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BULLETIN 1
Novel Method Detects Early Signs of Genetic Mutations
Researchers from New York University Langone Health developed a new method that can detect molecular changes in DNA before they become permanent mutations.
Most mutations originate in DNA changes that are found in only one DNA strand. These changes are the result of a DNA strand that is incorrectly copied during replication or when a strand is damaged due to heat or chemicals in the body. Unfortunately, single-strand changes cannot be identified using existing testing methods.
To address the issue, scientists from NYU Langone Health produced the Hairpin Duplex Enhanced Fidelity Sequencing (HiDEF-seq) technique. This novel method accurately detects double-strand mutations and identifies DNA changes in single strands before they turn into permanent double-strand mutations. Their research may help boost understanding of the causes of mutations and how genetic changes occur in cells as people get older.
For more information, read the press release of NYU Langone Health.
See https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=20865
Most mutations originate in DNA changes that are found in only one DNA strand. These changes are the result of a DNA strand that is incorrectly copied during replication or when a strand is damaged due to heat or chemicals in the body. Unfortunately, single-strand changes cannot be identified using existing testing methods.
To address the issue, scientists from NYU Langone Health produced the Hairpin Duplex Enhanced Fidelity Sequencing (HiDEF-seq) technique. This novel method accurately detects double-strand mutations and identifies DNA changes in single strands before they turn into permanent double-strand mutations. Their research may help boost understanding of the causes of mutations and how genetic changes occur in cells as people get older.
For more information, read the press release of NYU Langone Health.
See https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=20865
BULLETIN 2
MIT Researchers Develop Amber-Like Polymer for DNA Storage
MIT Researchers Develop Amber-Like Polymer for DNA Storage
Figure: Photo Source: MIT News
Scientists from the Massachusetts Institute of Technology (MIT) produced a novel method to store DNA in a new type of polymer. Their creation can fit the entire human genome and may store digital information on DNA.
Current methods of DNA storage require freezing temperatures, which are not feasible in other parts of the world. Those methods also consume a large amount of energy, which make them expensive and unscalable.
To address the DNA storage concerns, the MIT researchers developed Thermoset-REinforced Xeropreservation (T-REX) method. This technique stores DNA in a glassy, amber-like polymer at room temperature and protects DNA from heat and water damage. Their study also showed that the DNA can be retrieved from the polymer without any damage. The method only takes a few hours but can be shortened upon optimization.
The researchers are now working on improving the technology to form capsules for long-term storage. In the future, the technology may be used to preserve genomes for personalized medicine. The stored genomes may also undergo further analysis to better understand how they are related to disease.
Read the MIT press release for more information.
See https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=20864
Scientists from the Massachusetts Institute of Technology (MIT) produced a novel method to store DNA in a new type of polymer. Their creation can fit the entire human genome and may store digital information on DNA.
Current methods of DNA storage require freezing temperatures, which are not feasible in other parts of the world. Those methods also consume a large amount of energy, which make them expensive and unscalable.
To address the DNA storage concerns, the MIT researchers developed Thermoset-REinforced Xeropreservation (T-REX) method. This technique stores DNA in a glassy, amber-like polymer at room temperature and protects DNA from heat and water damage. Their study also showed that the DNA can be retrieved from the polymer without any damage. The method only takes a few hours but can be shortened upon optimization.
The researchers are now working on improving the technology to form capsules for long-term storage. In the future, the technology may be used to preserve genomes for personalized medicine. The stored genomes may also undergo further analysis to better understand how they are related to disease.
Read the MIT press release for more information.
See https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=20864
BULLETIN 3
The complex polyploid genome architecture of sugarcane
The complex polyploid genome architecture of sugarcane
A L Healey, O Garsmeur, J T Lovell, S Shengquiang, A Sreedasyam, J Jenkins, C B Plott, N Piperidis, N Pompidor, V Llaca, C J Metcalfe, J Doležel, P Cápal, J W Carlson, J Y Hoarau, C Hervouet, C Zini, A Dievart, A Lipzen, M Williams, L B Boston, J Webber, K Keymanesh, S Tejomurthula, S Rajasekar, R Suchecki, A Furtado, G May, P Parakkal, B A Simmons, K Barry, R J Henry, J Grimwood, K S Aitken, J Schmutz, A D'Hont
Nature; 2024 Apr; 628(8009):804-810. doi: 10.1038/s41586-024-07231-4.
Abstract
Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.
See https://pubmed.ncbi.nlm.nih.gov/38538783/
Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.
See https://pubmed.ncbi.nlm.nih.gov/38538783/
Fig.
Bru1 candidate gene locus.
a, Brown rust disease resistance in R570. Top panel shows selfed R570 offspring with the Bru1 locus, while the bottom panel shows offspring lacking Bru1. b, Gap-filled haplotype assembly identifies a TKP as candidate causal genes for Bru1 durable brown rust resistance. Blue pentagons represent curated gene models and grey pentagons are large transposable elements. Bru1 TKP7 and TKP8 candidate genes are indicated in red with their location on Chr. 3D.
Bru1 candidate gene locus.
a, Brown rust disease resistance in R570. Top panel shows selfed R570 offspring with the Bru1 locus, while the bottom panel shows offspring lacking Bru1. b, Gap-filled haplotype assembly identifies a TKP as candidate causal genes for Bru1 durable brown rust resistance. Blue pentagons represent curated gene models and grey pentagons are large transposable elements. Bru1 TKP7 and TKP8 candidate genes are indicated in red with their location on Chr. 3D.
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