For each frequency threshold i , the average number of SNPs per window n i was recorded. If a window showed a number of SNPs with P -value lower than 0. This procedure takes into account that SNPs with lower frequency are more numerous and thus more densely populate the genome, while providing a more conservative approach than simply removing regions with high SNP density regardless of their frequency.
The flagged regions were often shared among samples and annotated as repetitive regions in the reference genome. The remaining SNPs with corresponding frequency were then used to generate the clone size distribution in Fig.
The details on how we combined the SNPs from the different portions of colony 6 are reported in Supplementary Methods.
For the fluorescent marker experiments in budding yeast Fig. cerevisiae strain JRY derived from JRY ref. To grow colonies from single cells, saturated overnight culture was diluted in fresh media and grown for another 4. The resulting culture was diluted in PBS to give about 50 cells per ml.
For the timelapse movie Supplementary Movie 1 , single cells of JRY were inoculated on YPD plates, incubated in a stage-top incubator fitted to a Zeiss AxioZoom microscope and grown overnight.
For Fig. A z -stack was recorded and later combined by maximum intensity projection. Colonies were imaged on a Zeiss AxioZoom v16 upright microscope.
The red and green fluorescent channel were recorded separately, and exposure times were set automatically by the software for each colony and channel. To measure the mutant clone size distribution in the converting budding yeast strain, we used an automated thresholding algorithm with a locally adaptive threshold.
To detect large clones, we removed small object by computing the geodesic opening of the green channel image before binarizing with a locally 50 pixel radius adaptive threshold. For the detection of small bubbles, we computed the top hat transform of the green channel, using a 15 pixel radius disk as the structuring element, which effectively removes large elements from the image.
The resulting image was then segmented using an adaptive threshold in a 15 pixel radius neighbourhood. Finally, the two segmented images were overlaid and eroded by 1 pixel to obtain the final segmentation. In Fig. The imaged budding yeast colonies are not strictly 2D but have a roughly conical shape.
Small clones thus occupy stretched 3D volumes , of which only the projection can be observed under the microscope.
which serves as an upper bound for the case where bubbles are equally extended horizontally as they are vertically. Experimentally, the best fit to the low-frequency regime of the clone size distribution in Fig.
The alignment files obtained from sequencing the E. coli populations are available in the Sequence Read Archive SRA with access code SRP The rest of the data that support the findings of this study are available from the corresponding author upon request.
How to cite this article: Fusco, D. et al. Excess of mutational jackpot events in expanding populations revealed by spatial Luria—Delbrück experiments. Luria, S. Mutations of bacteria from virus sensitivity to virus resistance.
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Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01GM, by a National Science Foundation Career Award and by a Simons Investigator award from the Simons Foundation O.
The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
The library preparation and sequencing was performed by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR and S10RR The simulations were run on the Savio computational cluster resource provided by the Berkeley Research Computing programme.
Department of Physics, University of California, Berkeley, , California, USA. Department of Integrative Biology, University of California, Berkeley, , California, USA. You can also search for this author in PubMed Google Scholar.
and M. designed the study. performed E. coli experiments and analysed the sequencing data. performed S. cerevisiae experiment and image analysis. and J. recorded the time-lapse movie and the confocal images.
wrote and ran the simulations and performed the competitive release experiments. and O. performed the theoretical calculations. interpreted the data and wrote the manuscript.
Correspondence to Oskar Hallatschek. Supplementary Figure , Supplementary Table , Supplementary Note and Supplementary Methods and Supplementary References PDF kb.
Simulations showing the effect of antibiotic on the growth of colonies containing resistant bubbles yellow for three death rates.
Intermediate death rates show minimal growth and containment of resistance, while high death rates result in a large entirely resistant population MOV kb.
This work is licensed under a Creative Commons Attribution 4. Reprints and permissions. Fusco, D. Nat Commun 7 , Download citation. Received : 21 April Accepted : 28 July Published : 03 October Anyone you share the following link with will be able to read this content:.
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Abstract The genetic diversity of growing cellular populations, such as biofilms, solid tumours or developing embryos, is thought to be dominated by rare, exceptionally large mutant clones. High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast Article 13 November Selection in a growing colony biases results of mutation accumulation experiments Article Open access 14 September Mutability of demographic noise in microbial range expansions Article Open access 21 March Introduction One of the hallmarks of spontaneous mutations in growing populations is the emergence of mutational jackpot events—large mutant clones arising from mutations that by chance occur early in the development of a cellular population so that their progenitors benefit from prolonged growth.
Results Generalized Luria—Delbrück experiments To measure the size of mutational jackpot events, we employed population sequencing with low error rates see Methods section , which returned frequencies of new mutations at many genomic sites simultaneously and independently of their phenotypic effect.
Figure 1: Population sequencing reveals an excess of jackpot events in spatially growing populations. Full size image. Figure 2: Visualizing mutational jackpot events in colonies. Figure 3: Simulations of range expansions reproduce the measured distribution of clone sizes.
Figure 4: Fractal properties of clone boundaries control the size distribution of bubbles. Table 1 Predictions for the asymptotic behaviour of the clone size distribution.
Full size table. Figure 5: Gene surfing theory predicts an excess of jackpot events and its consequences. Figure 6: High drug concentration treatments can promote the spreading of resistance by unleashing mutants that are otherwise trapped within the colony bulk by competitive release.
Discussion In combination with a generalization of the Luria—Delbrück theory, our experiments show that the process of allele surfing generates an excess of high-frequency clones: mutations have a much higher chance of being carried by a high proportion of the population.
Methods Scaling of clone size distribution in expanding populations We consider a population expanding from one to N individuals without death. Additional information How to cite this article: Fusco, D.
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Article CAS PubMed Google Scholar Williams, M. Article CAS PubMed PubMed Central Google Scholar Lea, D. Article CAS PubMed Google Scholar Edmonds, C.
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Article PubMed Google Scholar Buttery, N. Article PubMed PubMed Central Google Scholar Nadell, C. Jackery Inc. Sold by. This item is non-returnable This item is non-returnable.
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Visit the Jackery Store. Amazon's Choice highlights highly rated, well-priced products available to ship immediately. Style: Explorer Explorer Solar Generator Purchase options and add-ons. About this item LONG LASTING ENDURANCE: The Explorer portable power station is built with the lithium-ion battery pack, in a safely designed frame structure to maximize, and long last the power for every single use of outdoor adventures and home use.
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Jackery sent me a replacement unit to replace a defective unit. I have built my own testing equipment to check on voltages, wattage and test capacities. This new unit performs just like I expected it to.
The Jackery has a regulated 12v DC output. That is very important, and the main reason for selecting the Jackery. My tester immediately showed that the 12v DC output is working on this unit. I checked the AC output at over W load for 6 minutes with no problem. The USB ports worked fine as well. That is quality and reliability.
I shut it down, and then took it to my garage to test the solar charging, It was connected to two 50W panels and the input varied, but I was able to see a 62W input at one point. I did not observer the input all day, however the unit fully charged by 5 PM when I checked on it.
This is a great unit that performs like I expected it to. It is a great value for the price, and it beats out the competition in the same power class with its regulated 12v DC output. This now gets 5 stars form me. I will continue to test the unit for capacity and efficiency, and I don't expect to be disappointed.
After two months of trying to get a defective unit replaced that has a DC output voltage problem. The DC regulated output did not work, and voltage constantly dropped during use causing failures and errors. This defect caused endless issues with DC devices that rely on a constant 12V.
The Jackery has a regulated 12V DC output, and that is one of the reasons for purchasing it. The Jackery is one of only a few power stations of this size and capacity, to my knowledge, having this feature.
It is very important and shows quality in design and manufacture. Thank you to Jackery for finally reaching out to me, and now trying to resolve the issue. I am raising my rating to 4 stars. This is my last update, as this has gone on too long for me. They did not address my issue at all, only to tell me that the 12V output was regulated.
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Just a tip, these may be great products, but if you have an issue, your left out in the cold. Because this is a battery, there is no returning it.
You get stuck with it as there is no customer service from Jackery either. I will just continue to try. If there are no further posts, consider this to be 1 star, you can imagine why.
If by any luck Jackery contacts me, I will update. As of now, Jackery is dead for me. It wasn't support, as I guess they are all out of town. So I expressed my issue, and it is supposed to be handed off to someone who can help me.
By the way, we did a reset, but my issue still persists. They will contact me at a later time. Let's hope! Meanwhile, I still have a paper weight. Original review 2 stars: I have been having issues with my Jackery that is only 3 weeks old, and have attempted to contact them multiple times with no response at all.
There is a telephone number that gets you absolutely nowhere, email that goes unanswered, and a website that is sparse in information. By the way, Jackery offers a 30 return policy on their products, but not if you order on Amazon.
They only honor the free 30 day returns on their products bought directly from their website. So Amazon customers are treated differently.
Jackery seems not to care about their Amazon customers, and obviously make it too difficult for customers to claim warranty issues. I warn all that want to purchase from Jackery, to reconsider.
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Sort reviews by Top reviews Most recent Top reviews. Top reviews from the United States. There was a problem filtering reviews right now. Please try again later. Style: Explorer Verified Purchase. I've been a car camper most of my life. And, those adventures have usually taken me and friends off road so there's no convenient electricity to power all our devices.
My first solution was to install a Marine Battery in the diamond plate tool box mounted on a cargo carrier inserted in the trailer hitch. Worked beautifully, supplied all the power I needed, but I couldn't take it with me on the trail.
Needing to upgrade my vehicle recently, I decided to see what was available for 'portable' power, for those trips away from my vehicle rather than install the Marine Battery again.
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