AI for plant breeding in an ever-changing climate

November 14, 2019 | 62 views

How might artificial intelligence (AI) impact agriculture, the food industry, and the field of bioengineering? Dan Jacobson, a research and development staff member in the Biosciences Division at the US Department of Energy's (DOE's) Oak Ridge National Laboratory (ORNL), has a few ideas. For the past 5 years, Jacobson and his team have studied plants to understand the genetic variables and patterns that make them adaptable to changing environments and climates. As a computational biologist, Jacobson uses some of the world's most powerful supercomputers for his work--including the recently decommissioned Cray XK7 Titan and the world's most powerful and smartest supercomputer for open science, the IBM AC922 Summit supercomputer, both located at the Oak Ridge Leadership Computing Facility (OLCF), a DOE Office of Science User Facility at ORNL.

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Cynvenio Biosystems, Inc.

Cynvenio Biosystems, Inc. is a leader in the development of more affordable and clinically actionable precision medicine strategies for the individual cancer patient.

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Top 10 biotech IPOs in 2019

Article | July 16, 2022

The big question at the start of 2019 was whether the IPO window would stay open for biotech companies, particularly those seeking to pull off ever-larger IPOs at increasingly earlier stages of development. The short answer is yes—kind of. Here’s the long answer: In the words of Renaissance Capital, the IPO market had “a mostly good year.” The total number of deals fell to 159 from 192 the year before, but technology and healthcare companies were standout performers. The latter—which include biotech, medtech and diagnostics companies—led the pack, making up 43% of all IPOs in 2019. By Renaissance’s count, seven companies went public at valuations exceeding $1 billion, up from five the year before

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MEDTECH

Cell Out? Lysate-Based Expression an Option for Personalized Meds

Article | July 12, 2022

Cell-free expression (CFE) is the practice of making a protein without using a living cell. In contrast with cell line-based methods, production is achieved using a fluid containing biological components extracted from a cell, i.e., a lysate. CFE offers potential advantages for biopharma according to Philip Probert, PhD, a senior scientist at the Centre for Process Innovation in the U.K.

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MEDTECH

Closing bacterial genomes from the human gut microbiome using long-read sequencing

Article | July 11, 2022

In our lab, we focus on the impact of the gut microbiome on human health and disease. To evaluate this relationship, it’s important to understand the particular functions that different bacteria have. As bacteria are able to exchange, duplicate, and rearrange their genes in ways that directly affect their phenotypes, complete bacterial genomes assembled directly from human samples are essential to understand the strain variation and potential functions of the bacteria we host. Advances in the microbiome space have allowed for the de novo assembly of microbial genomes directly from metagenomes via short-read sequencing, assembly of reads into contigs, and binning of contigs into putative genome drafts. This is advantageous because it allows us to discover microbes without culturing them, directly from human samples and without reference databases. In the past year, there have been a number of tour de force efforts to broadly characterize the human gut microbiota through the creation of such metagenome-assembled genomes (MAGs)[1–4]. These works have produced hundreds of thousands of microbial genomes that vastly increase our understanding of the human gut. However, challenges in the assembly of short reads has limited our ability to correctly assemble repeated genomic elements and place them into genomic context. Thus, existing MAGs are often fragmented and do not include mobile genetic elements, 16S rRNA sequences, and other elements that are repeated or have high identity within and across bacterial genomes.

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Selexis Cell Line Development Strategies

Article | February 11, 2020

In today’s biotechnology landscape, to be competitive, meet regulations, and achieve market demands, “we must apply Bioprocessing 4.0,” said Igor Fisch, PhD, CEO, Selexis. In fact, in the last decade, “Selexis has evolved from cloning by limiting dilution to automated cell selection to nanofluidic chips and from monoclonality assessment by statistical calculation to proprietary bioinformatic analysis,” he added. Single-use processing systems are an expanding part of the biomanufacturing world; as such, they are a major component of Bioprocessing 4.0. “At Selexis, we use single use throughout our cell line development workflow. Currently, we have incorporated single-use automated bioprocessing systems such as ambr® and the Beacon® optofluidic platform for accelerated cell line development. By using these systems and optimizing our parameters, we were able to achieve high titers in shake flasks. Additionally, the Beacon systems integrate miniaturized cell culture with high-throughput liquid handling automation and cell imaging. This allows us to control, adjust, and monitor programs at the same time,” noted Fisch.

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Cynvenio Biosystems, Inc.

Cynvenio Biosystems, Inc. is a leader in the development of more affordable and clinically actionable precision medicine strategies for the individual cancer patient.

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Labiotech.eu | November 07, 2019

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The Pectin Is Protectin’

Technology Networks | October 25, 2019

Aluminum toxicity has long been known to damage plant cells and inhibit the growth of plants. Aluminum is widely found in soils that are too acidic, and as human activities have increased soil acidity across the globe, aluminum toxicity has become a leading cause of low crop yield worldwide. While the effect of aluminum on plants is widely known, precisely how aluminum enters plant cells and causes harm is not well understood. In a new study published in Frontiers in Plant Science, researchers at the University of Tsukuba have found that an integral part of a plant’s cell wall may play a role in protecting rice plants from soil aluminum. The study focused on Oryza sativa, a species of rice widely grown in Asiatic countries. The group took advantage of a mutant strain of the rice called star1 (Sensitive To Aluminum Rhizotoxicity 1). As its name suggests, the mutant is highly sensitive to the toxic effects of aluminum, and its root tips grow very poorly when aluminum is in the soil. The mutant strain allowed the researchers to piece apart how rice plant cells respond, at the molecular level, to aluminum. “Earlier work suggested that the cell wall somehow plays a mechanistic role in aluminum susceptibility, including a possible role by pectin,” says Hiroaki Iwai, lead author of the study. “We focused on pectin because it is a major polysaccharide component of the cell wall, and because prior evidence suggests that the sensitivity of star1 to aluminum might be related to a pectin deficiency.”

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New dairy cattle breeding method increases genetic selection efficiency

phys.org | July 05, 2019

Brazilian scientists at Sao Paulo State University (UNESP) collaborating with colleagues at the University of Maryland and the United States Department of Agriculture (USDA) have developed a dairy cattle breeding method that adds a new parameter to genetic selection and conserves or even improves a population's genetic diversity. The study, which is published in Journal of Dairy Science, was funded by the São Paulo Research Foundation—FAPESP and USDA. Besides genetic value associated with milk, fat and protein yields, the new method also takes into consideration the variance in gametic diversity and what the authors call "relative predicted transmitting ability," defined as an individual animal's capacity to transmit its genetic traits to the next generation based on this variance."Not all progeny of highly productive animals inherit this quality. The new method selects animals that will produce extremely productive offspring," said Daniel Jordan de Abreu Santos, who conducted the study while he was a postdoctoral fellow at UNESP's School of Agricultural and Veterinary Sciences (FCAV) in Jaboticabal, São Paulo State.

Read More

Avantium Builds 10-Ton Demonstration Plant to Produce Bioplastics

Labiotech.eu | November 07, 2019

The Dutch bioplastics company Avantium has opened a demonstration plant capable of producing 10 tons per year of mono-ethylene glycol (MEG), a compound used to make plastics, using plants as the starting material. Construction of Avantium’s plant began at Chemie Park Delfzijl, the Netherlands, last year. The plant will extract carbohydrates from agricultural waste and crops such as sugar beet, and then use a chemical process called hydrogenolysis to turn them into MEG, an essential ingredient in textiles and plastic bottles. This plant will model the manufacturing process and allow early troubleshooting. Avantium aims to have a fully commercial plant up and running by 2024. At present, 99% of MEG comes from the petrochemical industry, which generates high greenhouse gas emissions. Avantium aims to reduce society’s reliance on non-renewable fossil fuels by instead producing the material from crops and unwanted plant waste. The company estimates that its technology could reduce carbon emissions by 70% compared with traditional sources of MEG.

Read More

The Pectin Is Protectin’

Technology Networks | October 25, 2019

Aluminum toxicity has long been known to damage plant cells and inhibit the growth of plants. Aluminum is widely found in soils that are too acidic, and as human activities have increased soil acidity across the globe, aluminum toxicity has become a leading cause of low crop yield worldwide. While the effect of aluminum on plants is widely known, precisely how aluminum enters plant cells and causes harm is not well understood. In a new study published in Frontiers in Plant Science, researchers at the University of Tsukuba have found that an integral part of a plant’s cell wall may play a role in protecting rice plants from soil aluminum. The study focused on Oryza sativa, a species of rice widely grown in Asiatic countries. The group took advantage of a mutant strain of the rice called star1 (Sensitive To Aluminum Rhizotoxicity 1). As its name suggests, the mutant is highly sensitive to the toxic effects of aluminum, and its root tips grow very poorly when aluminum is in the soil. The mutant strain allowed the researchers to piece apart how rice plant cells respond, at the molecular level, to aluminum. “Earlier work suggested that the cell wall somehow plays a mechanistic role in aluminum susceptibility, including a possible role by pectin,” says Hiroaki Iwai, lead author of the study. “We focused on pectin because it is a major polysaccharide component of the cell wall, and because prior evidence suggests that the sensitivity of star1 to aluminum might be related to a pectin deficiency.”

Read More

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phys.org | July 05, 2019

Brazilian scientists at Sao Paulo State University (UNESP) collaborating with colleagues at the University of Maryland and the United States Department of Agriculture (USDA) have developed a dairy cattle breeding method that adds a new parameter to genetic selection and conserves or even improves a population's genetic diversity. The study, which is published in Journal of Dairy Science, was funded by the São Paulo Research Foundation—FAPESP and USDA. Besides genetic value associated with milk, fat and protein yields, the new method also takes into consideration the variance in gametic diversity and what the authors call "relative predicted transmitting ability," defined as an individual animal's capacity to transmit its genetic traits to the next generation based on this variance."Not all progeny of highly productive animals inherit this quality. The new method selects animals that will produce extremely productive offspring," said Daniel Jordan de Abreu Santos, who conducted the study while he was a postdoctoral fellow at UNESP's School of Agricultural and Veterinary Sciences (FCAV) in Jaboticabal, São Paulo State.

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