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Last Updated: 03 September 2022

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Comparative genomics analysis of drought response between obligate CAM and C 3 photosynthesis plants

Through an inverted pattern of day/night stomatal closure and opening for CO 2 assimilation, Crassulacean acid metabolism plants show enhanced drought and heat tolerance in comparison to C 3 and C 4 plants. In K. fedtschenkoi, we found that the expression of CAM-related genes was not influenced by drought stimuli. CAM species and C3 species displayed some common transcriptional changes in genes involved in a variety of biological processes in response to drought, including ABA signaling and biosynthesis of secondary metabolites, according to our comparative analysis.

Source link: https://www.osti.gov/biblio/1883991


Identifying intragenic functional modules of genomic variations associated with cancer phenotypes by learning representation of association networks

Since GWAS is primarily concerned with discovering correlations between individual genomic variations and cancer phenotypes, there are gaps in understanding the mechanisms by which cancer phenotypes are coerced by more than one genomic variation. The results This paper introduces a network representation learning scheme to explore associations among genomic variations among genomic variations using a prostate cancer cohort. The proposed strategy was applied to a prostate cancer registry run by the Veterans Administration's Million Veteran Program to identify candidates for surgical modules associated with early-onset prostate cancer. The proposed approach's reproducibility demonstrated that the proposed strategy would improve the model's robustness in terms of robustness. Conclusions To our knowledge, this is the first attempt to investigate relationships among genomic variations within genes by using a network representation learning approach.

Source link: https://www.osti.gov/biblio/1876318


Precision genome editing in plants using gene targeting and prime editing: existing and emerging strategies

Gene targeting and prime editing are currently the best options for this purpose. In addition, improved prime editing gRNA design, the use of engineered reverse transcriptase enzymes, and splitting prime editing components have all improved prim editing in plants' effectiveness. Plants are reviewed alongside various perspectives on their future and the creation of robust precision genome editing services.

Source link: https://www.osti.gov/biblio/1876324


Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes

Objectives: This research sought to discover the population structure and demographic history of Lentinula edodes, dissect the evolutionary basis of adaptive evolution in L. edodes, and determine if genes related to fruiting body development are involved in adaptive evolution. Methods: In 133 L. edodes strains, we analyzed genomes and fruiting body characteristics, as well as RNA-seq analysis of fruiting body development in the YS69 strain. Results: We found three distinct subgroups of L. edodes by single nucleotide polymorphisms, which demonstrated a robust phenotypic and temperature response differentiation, as well as geographic distribution. In addition, L. edodes cultivars in China may have originated from the region of Northeast China. A total of 364 genes related to fruiting body formation were involved in genetic variation and phenotypic differentiation. Conclusion: The adaptation of L. edodes to the local environment, particularly temperature, resulted in genetic variation and phenotypic differentiation.

Source link: https://www.osti.gov/biblio/1880989


A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes

Antimicrobial resistance is a significant global health issue that affects millions of people each year. Many funding agencies around the world and the international research community have invested considerable money and time investigating AMR's evolution and distribution by isolating and sequencing bacterial strains and performing antimicrobial susceptibility testing. We have been covering these efforts for several years by gathering evidence from the literature and data sources and assembling a set of assembled bacterial genome sequences that are matched to laboratory-derived AST results for the last several years. It also serves as a useful starting point for developing machine learning models for predicting AMR phenotypes in addition to using the data to track AMR evolution and dissemination. Until now, we'll illustrate this by comparing two machine learning algorithms that are designed from the entire dataset to indicate whether predictive power is notably high or low.

Source link: https://www.osti.gov/biblio/1880127


A CRISPR-Cas9–integrase complex generates precise DNA fragments for genome integration

In bacteria, RNA molecules that guide Cas9's development derive from foreign DNA fragments that are captured and integrated into the host CRISPR genomic locus by the Cas1-CRISPR integrase, including foreign DNA fragments. Here, we demonstrate that an integrated integrase supercomplex made up of guide RNA and the proteins Cas1, Cas2, Csn2, and Cas9 provides precisely cut 30-base pair DNA molecules that are required for genome integration. Exonucleolytic DNA trimming is carried out by a procedure that is independent of the guide RNA sequence by the HNH Cas9's active site.

Source link: https://www.osti.gov/biblio/1815949


Genome-resolved metagenomics and metatranscriptomics of microbial communities in three meander-bound floodplain soils along the East River, Colorado.

This collection includes matched environmental and genomic results for soil samples collected across meander-bound floodplains G, L, and Z. 96 soil samples from the 10-25 cm layer were obtained in September 2015, during base flow conditions. In September 2016, three soil samples were collected from ERML, including three samples from a depth just above the water table. TOC + TIC, total inorganic carbon TIC, total nitrogen TN, TOC + TIC, total nitrogen TN, total nitrogen TN, TOC + TIC, total nitrogen TN, TOC + TIC, total nitrogen TN, and TOC:N ratio from 2015 subsamples. 2 Soil chemistry for 2016 subsamples. For each site sampled in 2015, a 4 A spread sheet with elevation, Easting, Northing, and a topographic position index TPI was available. The locations of the 96 soil sampling sites along the East River Watershed Floodplain in Colorado can be seen in a Google Earth file, which can be viewed in Google Earth.

Source link: https://www.osti.gov/biblio/1631979


Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics

A significant challenge in microbial ecology is linking uncultivated microbes' genomic content to their metabolic functions. The genomes of populations enriched in 13 C were recovered by this study, which was published in [13 C]butyrate. Two metagenome-assembled genomes that were significantly rich in heavy [13 C]DNA were discovered by differing abundance analysis of recovered genomic bins from the SIP metagenomes. According to the genus Syntrophomonas, one MAG was assigned to the genus Syntrophomonas and the other MAG to the genus Methanothrix, and the other MAG to the genus Methanothrix. The Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron exchange via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases, according to a morphometric reconstruction of the annotated genomes.

Source link: https://www.osti.gov/biblio/1626172

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions