DAF-16 and SMK-1 Contribute to Innate Immunity During Adulthood in Caenorhabditis elegans
Aging is accompanied by a progressive decline in immune function termed "immunosenescence". Deficient surveillance coupled with the impaired function of immune cells compromises host defense in older animals. The dynamic activity of regulatory modules that control immunity appears to underlie age-dependent modifications to the immune system. In the roundworm Caenorhabditis elegans levels of PMK-1 p38 MAP kinase diminish over time, reducing the expression of immune effectors that clear bacterial pathogens. Along with the PMK-1 pathway, innate immunity in C. elegans is regulated by the insulin signaling pathway. Here we aske...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: McHugh, D. R., Koumis, E., Jacob, P., Goldfarb, J., Schlaubitz-Garcia, M., Bennani, S., Regan, P., Patel, P., Youngman, M. J. Tags: Investigations Source Type: research
Species-Specific Duplication Event Associated with Elevated Levels of Nonstructural Carbohydrates in Sorghum bicolor
Simple sugars are the essential foundation to plant life, and thus, their production, utilization, and storage are highly regulated processes with many complex genetic controls. Despite their importance, many of the genetic and biochemical mechanisms remain unknown or uncharacterized. Sorghum, a highly productive, diverse C4 grass important for both industrial and subsistence agricultural systems, has considerable phenotypic diversity in the accumulation of nonstructural sugars in the stem. We use this crop species to examine the genetic controls of high levels of sugar accumulation, identify genetic mechanisms for the acc...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Brenton, Z. W., Juengst, B. T., Cooper, E. A., Myers, M. T., Jordan, K. E., Dale, S. M., Glaubitz, J. C., Wang, X., Boyles, R. E., Connolly, E. L., Kresovich, S. Tags: Investigations Source Type: research
The UCSF Mouse Inventory Database Application, an Open Source Web App for Sharing Mutant Mice Within a Research Community
The UCSF Mouse Inventory Database Application is an open-source Web App that provides information about the mutant alleles, transgenes, and inbred strains maintained by investigators at the university and facilitates sharing of these resources within the university community. The Application is designed to promote collaboration, decrease the costs associated with obtaining genetically-modified mice, and increase access to mouse lines that are difficult to obtain. An inventory of the genetically-modified mice on campus and the investigators who maintain them is compiled from records of purchases from external sources, trans...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Wall, E., Scoles, J., Joo, A., Klein, O., Quinonez, C., Bush, J. O., Martin, G. R., Laird, D. J. Tags: Software and Data Resources Source Type: research
De novo Genome Assembly of the indica Rice Variety IR64 Using Linked-Read Sequencing and Nanopore Sequencing
IR64 is a rice variety with high-yield that has been widely cultivated around the world. IR64 has been replaced by modern varieties in most growing areas. Given that modern varieties are mostly progenies or relatives of IR64, genetic analysis of IR64 is valuable for rice functional genomics. However, chromosome-level genome sequences of IR64 have not been available previously. Here, we sequenced the IR64 genome using synthetic long reads obtained by linked-read sequencing and ultra-long reads obtained by nanopore sequencing. We integrated these data and generated the de novo assembly of the IR64 genome of 367 Mb, equivalen...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Tanaka, T., Nishijima, R., Teramoto, S., Kitomi, Y., Hayashi, T., Uga, Y., Kawakatsu, T. Tags: Genome Report Source Type: research
Long-Read Genome Sequencing and Assembly of Leptopilina boulardi: A Specialist Drosophila Parasitoid
Leptopilina boulardi (Hymenoptera: Figitidae) is a specialist parasitoid of Drosophila. The Drosophila-Leptopilina system has emerged as a suitable model for understanding several aspects of host-parasitoid biology. However, a good quality genome of the wasp counterpart was lacking. Here, we report a whole-genome assembly of L. boulardi to bring it in the scope of the applied and fundamental research on Drosophila parasitoids with access to epigenomics and genome editing tools. The 375Mb draft genome has an N50 of 275Kb with 6315 scaffolds >500bp and encompasses >95% complete BUSCOs. Using a combination of ab-initio ...
Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: Khan, S., Sowpati, D. T., Srinivasan, A., Soujanya, M., Mishra, R. K. Tags: Genome Report Source Type: research
