by Liu Xu, Yibing Chen, Lingling Liu, Xinyu Hu, Chengsi He, Yuan Zhou, Xinyi Ding, Minhua Luo, Jiajing Yan, Quentin Liu, Hongsheng Li, Dongming Lai, Zhengzhi Zou Tumor-associated macrophages (TAM) subtypes have been shown to impact cancer prognosis and resistance to immunotherapy. However, there is still a lack of systematic investigation into their molecular characteristics and clinical relevance in different cancer types. Single-cell RNA sequencing data from three different tumor types were used to cluster and type macrophages. Functional analysis and communication of TAM subpopulations were ..read more

by Peiyao Wang, Zhaotong Lin, Haoran Xue, Wei Pan Genome-wide association studies (GWAS) have identified many genetic loci associated with complex traits and diseases in the past 20 years. Multiple heritable covariates may be added into GWAS regression models to estimate direct effects of genetic variants on a focal trait, or to improve the power by accounting for environmental effects and other sources of trait variations. When one or more covariates are causally affected by both genetic variants and hidden confounders, adjusting for them in GWAS will produce biased estimation of SNP effects ..read more

by Iain R. Timmins, The PRACTICAL Consortium , Frank Dudbridge Population differences in risk of disease are common, but the potential genetic basis for these differences is not well understood. A standard approach is to compare genetic risk across populations by testing for mean differences in polygenic scores, but existing studies that use this approach do not account for statistical noise in effect estimates (i.e., the GWAS betas) that arise due to the finite sample size of GWAS training data. Here, we show using Bayesian polygenic score methods that the level of uncertainty in estimates of ..read more

by Paris Veltsos, John K. Kelly Gene expression can be influenced by genetic variants that are closely linked to the expressed gene (cis eQTLs) and variants in other parts of the genome (trans eQTLs). We created a multiparental mapping population by sampling genotypes from a single natural population of Mimulus guttatus and scored gene expression in the leaves of 1,588 plants. We find that nearly every measured gene exhibits cis regulatory variation (91% have FDR ..read more

by Beth L. Dumont, Daniel M. Gatti, Mallory A. Ballinger, Dana Lin, Megan Phifer-Rixey, Michael J. Sheehan, Taichi A. Suzuki, Lydia K. Wooldridge, Hilda Opoku Frempong, Raman Akinyanju Lawal, Gary A. Churchill, Cathleen Lutz, Nadia Rosenthal, Jacqueline K. White, Michael W. Nachman The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for over a century. However, laboratory mice capture only a subset of the genetic variation found in wild mouse populations, ultimately limiting the potential of classical inbred strains to uncover phenot ..read more

by Manuela Alvarado Obando, Diego Rey-Varela, Felipe Cava, Tobias Dörr Peptidoglycan (PG) is the main component of the bacterial cell wall; it maintains cell shape while protecting the cell from internal osmotic pressure and external environmental challenges. PG synthesis is essential for bacterial growth and survival, and a series of PG modifications are required to allow expansion of the sacculus. Endopeptidases (EPs), for example, cleave the crosslinks between adjacent PG strands to allow the incorporation of newly synthesized PG. EPs are collectively essential for bacterial growth and must ..read more

by Suhan Ma, Xuyang Ni, Shimin Chen, Xiaomu Qiao, Xuejiao Xu, Weizhe Chen, Jackson Champer, Jia Huang CRISPR-based gene drives offer promising prospects for controlling disease-transmitting vectors and agricultural pests. A significant challenge for successful suppression-type drive is the rapid evolution of resistance alleles. One approach to mitigate the development of resistance involves targeting functionally constrained regions using multiple gRNAs. In this study, we constructed a 3-gRNA homing gene drive system targeting the recessive female fertility gene Tyrosine decarboxylase 2 (Tdc2 ..read more

by Egill Richard, Baptiste Darracq, Eloi Littner, Gael A. Millot, Valentin Conte, Thomas Cokelaer, Jan Engelstädter, Eduardo P. C. Rocha, Didier Mazel, Céline Loot Integrons are adaptive devices that capture, stockpile, shuffle and express gene cassettes thereby sampling combinatorial phenotypic diversity. Some integrons called sedentary chromosomal integrons (SCIs) can be massive structures containing hundreds of cassettes. Since most of these cassettes are non-expressed, it is not clear how they remain stable over long evolutionary timescales. Recently, it was found that the experimental inv ..read more

by Anna Cho, Gordon Lax, Samuel J. Livingston, Yumiko Masukagami, Mariia Naumova, Olivia Millar, Filip Husnik, Patrick J. Keeling Symbiomonas scintillans Guillou et Chrétiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC ..read more

by Rachel N. DuMez-Kornegay, Lillian S. Baker, Alexis J. Morris, Whitney L. M. DeLoach, Robert H. Dowen The popularity of the ancient, probiotic-rich beverage Kombucha Tea (KT) has surged in part due to its purported health benefits, which include protection against metabolic diseases; however, these claims have not been rigorously tested and the mechanisms underlying host response to the probiotics in KT are unknown. Here, we establish a reproducible method to maintain C. elegans on a diet exclusively consisting of Kombucha Tea-associated microbes (KTM), which mirrors the microbial community ..read more