scholarly journals Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages

PLoS Genetics ◽  
2021 ◽  
Vol 17 (9) ◽  
pp. e1009829
Author(s):  
Jessica K. Calland ◽  
Ben Pascoe ◽  
Sion C. Bayliss ◽  
Evangelos Mourkas ◽  
Elvire Berthenet ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Large Scale ◽  
Time Frame ◽  
Comparative Genomic ◽  
Campylobacter Coli ◽  
Common Ancestry ◽  
Nucleotide Change ◽  
Human Pathogens ◽  
Birthday Problem ◽  
In The Wild

Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the ‘birthday problem’. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10−6 s/s/y) and Campylobacter jejuni (3.4 x 10−6 s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time-frame–analogous to a shared birthday–and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.

scholarly journals Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages

2020 ◽  
Author(s):  
Jessica K. Calland ◽  
Ben Pascoe ◽  
Sion C. Bayliss ◽  
Evangelos Mourkas ◽  
Elvire Berthenet ◽  
...  
Keyword(s):  
Large Scale ◽  
Time Frame ◽  
Mutation Rates ◽  
Comparative Genomic ◽  
Campylobacter Coli ◽  
Common Ancestry ◽  
Human Pathogens ◽  
Birthday Problem ◽  
In The Wild ◽  
Environmental Bacteria

AbstractMeasuring molecular evolution in bacteria typically requires estimation of the rate at which mutations accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the ‘birthday problem’. Using large genomic datasets and comparative genomic approaches, we identify isolate pairs where common ancestry is inferred within the sample time-frame – analogous to a shared birthday. Identifying synonymous and non-synonymous substitions, both within and outside of recombinant regions of the genome, we quantify clock-like diversification to estimate mutation rates for the common pathogenic species Campylobacter coli (2.4 × 10-6 s/s/y) and Campylobacter jejuni (3.4 × 10-6 s/s/y). Finally, using estimated mutation rates we assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating mutation rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.

scholarly journals Phenotypic and Genetic Comparison of a Plant-Internalized and an Animal-Isolated Salmonella Choleraesuis Strain

2021 ◽  
Vol 9 (8) ◽  
pp. 1554
Author(s):  
Irene Esteban-Cuesta ◽  
Mirian Labrador ◽  
Katharina Hunt ◽  
Sven Reese ◽  
Jennie Fischer ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Evolutionary Process ◽  
Growth Curves ◽  
Animal Origin ◽  
Comparative Genomic ◽  
Nucleotide Polymorphisms ◽  
Human Pathogens ◽  
Single Nucleotide ◽  
Ionization Time ◽  
Hygienic Measures

Contamination of fresh produce with human pathogens poses an important risk for consumers, especially after raw consumption. Moreover, if microorganisms are internalized, no removal by means of further hygienic measures would be possible. Human pathogenic bacteria identified in these food items are mostly of human or animal origin and an adaptation to this new niche and particularly for internalization would be presumed. This study compares a plant-internalized and an animal-borne Salmonella enterica subsp. enterica serovar Choleraesuis aiming at the identification of adaptation of the plant-internalized strain to its original environment. For this purpose, a phenotypical characterization by means of growth curves under conditions resembling the indigenous environment from the plant-internalized strain and further analyses using Pulsed-field gel electrophoresis and Matrix-assisted laser desorption ionization time of flight spectrometry were assessed. Furthermore, comparative genomic analyses by means of single nucleotide polymorphisms and identification of present/absent genes were performed. Although some phenotypical and genetic differences could be found, no signs of a specific adaptation for colonization and internalization in plants could be clearly identified. This could suggest that any Salmonella strain could directly settle in this niche without any evolutionary process being necessary. Further comparative analysis including internalized strains would be necessary to assess this question. However, these kinds of strains are not easily available.

Free-living amoebae and squatters in the wild: ecological and molecular features

2019 ◽  
Vol 43 (4) ◽  
pp. 415-434 ◽  
Author(s):  
Ascel Samba-Louaka ◽  
Vincent Delafont ◽  
Marie-Hélène Rodier ◽  
Estelle Cateau ◽  
Yann Héchard
Keyword(s):  
Pathogenic Bacteria ◽  
Human Pathogens ◽  
Molecular Tools ◽  
Free Living ◽  
Comprehensive Overview ◽  
Molecular Features ◽  
New Information ◽  
Gene Functions ◽  
Free Living Amoeba ◽  
In The Wild

ABSTRACTFree-living amoebae are protists frequently found in water and soils. They feed on other microorganisms, mainly bacteria, and digest them through phagocytosis. It is accepted that these amoebae play an important role in the microbial ecology of these environments. There is a renewed interest for the free-living amoebae since the discovery of pathogenic bacteria that can resist phagocytosis and of giant viruses, underlying that amoebae might play a role in the evolution of other microorganisms, including several human pathogens. Recent advances, using molecular methods, allow to bring together new information about free-living amoebae. This review aims to provide a comprehensive overview of the newly gathered insights into (1) the free-living amoeba diversity, assessed with molecular tools, (2) the gene functions described to decipher the biology of the amoebae and (3) their interactions with other microorganisms in the environment.

Zeitstrukturen im Jazz

2014 ◽  
Vol 59 (1) ◽  
pp. 79-92
Author(s):  
Alexander Becker
Keyword(s):  
Large Scale ◽  
Large Scale Structure ◽  
Time Frame ◽  
Scale Structure ◽  
Classical Form ◽  
Jazz Music ◽  
The Moment

Wie erlebt der Hörer Jazz? Bei dieser Frage geht es unter anderem um die Art und Weise, wie Jazz die Zeit des Hörens gestaltet. Ein an klassischer Musik geschultes Ohr erwartet von musikalischer Zeitgestaltung, den zeitlichen Rahmen, der durch Anfang und Ende gesetzt ist, von innen heraus zu strukturieren und neu zu konstituieren. Doch das ist keine Erwartung, die dem Jazz gerecht wird. Im Jazz wird der Moment nicht im Hinblick auf ein Ziel gestaltet, das von einer übergeordneten Struktur bereitgestellt wird, sondern so, dass er den Bewegungsimpuls zum nächsten Moment weiterträgt. Wie wirkt sich dieses Prinzip der Zeitgestaltung auf die musikalische Form im Großen aus? Der Aufsatz untersucht diese Frage anhand von Beispielen, an denen sich der Weg der Transformation von einer klassischen zu einer dem Jazz angemessenen Form gut nachverfolgen lässt.<br><br>How do listeners experience Jazz? This is a question also about how Jazz music organizes the listening time. A classically educated listener expects a piece of music to structure, unify and thereby re-constitute the externally given time frame. Such an expectation is foreign to Jazz music which doesn’t relate the moment to a goal provided by a large scale structure. Rather, one moment is carried on to the next, preserving the stimulus potentially ad infinitum. How does such an organization of time affect the large scale form? The paper tries to answer this question by analyzing two examples which permit to trace the transformation of a classical form into a form germane to Jazz music.

The Green New Deal

2019 ◽  
Author(s):  
Robert C. Hockett
Keyword(s):  
New Deal ◽  
Large Scale ◽  
Public Investment ◽  
Climate Science ◽  
Time Frame ◽  
White Paper ◽  
Good News ◽  
Carbon Neutrality ◽  
The One ◽  
In Virtue Of

This white paper lays out the guiding vision behind the Green New Deal Resolution proposed to the U.S. Congress by Representative Alexandria Ocasio-Cortez and Senator Bill Markey in February of 2019. It explains the senses in which the Green New Deal is 'green' on the one hand, and a new 'New Deal' on the other hand. It also 'makes the case' for a shamelessly ambitious, not a low-ball or slow-walked, Green New Deal agenda. At the core of the paper's argument lies the observation that only a true national mobilization on the scale of those associated with the original New Deal and the Second World War will be up to the task of comprehensively revitalizing the nation's economy, justly growing our middle class, and expeditiously achieving carbon-neutrality within the twelve-year time-frame that climate science tells us we have before reaching an environmental 'tipping point.' But this is actually good news, the paper argues. For, paradoxically, an ambitious Green New Deal also will be the most 'affordable' Green New Deal, in virtue of the enormous productivity, widespread prosperity, and attendant public revenue benefits that large-scale public investment will bring. In effect, the Green New Deal will amount to that very transformative stimulus which the nation has awaited since the crash of 2008 and its debt-deflationary sequel.

scholarly journals TO STUDY THE ANTIBACTERIAL ACTIVITY OF VARIOUS EXTRACTS OF CLAUSENA DENTATA (WILLD.) ROEM.

2019 ◽  
pp. 69-73
Author(s):  
ANNAMALAI MADURAM ◽  
RAJU KAMARAJ
Keyword(s):  
Antibacterial Activity ◽  
Tamil Nadu ◽  
Pathogenic Bacteria ◽  
Volatile Oil ◽  
Stem Bark ◽  
Salmonella Typhi ◽  
Chloroform Extract ◽  
Klebsiella Pneumonia ◽  
Human Pathogens ◽  
Human Pathogenic Bacteria

Objectives: The objectives of the study were to study the antibacterial activity for the various extracts of Clausena dentata against human pathogens. Clausena (Rutaceae) is a genus of about 23 species of unarmed trees and shrubs. The stem bark of C. dentata is used in veterinary medicine for the treatment of wounds and sprains. Even though C. dentata has a lot of potential medical uses, the study of microbiological properties is very scarce. Methods: The plant C. dentata was collected from Kadagaman, near Tiruvannamalai, Tamil Nadu, India, and authenticated by Centre for Advanced Study in Botany, University of Madras, Chennai. The dry powder of stem bark was extracted with hexane, chloroform, and methanol. The extracts were subjected to qualitative phytochemical screening and antibacterial activity against human pathogenic bacteria such as Escherichia coli, Salmonella Typhi, Klebsiella pneumonia, Vibrio cholerae, and Staphylococcus aureus and compared with ciprofloxacin. Results: Qualitative chemical tests revealed the presence of various phytochemicals such as alkaloids, glycosides, carbohydrate, proteins and amino acids, phytosterols, and volatile oil. The antibacterial activity result reveals that all the extracts were are more active against V. cholerae. The activity against Pseudomonas aeruginosa was mild. Conclusion: The activity against V. cholerae was comparable with that of 5 μg/mL ciprofloxacin at the concentration of C. dentata 40 μg/mL. The orders of antibacterial activity against human pathogenic bacteria are hexane, methanol, and chloroform extract of C. dentata.

scholarly journals Shape My Face: Registering 3D Face Scans by Surface-to-Surface Translation

2021 ◽  
Author(s):  
Mehdi Bahri ◽  
Eimear O’ Sullivan ◽  
Shunwang Gong ◽  
Feng Liu ◽  
Xiaoming Liu ◽  
...  
Keyword(s):  
Large Scale ◽  
Training Time ◽  
3D Face ◽  
In The Wild ◽  
Previous State ◽  
Surface Translation ◽  
Visual Attention Mechanism ◽  
Diverse Data ◽  
Human Faces ◽  
Robust To Noise

AbstractStandard registration algorithms need to be independently applied to each surface to register, following careful pre-processing and hand-tuning. Recently, learning-based approaches have emerged that reduce the registration of new scans to running inference with a previously-trained model. The potential benefits are multifold: inference is typically orders of magnitude faster than solving a new instance of a difficult optimization problem, deep learning models can be made robust to noise and corruption, and the trained model may be re-used for other tasks, e.g. through transfer learning. In this paper, we cast the registration task as a surface-to-surface translation problem, and design a model to reliably capture the latent geometric information directly from raw 3D face scans. We introduce Shape-My-Face (SMF), a powerful encoder-decoder architecture based on an improved point cloud encoder, a novel visual attention mechanism, graph convolutional decoders with skip connections, and a specialized mouth model that we smoothly integrate with the mesh convolutions. Compared to the previous state-of-the-art learning algorithms for non-rigid registration of face scans, SMF only requires the raw data to be rigidly aligned (with scaling) with a pre-defined face template. Additionally, our model provides topologically-sound meshes with minimal supervision, offers faster training time, has orders of magnitude fewer trainable parameters, is more robust to noise, and can generalize to previously unseen datasets. We extensively evaluate the quality of our registrations on diverse data. We demonstrate the robustness and generalizability of our model with in-the-wild face scans across different modalities, sensor types, and resolutions. Finally, we show that, by learning to register scans, SMF produces a hybrid linear and non-linear morphable model. Manipulation of the latent space of SMF allows for shape generation, and morphing applications such as expression transfer in-the-wild. We train SMF on a dataset of human faces comprising 9 large-scale databases on commodity hardware.

scholarly journals Codon usage bias and environmental adaptation in microbial organisms

2021 ◽  
Author(s):  
Davide Arella ◽  
Maddalena Dilucca ◽  
Andrea Giansanti
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Pathogenic Bacteria ◽  
Large Scale ◽  
Synonymous Codon ◽  
Principal Component ◽  
Gene Copy ◽  
Phenotypic Traits ◽  
Translational Efficiency ◽  
Microbial Organisms

AbstractIn each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism’s lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.

scholarly journals Antimicrobial Activities of Marine Sponge-Associated Bacteria

2021 ◽  
Vol 9 (1) ◽  
pp. 171
Author(s):  
Yitayal S. Anteneh ◽  
Qi Yang ◽  
Melissa H. Brown ◽  
Christopher M. M. Franco
Keyword(s):  
Pathogenic Bacteria ◽  
South Australia ◽  
Multidrug Resistant ◽  
Antimicrobial Activities ◽  
Marine Sponges ◽  
Bioactive Metabolites ◽  
Human Pathogens ◽  
Sponge Associated Bacteria ◽  
Microbial Symbionts ◽  
Bacteria And Fungi

The misuse and overuse of antibiotics have led to the emergence of multidrug-resistant microorganisms, which decreases the chance of treating those infected with existing antibiotics. This resistance calls for the search of new antimicrobials from prolific producers of novel natural products including marine sponges. Many of the novel active compounds reported from sponges have originated from their microbial symbionts. Therefore, this study aims to screen for bioactive metabolites from bacteria isolated from sponges. Twelve sponge samples were collected from South Australian marine environments and grown on seven isolation media under four incubation conditions; a total of 1234 bacterial isolates were obtained. Of these, 169 bacteria were tested in media optimized for production of antimicrobial metabolites and screened against eleven human pathogens. Seventy bacteria were found to be active against at least one test bacterial or fungal pathogen, while 37% of the tested bacteria showed activity against Staphylococcus aureus including methicillin-resistant strains and antifungal activity was produced by 21% the isolates. A potential novel active compound was purified possessing inhibitory activity against S. aureus. Using 16S rRNA, the strain was identified as Streptomyces sp. Our study highlights that the marine sponges of South Australia are a rich source of abundant and diverse bacteria producing metabolites with antimicrobial activities against human pathogenic bacteria and fungi.

The adoption of biometric point-of-sale terminal for payments

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Siti Nurdiyana Atikah Sulaiman ◽  
Mohammad Nabil Almunawar
Keyword(s):  
Technology Acceptance ◽  
Large Scale ◽  
Time Frame ◽  
Ease Of Use ◽  
Perceived Usefulness ◽  
Perceived Ease Of Use ◽  
Content Type ◽  
Point Of Sale ◽  
Scale Point ◽  
Acceptance Model

Purpose The purpose of this paper is to investigate factors that influence customers’ adoption of biometric-based point-of-sale in Brunei. Design/methodology/approach This paper extends technology acceptance model constructs with trust and some other variables as the framework to investigate their influence on the attitude toward the usage of a biometric point-of-sale terminal for payments in Brunei. Nine variables may influence user’s perception toward usage. The nine variables are needed, perceived ease of use, perceived usefulness, experience, innovativeness, privacy, security, trust and attitude toward usage. Multiple regression analysis was conducted to test hypotheses related to these nine variables. Findings It is found that the innovativeness of an individual and similar experience corresponds toward trust, which is positively related to attitude toward usage. Perceived usefulness and trust have significantly influenced the intention of individuals to use biometrics as an authentication method for payment. Research limitations/implications The nature of this research is to gather the public’s opinion and perception as much as it is deemed possible to get a bigger and clearer picture of the study. As the target respondence is citizens and residents of Brunei without any specification or exclusion, a large response would be needed to have a more reliable and accurate result. However, only 205 respondents can be gathered in this study. Had there been a longer time frame, it would be best to gather a lot more responses. Originality/value This paper explores the adoption of biometric authentication in large-scale point-of-terminals. It identifies factors that influence adoption. The results of this study could assist future researchers in which direction to take to further explore biometric as an authentication method for payment. In addition to this, it could also provide banks and financial technology in Brunei a clearer picture of the Brunei market and Bruneians perspective on the biometric system.

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