Feeds:
Posts
Comments

Archive for the ‘DNA’ Category

What role can genetics play in ‘designing’ more sustainable crops, livestock and trees?

Rodolphe Barrangou | National Academy of Engineering | July 1, 2022

Print Friendly, PDF & Email
Plants, animals and microbes can be improved with gene editing. Credit: Carys-ink
Plants, animals and microbes can be improved with gene editing. Credit: Carys-ink

The ability to engineer genomes and tinker with DNA sequences with unprecedented ease, speed, and scale is inspiring breeders of all biological entities. Genome engineers have deployed CRISPR tools in species from viruses and bacteria to plants and trees (whose genome can be 10 times larger than the human genome), including species used in food and agriculture (Zhu et al. 2020).

Follow the latest news and policy debates on agricultural biotech and biomedicine? Subscribe to our newsletter.

SIGN UP

Starting small, bacteria used in food fermentations have had their genomes enhanced to optimize their functional attributes linked to the flavor and texture of fermented dairy products such as yogurt and cheese. The fact that CRISPR-Cas systems provide adaptive immunity against viruses in dairy bacteria led to the commercial launch, more than a decade ago, of bacterial starter cultures with enhanced phage immunity in industrial settings. Most fermented dairy products are now manufactured using CRISPR-enhanced starter cultures. Since then, a variety of bacteria, yeast, and fungi (figure 2) involved in the manufacturing of bioproducts has also been CRISPR enhanced to yield commercial products such as enzymes, detergents, and dietary supplements.

Moving along the farm-to-fork spectrum, most commercial crops—from corn, soy, wheat, and rice to fruits and vegetables—have had their genomes altered (figure 2). Genome engineering is used to increase yield (e.g., meristem size, grain weight) and improve quality (e.g., starch and gluten content), pest resistance (e.g., to bacteria, fungi, viruses), and environmental resilience (e.g., to drought, heat, frost). For instance, nonbrowning mushrooms with extended shelf life can be generated, and tomatoes with increased amounts of gamma aminobutyric acid (GABA) to enhance brain health have been commercialized. In addition, efforts are underway to enhance nutritional value.

Follow the latest news and policy debates on agricultural biotech and biomedicine? Subscribe to our newsletter.

SIGN UP

Credit: NAE

Livestock breeders have joined the fray, with genome engineering of main farm species such as swine (leaner bacon), poultry (CRISPR chicken), and cattle (for both meat and dairy). Swine have also been edited with a viral receptor knockout to prevent porcine reproductive and respiratory syndrome; the approach is being evaluated for regulatory approval (Burkard et al. 2017). Breeding applications include hornless cows (for more humane treatment), resistance to infectious disease (tuberculosis in cattle), and removal of viral sequences in the genome of elite commercial livestock,[1] notably swine. The CRISPR zoo also encompasses genetically diverse species—fish (tiger-puffer and red sea bream), cats (efforts are underway to develop hypoallergenic variants), and even butterflies (wing pattern)—illustrating the ability to deploy this technology broadly.

This is an excerpt. Read the original post here

Read Full Post »

new soil viruses

Scientists discover new soil viruses

by Sarah Wong, Pacific Northwest National Laboratory

seedling
Credit: Unsplash/CC0 Public Domain

Soil is the unsung hero of our lives. It provides nourishment to crops to provide us with food, offers drainage for rainwater into aquifers, and is a habitat for a variety of organisms. On the microscopic level, soil thrives with life, harboring microbes, such as fungi and bacteria that work cooperatively with plants. Despite being such an important part of our lives, not much is known about exactly what exists just below the Earth’s surface.

In new research from Pacific Northwest National Laboratory (PNNL), scientists used bioinformatics and deep sequencing to identify soil viruses and better understand their roles in the Earth. Most of these viruses infect bacteria, and are thus thought to play an important part in maintaining microbial populations.

“Viruses are abundant in nature,” said Janet Jansson, chief scientist for biology and PNNL Laboratory Fellow. “Because there are so many of them in every soil sample, identifying different viruses becomes a challenge.”

Jansson worked with Computational Scientist Ruonan Wu and Earth Scientist and Microbiome Science Team Leader Kirsten Hofmockel in the Biological Sciences Division at PNNL to meet this challenge.

Along with collaborators from Washington State University; Oregon Heath & Science University; Iowa State University; and EMSL, the Environmental Molecular Sciences Laboratory, a Department of Energy Office of Science user facility at PNNL; the PNNL scientists collected soil samples from grasslands in Washington, Iowa, and Kansas and began a deep dive into the soil composition. They leveraged the massive DNA sequencing abilities of the Joint Genome Institute, computing power of the National Energy Research Scientific Computing Center, and multi-omics expertise from EMSL to unearth previously unknown soil viruses. Their results were published in mBio and Communications Biology.

Different viruses for different climates

The scientists chose Washington, Iowa, and Kansas for their soil samples because each location gets a different amount of rainfall. Eastern Washington is much drier compared to Iowa, while Kansas sits in the crossroads between the two in terms of soil moisture.

“We chose to take samples from places with different amounts of soil moisture to see if this made a difference in the types and amounts of viruses there,” said Wu. “Wetter soil contains more bacteria, and many soil viruses infect bacteria.”

The scientists noticed that certain viruses are much more abundant in dry soil than wet soil.

“In drier climates, there tend to be fewer, but more diverse, microbes in the soil,” said Wu. “The relative scarcity of bacterial hosts means that it’s in the virus‘s best interest to keep the host alive.”

The researchers also discovered that in drier soil, viruses were more likely to contain special genes that they could potentially transfer to their bacterial hosts.

“These genes could potentially give their bacterial hosts ‘superpowers'” said Jansson. “These virus genes could be passed to their bacterial hosts to help them survive in dry soils.”

Though more research is necessary to better understand the role of these special viral genes, the possibility that they could be useful to bacteria living in the soil is exciting. These genes could be useful to bacteria by increasing their ability to recycle carbon and thus increase soil health.


Explore further

Distribution of soil bacterial community in surface and deep layers reported along elevational gradient


More information: Ruonan Wu et al, DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes, mBio (2021). DOI: 10.1128/mBio.02595-21

Ruonan Wu et al, Moisture modulates soil reservoirs of active DNA and RNA viruses, Communications Biology (2021). DOI: 10.1038/s42003-021-02514-2

Journal information: Communications Biology  mBio 

Provided by Pacific Northwest National Laboratory 

Read Full Post »

Are Scientists Being Fooled by Bacteria? New Machine Learning Algorithm Reveals the Truth About DNA

TOPICS:CancerDNAGeneticsMachine LearningMount Sinai Health SystemMount Sinai HospitalMount Sinai School Of MedicinePopular

By THE MOUNT SINAI HOSPITAL / MOUNT SINAI SCHOOL OF MEDICINE FEBRUARY 3, 2022

DNA Genetics

Previous studies of a genetic on/off switch may have been confounded by contamination, but Mount Sinai scientists have created a new tool for accurately determining whether it plays a role in human disease.

For decades, a small group of cutting-edge medical researchers have been studying a biochemical, DNA tagging system, which switches genes on or off. Many have studied it in bacteria and now some have seen signs of it in, plants, flies, and even human brain tumors. However, according to a new study by researchers at the Icahn School of Medicine at Mount Sinai, there may be a hitch: much of the evidence of its presence in higher organisms may be due to bacterial contamination, which was difficult to spot using current experimental methods.

To address this, the scientists created a tailor-made gene sequencing method that relies on a new machine learning algorithm to accurately measure the source and levels of tagged DNA. This helped them distinguish bacterial DNA from that of human and other non-bacterial cells. While the results published in Science supported the idea that this system may occur naturally in non-bacterial cells, the levels were much lower than some previous studies reported and were easily skewed by bacterial contamination or current experimental methods. Experiments on human brain cancer cells produced similar results.

“Pushing the boundaries of medical research can be challenging. Sometimes the ideas are so novel that we have to rethink the experimental methods we use to test them out,” said Gang Fang, PhD, Associate Professor of Genetics and Genomic Sciences at Icahn Mount Sinai. “In this study, we developed a new method for effectively measuring this DNA mark in a wide variety of species and cell types. We hope this will help scientists uncover the many roles these processes may play in evolution and human disease.”

Researchers at the Icahn School of Medicine at Mount Sinai developed an advanced method for determining whether cells may use an obscure DNA tagging system for turning genes on or off. Credit: Courtesy of Do lab, Mount Sinai, N.Y., N.Y.

The study focused on DNA adenine methylation, a biochemical reaction which attaches a chemical, called a methyl group, to an adenine, one of the four building block molecules used to construct lengthy DNA strands and encode genes. This can “epigenetically” activate or silence genes without actually altering DNA sequences. For instance, it is known that adenine methylation plays a critical role in how some bacteria defend themselves against viruses.

For decades, scientists thought that adenine methylation strictly happened in bacteria whereas human and other non-bacterial cells relied on the methylation of a different building block—cytosine—to regulate genes. Then, starting around 2015, this view changed. Scientists spotted high levels of adenine methylation in plant, fly, mouse, and human cells, suggesting a wider role for the reaction throughout evolution.

However, the scientists who performed these initial experiments faced difficult trade-offs. Some used techniques that can precisely measure adenine methylation levels from any cell type but do not have the capacity to identify which cell each piece of DNA came from, while others relied on methods that can spot methylation in different cell types but may overestimate reaction levels.

In this study, Dr. Fang’s team developed a method called 6mASCOPE which overcomes these trade-offs. In it, DNA is extracted from a sample of tissue or cells and chopped up into short strands by proteins called enzymes. The strands are placed into microscopic wells and treated with enzymes that make new copies of each strand. An advanced sequencing machine then measures in real time the rate at which each nucleotide building block is added to a new strand. Methylated adenines slightly delay this process. The results are then fed into a machine learning algorithm which the researchers trained to estimate methylation levels from the sequencing data.

“The DNA sequences allowed us to identify which cells—human or bacterial—methylation occurred in while the machine learning model quantified the levels of methylation in each species separately,” said Dr. Fang,

Initial experiments on simple, single-cell organisms, such as green algae, suggested that the 6mASCOPE method was effective in that it could detect differences between two organisms that both had high levels of adenine methylation.

The method also appeared to be effective at quantifying adenine methylation in complex organisms. For example, previous studies had suggested that high levels of methylation may play a role in the early growth of the fruit fly Drosophila melanogaster and of the flowering weed Arabidopsis thaliana. In this study, the researchers found that these high levels of methylation were mostly the result of contaminating bacterial DNA. In reality, the fly and the plant DNA from these experiments only had trace amounts of methylation.

Likewise, experiments on human cells suggested that methylation occurs at very low levels in both healthy and disease conditions. Immune cell DNA obtained from patient blood samples had only trace amounts of methylation.

Similar results were also seen with DNA isolated from glioblastoma brain tumor samples. This result was different than a previous study, which reported much higher levels of adenine methylation in tumor cells. However, as the authors note, more research may be needed to determine how much of this discrepancy may be due to differences in tumor subtypes as well as other potential sources of methylation.

Finally, the researchers found that plasmid DNA, a tool that scientists use regularly to manipulate genes, may be contaminated with high levels of methylation that originated from bacteria, suggesting this DNA could be a source of contamination in future experiments.

“Our results show that the manner in which adenine methylation is measured can have profound effects on the result of an experiment. We do not mean to exclude the possibility that some human tissues or disease subtypes may have highly abundant DNA adenine methylation, but we do hope 6mASCOPE will help scientists fully investigate this issue by excluding the bias from bacterial contamination,” said Dr. Gang. “To help with this we have made the 6mASCOPE analysis software and a detailed operating manual widely available to other researchers.”

Reference: “Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution” by Yimeng Kong, Lei Cao, Gintaras Deikus, Yu Fan, Edward A. Mead, Weiyi Lai, Yizhou Zhang, Raymund Yong, Robert Sebra, Hailin Wang, Xue-Song Zhang and Gang Fang, 3 February 2022, Science.
DOI: 10.1126/science.abe7489

This work was supported by the National Institutes of Health (GM139655, HG011095, AG071291); the Icahn Institute for Genomics and Multiscale Biology; the Irma T. Hirschl/Monique Weill-Caulier Trust; the Nash Family Foundation; and the Department of Scientific Computing at the Icahn School of Medicine at Mount Sinai. Methods validation using Mass Spectrometry was supported by the collaborators at the Chinese Academy of Sciences (XDPB2004) and the National Natural Science Foundation of China (22021003).

We recommend

  1. Most “Pathogenic” Genetic Variants Have a Low Risk of Actually Causing DiseaseMike ONeill, SciTechDaily, 2022
  2. Tangles in DNA Strands Can Help Predict Evolution of MutationsMike ONeill, SciTechDaily, 2021
  3. MIT Researchers Devised a Way To Program Memories Into Bacterial Cells by Rewriting Their DNAMike ONeill, SciTechDaily, 2021
  4. Mount Sinai Scientists: Potentially Serious Side Effect Seen in Patient After ImmunotherapyMike ONeill, SciTechDaily, 2021
  5. New Approach to Gene Therapy: Prime Editing System Inserts Entire Genes in Human CellsMike ONeill, SciTechDaily, 2021
  1. When genome editing goes off-targetHannah R. Kempton et al., Science, 2019
  2. Bacterial DNA MutationsShelby Watford et al., StatPearls, 2020
  3. Autism Sequencing Study Uncovers New Disease-Associated Genes, Functional Cluesstaff reporter, GenomeWeb, 2020
  4. The adenine methylation debateKonstantinos Boulias et al., Science, 2022
  5. Treatment of excessive daytime sleepiness (EDS) or cataplexy in adult patients with narcolepsySponsored by Drugs.com Profes

Read Full Post »

Amplicon technology: a new way to detect tobacco whitefly resistance

Tobacco whitefly (Bemisia tabaci) is a harmful pest distributed globally and can have a serious impact on vegetable production. Its resistance to crop protection is one of the difficulties in practice. Therefore, the detection of the resistance gene mutations can provide an important reference for pest management. However, the individual Bemisia tabaci is small, with a body length of less than 1mm. The traditional single-head sequencing operation is difficult, and often a small amount of gDNA is obtained, but it consumes a lot of time and resources, and new detection methods are urgently needed in scientific research.


© Tomasz Klejdysz | Dreamstime.com 

The Vegetable Pest Research Laboratory has established a method to detect gene mutation frequencies in micro-insects using amplicon technology and detected the frequency of two pyrethroid resistance-related point mutations of sodium ion channel genes in the Bemisia tabaci population. The method is efficient and reliable and solves the problem of detecting gene mutation frequency of micro-insects.

Amplicon sequencing was originally used to detect the community composition of soil, plant, or animal gut microbes, which can be used to analyze the interaction between microbes and animals and plants. The amplicon sequencing method is based on the Next-generation Sequencing technology, which has high sequencing efficiency and can perform centralized detection of a large number of samples.

The team established an efficient approach for detecting the frequency of mutation by amplicon sequencing. The frequencies of L925I and T929V in VGSC associated with pyrethroid resistance were detected in this study, which could provide foundational data for resistance management of B. tabaci.

This research provides an efficient and reliable method for detecting the frequency of gene mutations in micro-insects and is helpful to the development of pest control in the field. The research was published in the entomology professional journal Pest Management Science (impact factor 3.75), Q1 of the Chinese Academy of Sciences. The first author of the thesis is Wei Yiyun, a postdoctoral researcher at the Lab. Associate researcher Wang Ran, Dr. Qu Cheng, and Dr. Guan Fang from Nanjing Agricultural University participated in part of the work. Researcher Luo Chen is the corresponding author of the paper.

Source: https://doi.org/10.1002/ps.6327

Wei, Y., Guan, F., Wang, R., Qu, C. and Luo, C. (2021), Amplicon sequencing detects mutations associated with pyrethroid resistance in Bemisia tabaci (Hemiptera: Aleyrodidae). Pest Manag Sci, 77: 2914-2923. https://doi.org/10.1002/ps.6327 

Publication date: Thu 30 Sep 2021

Read Full Post »

AGWEEK

Silver scurf, caused by a fungus, is a common potato disease and found in all major production areas of the U.S., including the Red River Valley of western Minnesota and northeast North Dakota.(Photo by Andrew Robinson)

Silver scurf: Great name, but bad for spuds

GRAND FORKS, N.D. — Fans of colorful, alliterative language may like “silver scurf.” Not Red River Valley potato growers; they see the crop disease as a growing threat.

“I’m getting more questions about it at harvest,” said Andy Robinson, Fargo, N.D.-based potato extension agronomist for both North Dakota State University and the University of Minnesota.

 He helped to organize potato educational sessions during the recent International Crop Expo in Grand Forks, N.D., and brought in Amanda Gevens to speak on the crop disease on Feb. 22.Gevens, a professor in the plant pathology department at the University of Wisconsin, also is seeing more cases of silver scurf. She described the disease “as gray, silver and shiny patches” that are “more obvious on red and purples,” but seen on yellow and russet potatoes, too.

Silver scurf, caused by a fungus, is a common potato disease and found in all major production areas of the United States, including the Red River Valley of western Minnesota and northeast North Dakota.

 The disease, specific to potato tubers, causes blemishes on spuds. Though the effect is mostly cosmetic, some potatoes affected by the disease have been rejected by industry buyers. Efforts to combat silver scurf are complicated by its close resemblance to black dot, another crop disease. Even Gevens can have trouble distinguishing the two diseases on affected potatoes.

 

“Whodunnit? Is it a silver scurf problem? Or is it a black dot problem,” she said. “It’s hard to tell these apart. Sometimes you can’t tell them apart.”

One important difference: silver scurf is tied to infected seed, while black dot is more of a soil/field debris issue, Gevens said.

 No commercial cultivars resistant to silver scurf are available yet, though work to develop them is underway.

Use of uninfected seed, which can be hard to get, helps to control the disease, as does early harvest and chemical use,

Storage conditions also influence the extent of silver scurf in affected potatoes. “High humidity in storage encourages it,” Gevens said.

Research also shows that smaller storage volumes help to control core temperatures and hold down silver scurf. But limiting storage volumes may not always be feasible, she said.

Read Full Post »

Science Daily

 Linking virus sensing with gene expression, a plant immune system course-corrects
Date:
March 6, 2018
Source:
American Society for Biochemistry and Molecular Biology
 
FULL STORY

Plant immune systems, like those of humans and animals, face a difficult balancing act: they must mount responses against ever-evolving pathogens, but they must not overdo it. Immune responses require energy and resources and often involve plants killing their own infected cells to prevent the pathogens from spreading.

Researchers at Durham University in the UK have identified a crucial link in the process of how plants regulate their antiviral responses. The research is published in the March 2 issue of the Journal of Biological Chemistry.

Martin Cann’s lab at Durham, in collaboration with the laboratories of Aska Goverse at Wageningen University and Frank Takken at the University of Amsterdam, studied a receptor protein called Rx1, which is found in potato plants and detects infection by a virus called potato virus X.

Binding to a protein from the virus activates Rx1 and starts a chain of events that results in the plant mounting an immune response. But the exact sequence of cellular events — and how Rx1 activation was translated into action by the rest of the cell — was unknown.

“Our study revealed an exciting, and unexpected, link between pathogen attack and plant DNA,” Cann said.

Specifically, the study showed that Rx1 joins forces with a protein called Glk1. Glk1 is a transcription factor, meaning it binds to specific regions of DNA and activates genes involved in cell death and other plant immune responses. The team found that when Glk1 bound to virus-activated Rx1, it was able to turn on the appropriate defense genes.

Interestingly, when the viral protein was absent, Rx1 seemed to have the opposite effect — actually keeping Glk1 from binding to DNA. In this way, it prevented an inappropriate immune response.

“The immune response involves reprogramming the entire cell and also often the entire plant,” Cann said. “An important part of this regulatory process is not only allowing activation but also making sure the entire system is switched off in the absence of infection.”

As over a third of the annual potential global crop harvest is lost to pathogens and pests, breeding plants with better immune systems is an important challenge. Understanding how this immune system is regulated at the appropriate level of activity gives the researchers more ideas of points in the immune signaling pathway that could targeted to increase the plant’s baseline ability to resist disease.

“To increase (crop) yield, there is an urgent need for new varieties that are resilient to these stresses,” Cann said. “A mechanistic understanding of how plants resist or overcome pathogen attack is crucial to develop new strategies for crop protection.”

Story Source:

Materials provided by American Society for Biochemistry and Molecular Biology. Note: Content may be edited for style and length.


Journal Reference:

  1. Philip D. Townsend, Christopher H. Dixon, Erik J. Slootweg, Octavina C. A. Sukarta, Ally W. H. Yang, Timothy R. Hughes, Gary J. Sharples, Lars-Olof Pålsson, Frank L. W. Takken, Aska Goverse, Martin J. Cann. The intracellular immune receptor Rx1 regulates the DNA-binding activity of a Golden2-like transcription factor. Journal of Biological Chemistry, 2018; 293 (9): 3218 DOI: 10.1074/jbc.RA117.000485

American Society for Biochemistry and Molecular Biology. “Linking virus sensing with gene expression, a plant immune system course-corrects.” ScienceDaily. ScienceDaily, 6 March 2018. <www.sciencedaily.com/releases/2018/03/180306153726.htm>.

Read Full Post »