primary role of experimental data recording in rapid, accurate and consistent quantitative assessment of laboratory animal itch.

scholarly journals Genetic Algorithm – A Sensible Evolutionary Optimization Technique

2019 ◽  
Vol 8 (9) ◽  
pp. 2805-2809
Keyword(s):  
Genetic Algorithm ◽  
Optimization Problems ◽  
Search Algorithm ◽  
Random Search ◽  
Optimization Technique ◽  
Search Space ◽  
Effective Population ◽  
Natural Systems ◽  
Heuristic Search Algorithm ◽  
Feasible Solutions

The study presents a pragmatic outlook of genetic algorithm. Many biological algorithms are inspired for their ability to evolve towards best solutions and of all; genetic algorithm is widely accepted as they well suit evolutionary computing models. Genetic algorithm could generate optimal solutions on random as well as deterministic problems. Genetic algorithm is a mathematical approach to imitate the processes studied in natural evolution. The methodology of genetic algorithm is intensively experimented in order to use the power of evolution to solve optimization problems. Genetic algorithm is an adaptive heuristic search algorithm based on the evolutionary ideas of genetics and natural selection. Genetic algorithm exploits random search approach to solve optimization problems. Genetic algorithm takes benefits of historical information to direct the search into the convergence of better performance within the search space. The basic techniques of evolutionary algorithms are observed to be simulating the processes in natural systems. These techniques are aimed to carry effective population to the next generation and ensure the survival of the fittest. Nature supports the domination of stronger over the weaker ones in any kind. In this study, we proposed the arithmetic views of the behavior and operators of genetic algorithm that support the evolution of feasible solutions to optimized solutions.

scholarly journals Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia

2021 ◽  
Vol 12 ◽  
Author(s):  
Rúben M. Costa ◽  
Anny Cárdenas ◽  
Céline Loussert-Fonta ◽  
Gaëlle Toullec ◽  
Anders Meibom ◽  
...  
Keyword(s):  
Surface Topography ◽  
Carrying Capacity ◽  
Model Organism ◽  
Model Systems ◽  
Functional Studies ◽  
Stony Corals ◽  
Starting Point ◽  
Colony Forming Units ◽  
Surface Topographies ◽  
Microbial Host

Aiptasia is an emerging model organism to study cnidarian symbioses due to its taxonomic relatedness to other anthozoans such as stony corals and similarities of its microalgal and bacterial partners, complementing the existing Hydra (Hydrozoa) and Nematostella (Anthozoa) model systems. Despite the availability of studies characterizing the microbiomes of several natural Aiptasia populations and laboratory strains, knowledge on basic information, such as surface topography, bacterial carrying capacity, or the prospect of microbiome manipulation is lacking. Here we address these knowledge gaps. Our results show that the surface topographies of the model hydrozoan Hydra and anthozoans differ substantially, whereas the ultrastructural surface architecture of Aiptasia and stony corals is highly similar. Further, we determined a bacterial carrying capacity of ∼104 and ∼105 bacteria (i.e., colony forming units, CFUs) per polyp for aposymbiotic and symbiotic Aiptasia anemones, respectively, suggesting that the symbiotic status changes bacterial association/density. Microbiome transplants from Acropora humilis and Porites sp. to gnotobiotic Aiptasia showed that only a few foreign bacterial taxa were effective colonizers. Our results shed light on the putative difficulties of transplanting microbiomes between cnidarians in a manner that consistently changes microbial host association at large. At the same time, our study provides an avenue to identify bacterial taxa that exhibit broad ability to colonize different hosts as a starting point for cross-species microbiome manipulation. Our work is relevant in the context of microbial therapy (probiotics) and microbiome manipulation in corals and answers to the need of having cnidarian model systems to test the function of bacteria and their effect on holobiont biology. Taken together, we provide important foundation data to extend Aiptasia as a coral model for bacterial functional studies.

A numerical algorithm for constructing an individual mathematical model of HIV dynamics at cellular level

2018 ◽  
Vol 26 (6) ◽  
pp. 859-873 ◽  
Author(s):  
H. Thomas Banks ◽  
Sergey I. Kabanikhin ◽  
Olga I. Krivorotko ◽  
Darya V. Yermolenko
Keyword(s):  
Experimental Data ◽  
Mathematical Model ◽  
Inverse Problem ◽  
Cellular Level ◽  
Free Virus ◽  
Hiv Dynamics ◽  
Infection Parameters ◽  
Simulation Results ◽  
The Mathematical Model ◽  
Fixed Times

Abstract In this paper a problem of specifying HIV-infection parameters and immune response using additional measurements of the concentrations of the T-lymphocytes, the free virus and the immune effectors at fixed times for a mathematical model of HIV dynamics is investigated numerically. The problem of the parameter specifying of the mathematical model (an inverse problem) is reduced to a problem of minimizing an objective function describing the deviation of the simulation results from the experimental data. A genetic algorithm for solving the least squares function minimization problem is implemented and investigated. The results of a numerical solution of the inverse problem are analyzed.

Sign in / Sign up

Export Citation Format

Share Document