scholarly journals Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

2021 ◽  
Author(s):  
Samuel Martin ◽  
Darren Heavens ◽  
Yuxuan Lan ◽  
Samuel Horsfield ◽  
Matthew D Clark ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Web Application ◽  
Adaptive Sampling ◽  
Bacterial Species ◽  
Abundant Species ◽  
Read Length ◽  
Multiple Species ◽  
Sequencing Platforms ◽  
The Relationship ◽  
Pore Stability

Background: Adaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms recently implemented in Oxford Nanopore's own control software. By examining the first few hundred bases of a DNA molecule as it passes through a pore, software can determine if the molecule is sufficiently interesting to sequence in its entirety. If not, the molecule is ejected from the pore by reversing the voltage across it, freeing the pore for a new molecule. User supplied sequences define the targets to be sequenced or ejected. Here we explore the potential of using adaptive sampling for enrichment of rarer species within metagenomic samples. Results: We created a synthetic mock community consisting of seven bacterial species at different proportions ranging from 1.2% to 47% and used this as the basis for a series of enrichment and depletion experiments. To investigate the effect of DNA length on adaptive sampling efficiency, we created sequencing libraries with mean read lengths of 1.7 kbp, 4.7 kbp, 10.6 kbp, and 12.8 kbp and enriched or depleted for individual and multiple species over a series of sequencing runs. Across all experiments enrichment ranged from 1.67-fold for the most abundant species with the shortest read length to 13.87-fold for the least abundant species with the longest read length. Factoring in the reduction to sequence output associated with repeatedly rejecting molecules reduces the calculated efficiency of this enrichment to between 0.96-fold and 4.93-fold. We note that reducing ejections due to false negatives (approximately 36%) would significantly increase efficiency. We used the relationship between abundance, molecule length and enrichment factor to produce a mathematical model of enrichment based on molecule length and relative abundance, whose predictions correlated strongly with experimental data. A web application is provided to allow researchers to explore model predictions in advance of performing their own experiments. Conclusions: Our data clearly demonstrates the benefit for enriching low abundant species in adaptive sampling metagenomic experiments, especially with longer molecules, and our mathematical model can be used to determine whether a given experimental DNA sample is suitable for adaptive sampling. Notably, repeated voltage reversals have no effect on pore stability.

Temperature Influence on Performance of Oxidation Ponds

1991 ◽  
Vol 24 (5) ◽  
pp. 85-96 ◽  
Author(s):  
Qingliang Zhao ◽  
Zijie Zhang
Keyword(s):  
Mathematical Model ◽  
Temperature Influence ◽  
Field Scale ◽  
Experiment Data ◽  
Computer Technique ◽  
Oxidation Pond ◽  
Optimum Model ◽  
Oxidation Ponds ◽  
The Mathematical Model ◽  
The Relationship

By means of simulated tests of a laboratory–scale oxidation pond model, the relationship between BOD5 and temperature fluctuation was researched. Mathematical modelling for the pond's performance and K1determination were systematically described. The calculation of T–K1–CeCe/Ci) was complex but the problem was solved by utilizing computer technique in the paper, and the mathematical model which could best simulate experiment data was developed. On the basis of experiment results,the concept of plug–ratio–coefficient is also presented. Finally the optimum model recommended here was verified with the field–scale pond data.

Pulse-Width Modulated Amplifier for DC Servo System and Its Matlab Simulation

2015 ◽  
Vol 9 (1) ◽  
pp. 625-631
Author(s):  
Ma Xiaocheng ◽  
Zhang Haotian ◽  
Cheng Yiqing ◽  
Zhu Lina ◽  
Wu Dan
Keyword(s):  
Mathematical Model ◽  
Transfer Function ◽  
Input Signal ◽  
Pulse Width ◽  
Rotation Speed ◽  
Servo Motor ◽  
Matlab Simulation ◽  
Pulse Width Modulated ◽  
Signal Changes ◽  
The Relationship

This paper introduces a mathematical model for Pulse-Width Modulated Amplifier for DC Servo Motor. The relationship between pulse-width modulated (PWM) signal and reference rotation speed is specified, and a general model of motor represented by transfer function is also put forward. When the input signal changes, the rotation speed of the servo motor will change accordingly. By changing zeros and poles, transient performance of this system is discussed in detail, and optimal ranges of the parameters is recommended at the end of discussion.

scholarly journals Diversity of Epibionts Associated with Lepidochelys olivacea (Eschscholtz 1829) Sea Turtles Nesting in the Mexican South Pacific

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1734
Author(s):  
Brenda Sarahí Ramos-Rivera ◽  
Himmer Castro-Mondragon ◽  
José Gabriel Kuk-Dzul ◽  
Pedro Flores-Rodríguez ◽  
Rafael Flores-Garza
Keyword(s):  
Data Analysis ◽  
Sea Turtles ◽  
South Pacific ◽  
First Record ◽  
Abundant Species ◽  
Interspecific Relationships ◽  
Lepidochelys Olivacea ◽  
Significant Difference ◽  
The Relationship ◽  
Head Neck

The present study contributes to the knowledge of epibionts recorded on sea turtles that nested on a beach in the South Pacific of Mexico. A total of 125 Lepidochelys olivacea turtles nested on Llano Real beach, Guerrero, Mexico, were examined. We collected 450 conspicuous organisms from 8 species from 43 turtles. The corresponding data analysis was carried out to obtain the relative abundance, the relationship between turtle sizes and the presence of organisms, the similarity of species between the sampling months, and the interspecific relationships between the epibionts and the turtles observed. Chelonibia testudinaria was the most abundant species, while Remora remora was the least abundant species. The turtles were divided into six body sections, with the greatest abundance of these organisms located in the head–neck section of turtles, and there was a significant difference in the size of the turtles that presented epibionts and those that did not. C. testudinaria showed greater similarity between sampling months, and the interspecific relationships recorded were commensalism, parasitism, amensalism, and protocooperation. This research contributes the first record of epibionts in L. olivacea nesting in Guerrero, Mexico.

The bacteriome of the oral cavity in healthy dogs and dogs with periodontal disease

2022 ◽  
pp. 1-9
Author(s):  
Brook A. Niemiec ◽  
Jerzy Gawor ◽  
Shuiquan Tang ◽  
Aishani Prem ◽  
Janina A. Krumbeck
Keyword(s):  
Oral Cavity ◽  
Periodontal Disease ◽  
Bacterial Species ◽  
Abundant Species ◽  
Rrna Gene ◽  
Core Microbiome ◽  
The Core ◽  
Severe Periodontal Disease ◽  
Healthy Dogs ◽  
V3 Region

Abstract OBJECTIVE To compare the bacteriome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease. ANIMALS Dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease. PROCEDURES The maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the V1–V3 region of the 16S rRNA gene. RESULTS 714 bacterial species from 177 families were identified. The 3 most frequently found bacterial species were Actinomyces sp (48/51 samples), Porphyromonas cangingivalis (47/51 samples), and a Campylobacter sp (48/51 samples). The most abundant species were P cangingivalis, Porphyromonas gulae, and an undefined Porphyromonas sp. Porphyromonas cangingivalis and Campylobacter sp were part of the core microbiome shared among the 4 groups, and P gulae, which was significantly enriched in dogs with severe periodontal disease, was part of the core microbiome shared between all groups except dogs without periodontal disease. Christensenellaceae sp, Bacteroidales sp, Family XIII sp, Methanobrevibacter oralis, Peptostreptococcus canis, and Tannerella sp formed a unique core microbiome in dogs with severe periodontal disease. CONCLUSIONS AND CLINICAL RELEVANCE Results highlighted that in dogs, potential pathogens can be common members of the oral cavity bacteriome in the absence of disease, and changes in the relative abundance of certain members of the bacteriome can be associated with severity of periodontal disease. Future studies may aim to determine whether these changes are the cause or result of periodontal disease or the host immune response.

Modeling the Growth of Salmonella in Cut Red Round Tomatoes as a Function of Temperature

2010 ◽  
Vol 73 (8) ◽  
pp. 1502-1505 ◽  
Author(s):  
WENJING PAN ◽  
DONALD W. SCHAFFNER
Keyword(s):  
Mathematical Model ◽  
Growth Rates ◽  
Low Temperatures ◽  
Safety Concern ◽  
Time Intervals ◽  
Salmonella Serotypes ◽  
Increasing Temperature ◽  
Incubation Temperatures ◽  
Raw Poultry ◽  
The Relationship

Tomato-associated Salmonella outbreaks have recently become a significant food safety concern. Temperature abuse of cut tomatoes may have played a role in some of these outbreaks. The purpose of this study was to develop a mathematical model to describe the growth of Salmonella on cut tomatoes at various temperatures. Four Salmonella serotypes (Typhimurium, Newport, Javiana, and Braenderup) obtained from previous tomato-linked cases of salmonellosis were used in this study. These four serotypes were cultured separately, combined into a cocktail, and inoculated onto whole red round tomatoes and allowed to dry overnight. The tomatoes were then cut into pieces and incubated at a predetermined range of temperatures (10, 12.5, 15, 17.5, 20, 22.5, 25, 27.5, 30, and 35°C). Salmonella concentration was measured at specified time intervals to determine the growth curve for Salmonella on cut tomatoes at each temperature. The growth rates were calculated using DMFit and used to build a mathematical model to illustrate the relationship between the growth rates of Salmonella on tomatoes and incubation temperatures from 10 to 35°C. The resulting model compared favorably with a Salmonella growth model for raw poultry developed by our laboratory. The Pathogen Modeling Program underpredicted growth at low temperatures and overpredicted growth at high temperatures. ComBase predicted consistently slower growth rates than were observed in tomatoes but showed parallel increases in growth rate with increasing temperature.

scholarly journals Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

2019 ◽  
Author(s):  
Kathryn E. Holt ◽  
Florent Lassalle ◽  
Kelly L. Wyres ◽  
Ryan Wick ◽  
Rafal J. Mostowy
Keyword(s):  
Evolutionary Dynamics ◽  
Bacterial Species ◽  
Purifying Selection ◽  
Evolutionary Forces ◽  
Polysaccharide Synthesis ◽  
Surface Polysaccharides ◽  
Surface Polysaccharide ◽  
Selective Preservation ◽  
Multiple Species

Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically-relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps and kps, using 27,334 genomes from 45 genera. We identified high-quality cps loci in 22 genera and kps in 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages of Escherichia coli, Enterobacter hormachei and Klebsiella aerogenes most likely to share SP loci via recent exchange; and lineages of Salmonella enterica, Citrobacter sakazakii and Serratia marcescens most likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species.

scholarly journals THE INNOVATIVE POTENTIAL OF HUMAN RESOURCES AS A FACTOR IN THE DEVELOPMENT OF THE INNOVATIVE TECHNOLOGIES MARKET IN UKRAINE

2021 ◽  
Vol 23 (1(78)) ◽  
pp. 58-74
Author(s):  
I.V. GRYSHCHENKO ◽  
V.F. GRYSHCHENKO
Keyword(s):  
Mathematical Model ◽  
Human Resources ◽  
Market Development ◽  
Short Term ◽  
Model Calculations ◽  
Innovative Technologies ◽  
Innovation Capacity ◽  
Innovative Potential ◽  
The Impact ◽  
The Relationship

Topicality. The successful operation of an economic entity, in the development of the innovative technologies market, is largely determined by the innovative potential of its human resources - by the people who work for it - their knowledge, talents, and skills. The wrong combination of these elements, lack of employees who have the necessary qualifications, lack of harmony in the relationship between employers and employees can inevitably lead to serious financial and economic problems. Improving the efficiency of the use of the innovative potential of human resources in the development of the innovative technologies market is one of the most urgent tasks for any business entity. The competitive advantages of business entities, financial and economic indicators of their activity, ensuring sustainable development of entrepreneurship in general, are depending on the degree and balance of its use. Aim and tasks. The purpose of the work is to analyze and develop on its basis recommendations for increasing the level of the innovative potential of human resources in the context of the development of the innovative technologies market in Ukraine. Research results. The article analyzes the main structural elements of the innovative potential of human resources and identifies the factors influencing its level in Ukraine. The results of the analysis allowed us to build an economic and mathematical model of the relationship between innovation capacity, as an indicator of the development of the innovative technologies market and components of the innovative potential of human resources in Ukraine. This made it possible to predict the level of innovation capacity as an indicator of the innovative technologies market development in Ukraine in the short term. The obtained results allowed us to identify problems and develop recommendations for increasing the level of the innovative potential of human resources in the context of the innovative technologies market development in Ukraine. Conclusion. Based on the developed economic and mathematical model, calculations were made that characterize the relationship between innovation capacity as an indicator of the innovative technologies market development and components of the innovative potential of human resources in Ukraine. As shown in the calculations, the proposed economic and mathematical model with high accuracy allows to assess the impact of components of the innovative potential of human resources on innovation capacity and identify major obstacles for its development, which made it possible to predict trends in innovation capacity as an indicator of the innovative technologies market development in Ukraine in the short term.

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