Daily Archives: February 24, 2022

The projects administrative office is located at the UC Davis Genome Center, and it will seek to sequence the genomes of 1.8 million species over the course of 10 years

By SONORA SLATER science@theaggie.org

It took 13 years and three billion dollars to sequence the human genome but over the next 10 years, the Earth BioGenome Project (EBP) plans to sequence the genome of every other known eukaryotic organism on earth for a fraction of the comparative cost.

EBP was launched in November 2018, and is now entering a new phase, as it shifts from pilot projects to beginning the full-scale sequencing of the 1.8 million named plants, animals and fungi that make up Earths eukaryotes, according to a recent press release. The information will then be made available in the form of an open-access digital library.

The projects administrative office is located at the UC Davis Genome Center, and Harris Lewin, a distinguished professor in the Department of Evolution and Ecology at UC Davis, acts as the chair of the EBP Working Group. Lewin also co-authored four papers that were included in a 10-part special feature published in Proceedings of the National Academy of Sciences on Jan. 17 that describe the projects goals, challenges and future plans.

This set of papers, the special feature, represents sort of a series of milestones of where we are, or even where we were one year ago when we started putting these papers together, Lewin said. It is a representation of the work that includes 43 institutions around the world.

The papers include information about why the project matters, ethical, social and legal challenges that the project has faced, how the genome library will contribute to the conservation of endangered species and reflection on how credit will be attributed, according to Lewin.

There [are] a lot of ethical issues around [] how the benefits accrue, Lewin said. Lets say theres Indigenous knowledge about the medicinal properties of a plant. [] how would the benefits be shared with those peoples who might have shared the basic information pointing toward the medicinal qualities of the plant?

Jacob Sherkow, a professor of law at the University of Illinois, is the lead author of a paper for the special feature that detailed ethical, legal and social issues in the Earth BioGenome Project. He talked about one of the challenges detailed in the paper.

The library is going to be open-access, and open-access usually means free, Sherkow said. But we also have to make sure that were compensating countries for their work sequencing genomes. What weve learned in the last 20 years is that the value of genetic data is improved the more that its shared, [] so even though its a very complex and difficult issue, its worth solving, and I believe that the EBP will find a solution to allow open-access.

Carolyn Hogg, the science lead for the Threatened Species Initiative in Australia and the lead author of the EBP paper investigating how genomic resources can empower conservation action, described how the genomic work theyre doing is especially important when it comes to endangered species.

Some of our animals are technically extinct in the wild, theyre only found in captivity, Hogg said. So the value of those samples is exceedingly high. And the sequencing guys have one chance to get it right. If somebody makes a misstep, theres no other opportunity to get more samples.

Katherine Belov, a professor of comparative genomics at the University of Sydney and one of the co-authors of the same paper, elaborated on the value of gaining genomic information on endangered species.

In the worst case the project will provide us with a blueprint of the genetic diversity that existed in species that are now extinct, Belov said via email. I hope it wont come to that. In the best case, we will find ways to use the EBP genomes to better lobby for conservation of species that are at risk of extinction. Having their genome sequence wont save them only preservation of habitats will. But genomes provide information [that can] directly inform economically sound management decisions using scarce conservation dollars.

This kind of translation from information to action is being incorporated into the goals of the EBP, as they build partnerships between academia and those who work in policy and management spaces, according to Belov.

The critical step that cannot be forgotten is the importance of empowering conservation managers to be able to use this data to manage animals on the ground, Belov said via email. Otherwise, the data just sits in the cloud and gathers dust.

The benefits of the EBP arent only given to those species being sequenced for the first time. There are also direct benefits to humans, as it relates to agriculture, human health, renewable energy technologies in the form of biofuels and more, according to Hogg.

Genomes are an exceedingly powerful tool, Hogg said. If you think about human medicine, we published the human genome back in 2001. Think about the changes in human medicine back in 2001 versus now we can do targeted cancer therapy, work against Alzheimers.

Hogg said that the foundation of most pharmaceuticals such as Advil is found in nature, from plants with medicinal qualities or the venom of certain animals, before theyre synthesized and made more active. Additionally, the productivity and the type of food available in supermarkets is also dependent on biodiversity.

People [need] to understand that losing biodiversity is not just losing the nice stuff in the forests, Hogg said. Its all interrelated. Its not just a bunch of scientists trying to shoot for the moon.

Elaborating on the moon analogy, Hogg referenced a photograph called Earthrise taken in 1968 by Bill Anders from Apollo 8.

Its been declared as one of the most environmentally significant photos of all time, because it was the first time we saw our planet from space, Hogg said. So part of what Harris and the people who set up Earth BioGenome wanted to do is a moonshot. This is the next greatest moonshot.

Lewin offered some final thoughts on what the impact of this moonshot could be.

This is going to be the basis of advances in agriculture, in human health, in animal health, in environmental health and how climate change influences biodiversity, Lewin said. Having this knowledge is going to give us the fundamental scientific knowledge to make further advances and decisions and develop policies that are going to be effective in dealing with the major problems that are facing the world today.

EBP has been built on collaboration, with work being done in 22 countries on every continent except Antarctica. Hogg explained how essential she believes this is to the projects hopeful success.

I think the global challenges we face today are unsolvable by any one person, or any one research group, or any one university, Hogg said. I think we will only be able to address the challenges that we face as a species and that the planet faces by working collaboratively and cooperatively. So I think that EBP really is a testament to what can be achieved when everyone comes to the table with the same mindset of what is for the greater good.

Written by: Sonora Slater science@theaggie.org

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Earth BioGenome Project plans to sequence genome of every known eukaryotic organism - The Aggie - The Aggie

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The genome editing market is projected to reach US$ 16,986. 69 million by 2028 from US$ 5,199. 40 million in 2021; it is expected to grow at a CAGR of 18. 4% from 2021 to 2028. Over the past few years, advances in genome editing technologies have been making constant headlines.

New York, Feb. 22, 2022 (GLOBE NEWSWIRE) -- Reportlinker.com announces the release of the report "Genome Editing Market Forecast to 2028 - COVID-19 Impact and Global Analysis By Technology, Application, and End User" - https://www.reportlinker.com/p06232553/?utm_source=GNW Genome editing technologies can alter biological research and significantly impact human health, food security, and environmental sustainability since they are precise, relatively inexpensive, easy to use, and remarkably powerful.

The advances in genome editing can be traced back to quiet beginnings in the 1990s.The introduction of CRISPR-Cas9a genome-editing tool that can be used to make precise and targeted changes in the DNA sequence with easeis mainly responsible for the recent rise in the amount and scope of applications of genome editing technologies.

The CRISPR platforms ease of use, as compared to previous technologies, has resulted in its widespread adoption and application. Genome editing could have a favorable impact on sustainable development, environmental management, food security, and the introduction of affordable diagnostics and therapies for various diseases due to these advancements.

A team from MIT and Harvards Broad Institute has developed a novel CRISPR genome-editing technique that has the potential to fix up to 89% of disease-causing genetic abnormalities.CRISPR-Cas9 and reverse transcriptase, two of the most significant proteins in molecular biology, have been merged into a single machine by researchers.

Prime editing is a method that can alter human cells directly in a precise, efficient, and highly versatile manner.They have also developed a CRISPR RNA-cutting enzyme into an antiviral agent that can be programmed to detect and eliminate RNA-based viruses in human cells.

The Cas13 enzyme has previously been used to cut and alter human RNA and as a diagnostic approach for detecting the presence of viruses, bacteria, and other targets. This is one of the first studies to use Cas13, or any CRISPR system, as an antiviral in human cells in culture.

Recognizing the potential of genome editing techniques for studying and manipulating the genome., the Department of Biotechnology (DBT), Govt. of India has been fostering research and innovation in genome engineering technologies and applications to make them more accessible and inexpensive for research and development ( R&D). Through focused calls for proposals in different areas such as the development of new methods, tools, processes, and platforms for genome editing, improvement of existing genome-editing methods, and novel applications of genome editing technologies in agriculture, bioenergy, environmental research, and human health, efforts have been made to encourage R&D programs in emerging genome engineering technologies and their applications.

World Health Organization (WHO), Centers for Disease Control and Prevention (CDC), and National Health and Wellness Centers for Medicare and Medicaid Services (CMS), Federal Trade Commission (FTC) are among the primary and secondary sources referred to while preparing the report on the genome editing market.Read the full report: https://www.reportlinker.com/p06232553/?utm_source=GNW

About ReportlinkerReportLinker is an award-winning market research solution. Reportlinker finds and organizes the latest industry data so you get all the market research you need - instantly, in one place.

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Genome Editing Market Forecast to 2028 - COVID-19 Impact and Global Analysis By Technology, Application, and End User - Yahoo Finance

Genome Sequencing Marketresearch report can be primarily categorized into four major areas which are market definition, market segmentation, competitive analysis, and research methodology. Each of these topics is carefully researched and analyzed in detail for framing a comprehensive market research report. The report carries out the studies about the market with respect to general market conditions, market status, market improvement, key developments, cost and profit of the specified market regions, position, and comparative pricing between major players. The report seems to offer a thorough synopsis on the study, analysis, and estimation of the market and how it is affecting This industry. It also provides statistics on the current state of the industry and hence acts as an important source of guidance and direction for companies and investors interested in this market.

The genome sequencing market is expected to gain market growth in the forecast period of 2021 to 2028. Data Bridge Market Research analyses that the market is growing with the CAGR of 15.73% in the forecast period of 2021 to 2028 and is estimated to reach 41,151.61 USD million by 2028. The growing of the prevalence of the cancer will help in escalating the growth of the genome sequencing market.

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Genome sequencing is the procedure of mapping and sequencing of the unique DNA of a person. Genome signifies the entire blueprint of a persons human body. Genome sequencing aids to identify any important differences in the genes, which are a bundle of DNA, in a persons body which can cause a disease or upsurge the likelihood of a disease.

Segmentation:

Global Genome Sequencing MarketBy Product (Consumables, Systems & Software, Services), Technology (PCR, Sequencing, Microarray, Nucleic Acid Extraction & Purification, Others), Application (Diagnostics, Drug Discovery & Development, Precision Medicine, Agriculture & Animal Research, Others), End-User (Research Centers, Academic & Government Institutes, Hospitals & Clinics, Pharmaceutical & Biotechnology Companies, Others), Geography (North America, South America, Europe, Asia-Pacific, Middle East And Africa) Industry Trends & Forecast to 2026

List of Top Key Vendors:

The major players covered in the genome sequencing market report are Thermo Fisher Scientific, Illumina, Inc., QIAGEN, Eurofins Scientific, Agilent Technologies, Inc., Oxford Nanopore Technologies., F. Hoffmann-La Roche Ltd, Bio-Rad Laboratories, Inc., BGI, Danaher., General Electric Company, Eppendorf AG, Abbott, LI-COR, Inc., Siemens, PerkinElmer Inc., Macrogen Inc., DNASTAR, Geneious, Myriad Genetics, Inc., GATC Biotech, Biomatters, New England Biolabs, among other domestic and global players. Market share data is available for global, North America, Europe, Asia-Pacific (APAC), Middle East and Africa (MEA) and South America separately. DBMR analysts understand competitive strengths and provide competitive analysis for each competitor separately.

Complete Report is Available (Including Full TOC, List of Tables & Figures, Graphs, and Chart) @https://www.databridgemarketresearch.com/toc/?dbmr=global-genome-sequencing-market&shrikesh

The genome sequencing market is segmented on the basis of product, technology, application and end user. The growth amongst these segments will help you analyse meagre growth segments in the industries, and provide the users with valuable market overview and market insights to help them in making strategic decisions for identification of core market applications.

The genome sequencing market is analysed and market size insights and trends are provided by country, product, technology, application and end user as referenced above.

The countries covered in the genome sequencing market report are the U.S., Canada and Mexico in North America, Germany, France, U.K., Netherlands, Switzerland, Belgium, Russia, Italy, Spain, Turkey, Rest of Europe in Europe, China, Japan, India, South Korea, Singapore, Malaysia, Australia, Thailand, Indonesia, Philippines, Rest of Asia-Pacific (APAC) in the Asia-Pacific (APAC), Saudi Arabia, U.A.E, South Africa, Egypt, Israel, Rest of Middle East and Africa (MEA) as a part of Middle East and Africa (MEA), Brazil, Argentina and Rest of South America as part of South America.

North America dominates the genome sequencing market because of the nonstop technological advancements by the key players. Furthermore, the high investment in research and development, and the accessibility of scientifically developed of healthcare infrastructure which will boost the growth of the genome sequencing market in the region during the forecast period. Asia Pacific is projected to observe significant amount of growth in the genome sequencing market because of the calculated initiatives undertaken by the international firms to extend their occurrence because of the high customer base.

Provided for Major Regions as Follows:

Some Point of Table of Content:

Table of Content:

Chapter 1: Market Overview

Chapter 1.1: Study Assumptions

Chapter 1.2: Scope of the Study

Chapter 2: Market Economic Impact

Chapter 2.1: Analysis Methodology

Chapter 2.2: Research Phases

Chapter 3: Competition by Manufacturers

Chapter 3.1: Current Market Scenario

Chapter 3.2: Value Chain/Supply Chain Analysis

Chapter 3.3: Government Regulations and Initiatives

Chapter 4: Production, Revenue (Value) by Region

Chapter 5: Supply (Production), Consumption, Export, Import by Regions

Chapter 5.1: Market Drivers

Chapter 5.2: Market Restraints/Challenges

Chapter 5.3: Market Opportunities

Chapter 6: Production, Revenue (Value), Price Trend by Type

Chapter 7: Market Analysis by Application

Chapter 8: Market by Manufacturing Cost Analysis

Chapter 9: Industrial Chain, Sourcing Strategy and Downstream Buyers

Chapter 10: Marketing Strategy Analysis, Distributors/Traders

Chapter 11: Market Geographic Analyses

Chapter 12: Market Effect Factors Analysis

Highlights of this Study Market Research Report:1. To strategically profile key players and comprehensively analyze their market position in terms of ranking and core competencies, and detail the competitive landscape for market leaders2. To describe and forecast the market, in terms of value, for various segments, by region North America, Europe, Asia Pacific (APAC), and Rest of the World (RoW)3. Key parameters which are driving this market and restraining its growth4. What all challenges manufacturers will face as well as new opportunities and threats faced by them.5. Learn about the market strategies that are being adopted by your competitors and leading organizations

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Original post:
Genome Sequencing Market Size, Share, Application Analysis, Regional Outlook, Growth Trends, Key Players, Competitive Strategies and Forecasts to 2028...

Recently, scientists from the University of Tsukubadevelopeda novel CRISPR/Cas9-based genome-editing tool called Target activation-induced cytidine deaminase (Target-AID). They targeted SlDELLAand SlETRin the model tomato cultivar Micro-Tom and in commercial tomato cultivars to confirm and extend the applicability of the Target-AID genome-editing system. After confirming that nucleotide substitutions were induced by the Target-AID system, mutants that showed high GA sensitivity in both Micro-Tom and the commercial cultivars were isolated. Nucleotide substitution was also successfully induced by multi-targeting with a single sgRNA and multi-targeting with multiple sgRNAs in a single vector. In addition, the Target-AID system also produced a Target-AID-specific pattern of indelswith editing positions different from those of Cas9 vectors.

We demonstrate that the Target-AID system could efficiently edit sgRNA-targeting sites and facilitate a case study on the application of base-editing technology to translational research that aims at the commercialization of genome-edited crops, Prof Ezura said. These results demonstrated that the Target-AID genome-editing system is a promising tool for molecular breeding in tomato crops,highlighting the scientific and agricultural potential of the combined use of Target-AID with other base-editing systems.

###

Reference

Authors

Sachiko Kashojiya1,2,, Yu Lu1,2,, Mariko Takayama1, Hiroki Komatsu1, Luyen Hieu Thi Minh1, Keiji Nishida3,4, Kenta Shirasawa5, Kenji Miura1,Satoko Nonaka1, Jun-ichiroMasuda1,6, Akihiko Kondo3,4, Hiroshi Ezura1,7,* and Tohru Ariizumi1,7,*

Affiliations

1Faculty of Life and Environmental Sciences, University of Tsukuba, Gene Research Center, Tsukuba, Ibaraki 305-8572, Japan

2Japan Society for Promotion of Science, 5-3-1, Kojimachi, Tokyo 102-0083, Japan

3Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo 657-8501, Japan

4Engineering Biology Research Center, Kobe University, 7-1-49, Minatojima Minami Machi, Chuo-ku, Kobe 650-0047, Japan

5Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan

6Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan

7Tsukuba Plant Innovation Research Center, University of Tsukuba, Ibaraki 305-8572, Japan

About Dr.Hiroshi Ezura and Dr. Tohru Ariizumi

Dr. Hiroshi Ezura is a professor in the Faculty of Life and Environmental Sciencesatthe University of TsukubainJapan, as well as the director of the Plant Innovation Research Center at the University of Tsukuba. Prof. Ezura received his Ph.D. from Hokkaido Universityin 1993andhas been working at the University of Tsukuba since 2005. Prof. Ezura is amember of the Japanese Science Committee and has served as the chairman of the Japanese Society for Plant Cell and Molecular Biology. He is mainly engaged in research on the functional genomics and genetic breeding of Solanaceae and Cucurbitaceae vegetable crops.His group used gene-editing technology to breed the first Japanesetomato varietywithbloodpressurelowering effects. Prof. Ezurahas published numerous papers in Nature Biotechnology,Plant Cell, New Phytologist, Plant Physiology, Plant Journal, and other journals.

Dr.Tohru Ariizumigraduated from the Faculty of Agriculture, Tohoku University, completed the applied life science course at the Graduate School of Agriculture, University of Tokyo in 2004, and became a Doctor of Agriculture (Tohoku University). He was an assistant professor at Washington State Universityand becamean assistant professor at the Graduate School of Life and Environmental Sciences at Tsukuba University in 2015.

Not applicable

Modification of tomato breeding traits and plant hormone signaling by Target-AID, the genome-editing system inducing efficient nucleotide substitution

28-Jan-2022

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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Modification of tomato breeding traits and plant hormone signaling by Target-AID, the genome-editing system inducing efficient nucleotide substitution...

MarketsandResearch.biz releases a Global Whole Genome and Exome Sequencing Market from 2021 to 2027 research report that examines the industry and significant market trends, as well as historical and forecasted market statistics. The research includes a market overview, as well as definitions and applications. In terms of volume and value, the market is divided by application, type, and geography.

The design of a research is selected to highlight possible trends and opportunities in the global Whole Genome and Exome Sequencing market over the next several years. Several drivers and obstacles, opportunities, and issues will indeed be explored during the predicted time period, according to the market analysis.

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In addition, the study looks at market regional patterns that might affect growth from 2021 to 2027. The study assists in the discovery of new marketing possibilities and offers a complete picture of the global Whole Genome and Exome Sequencing market.

The following manufacturers are represented on the international market:

Market segmentation based on application:

Both the market and the product category are segmented:

Geographical division of the market:

The findings of the survey are provided in the next chapter of the report. Our analysts supply all of the data that customers require to build long-term strategic growth strategies and policies. In order to properly assess and give expert insights to financial backers on worldwide Whole Genome and Exome Sequencing market trends, the analyst conducts a thorough analysis of size of the market, distribution, trends, and overall revenue.

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Global Whole Genome and Exome Sequencing Market 2021 Industry Demand, Growth Opportunities, Future Trends, Key Players, and Forecast to 2027 ZNews...

Japanese researchers said they pinpointed the causes of previously undetected diseases among small children through genome analysis in half of the cases they examined.

Team members, primarilyfrom Keio University in Tokyo, said courses of testing and therapy improved in half of the cause-identified instances. Looking into the complete set of genes proved to be the key for correct diagnoses and treatment of newborns suffering from serious disorders, they added.

We want to help protect infants, who are in the most vulnerable position in society, through the latest technological advances in genome analysis, said Toshiki Takenouchi, a full-time lecturer of pediatrics at Keio University, who is a member of the team.

The study involved 17 perinatal medical centers in eight prefectures.

Blood samples underwent genome analysis for 85 seriously ill infants hospitalized in neonatal intensive care units from April 2019 through March 2021 whose cause of symptoms went undetected.

The findingsshowed that 41 of the newborns suffered from a hereditary condition. While humankinds genetic code in DNA consists of 3 billion base pairs represented by the letters A, T, G and C, only one or two of the characters were replaced to result in the onset of symptoms in most cases.

The genetic anomalies not only emanated from the parents themselves but alsoemerged in the newborns via mutations in many instances, team members said.

Genome analysis saved 20 of the 41 children theordeal of undergoing onerous biopsies that collect muscle or skin samplesfor analysis. This also led to more effective therapeutic methods, including theuse of drugs more suited to eliminating individual health problems.

The research findings were published in the specialized pediatrics magazine Journal of Pediatrics at (https://www.jpeds.com/article/S0022-3476(22)00064-6/fulltext).

Link:
Gene analysis proves key to treating seriously ill newborns | The Asahi Shimbun: Breaking News, Japan News and Analysis - Asahi Shimbun

This article was originally published here

Oncogene. 2022 Feb 22. doi: 10.1038/s41388-022-02235-8. Online ahead of print.

ABSTRACT

Limited understanding of bladder cancer aetiopathology hampers progress in reducing incidence. Mutational signatures show the anti-viral apolipoprotein B mRNA editing enzyme catalytic polypeptide (APOBEC) enzymes are responsible for the preponderance of mutations in bladder tumour genomes, but no causative viral agent has been identified. BK polyomavirus (BKPyV) is a common childhood infection that remains latent in the adult kidney, where reactivation leads to viruria. This study provides missing mechanistic evidence linking reactivated BKPyV-infection to bladder cancer risk. We used a mitotically-quiescent, functionally-differentiated model of normal human urothelium to examine BKPyV-infection. BKPyV-infection led to significantly elevated APOBEC3A and APOBEC3B protein, increased deaminase activity and greater numbers of apurinic/apyrimidinic sites in the host urothelial genome. BKPyV Large T antigen (LT-Ag) stimulated re-entry from G0 into the cell cycle through inhibition of retinoblastoma protein and activation of EZH2, E2F1 and FOXM1, with cells arresting in G2. The single-stranded DNA displacement loops formed in urothelial cells during BKPyV-infection interacted with LT-Ag to provide a substrate for APOBEC3-activity. Addition of interferon gamma (IFN) to infected urothelium suppressed expression of the viral genome. These results support reactivated BKPyV infections in adults as a risk factor for bladder cancer in immune-insufficient populations.

PMID:35194151 | DOI:10.1038/s41388-022-02235-8

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Induction of APOBEC3-mediated genomic damage in urothelium implicates BK polyomavirus (BKPyV) as a hit-and-run driver for bladder cancer - DocWire...