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Nature Papers Present Arctic Ocean Metagenomes, Gene Knock-Up in Rice, More

A collection of hundreds of metagenome-assembled bacterial and archaeal genomes from the Arctic Ocean is presented in Nature Microbiology this week. Given the growing pressure of climate change on the Arctic and the importance of microorganisms to the marine food web, a team led by scientists from the Institut de Ciències del Mar in Barcelona applied genome-resolved metagenomics to 41 Arctic seawater samples, collected at various depths in different seasons during a 2013 polar circle expedition, and generated a catalog of 530 metagenome-assembled genomes (MAGs) comprising 526 species. A total of 441 MAGs belonged to previously unreported species, highlighting the limited knowledge of prokaryotic communities in the Arctic Ocean, while 299 of the genomes showed an exclusively polar distribution. The catalog, the researchers write, "will inform our understanding of polar microorganisms that drive global biogeochemical cycles."

A CRISPR-based method for gene knock-up in rice is reported in Nature Plants this week, pointing to new possibilities for the use of the genome-editing technology in agriculture. While CRISPR gene editing is widely used in plant and animal breeding, applications focus largely on knocking down or knocking out genes. Increasing expression of a gene of interest for plant or animal trait improvement can be achieved by inserting donor DNA as a transcriptional or translational enhancer element at desired positions, but a donor-DNA-free approach is an attractive alternative as it would likely simplify regulatory approval. To that end, a group led by investigators from China Agricultural University developed a technique that uses CRISRP-Cas9 to create new genes and traits via large-scale genomic inversion or duplication and demonstrated that the technique could boost herbicide resistance in rice without affecting important agronomic traits. "Our results indicate that the designed [structural variations] are a powerful approach to gene knock-ups and thus may open up an unexplored horizon to plant and animal improvements using CRISPR/Cas tools," the study's authors write.

A multi-omics analysis of two types of motor neurons affected in amyotrophic lateral sclerosis (ALS) is published in Nature Neuroscience this week, revealing aberrant lipid metabolism in the disease. In the study, a Johns Hopkins University-led team applied transcriptomics and metabolomics profiling to human induced pluripotent stem cell-derived spinal motor neurons (sMNs) and ocular motor neurons to identify shared metabolic perturbations in inherited and sporadic forms of ALS. They uncovered dysregulation in various pathways in lipid metabolism and, notably, were able to partially rescue ALS-related phenotypes in human sMNs and animal models of the disease by pharmacologically targeting one of the pathways. "These findings pinpoint a catalytic step of lipid metabolism as a potential therapeutic target for ALS," the researchers write. GenomeWeb has more on this, here.

A method for profiling the expression of transposable elements (TEs) and other full-length molecules in single cells is reported by University of Cambridge scientists in Nature Biotechnology this week. Called single-cell long-read RNA-sequencing, or CELLO-seq, the approach combines long-read single cell RNA-sequencing with computational analyses to measure TE expression at unique loci. The inventors demonstrate CELLO-seq by using it to assess the widespread expression of TEs in two-cell mouse blastomeres, as well as in human induced pluripotent stem cells. "CELLO-seq enables analysis of isoform, allelic, and TE expression at unique loci at single-cell resolution," they write. "Our simulations show that we are able to map autonomous TEs with high specificity at most loci. The potential to study the role of TEs at unique loci — in the same way that we study protein-coding genes — will provide insight into TE biology and the role of TEs in regulating gene expression."