Dual gene activation and knockout screen reveals directional dependencies in genetic networks.

Understanding the direction of information flow is essential for characterizing how genetic networks affect phenotypes. However, methods to find genetic interactions largely fail to reveal directional dependencies. We combine two orthogonal Cas9 proteins from Streptococcus pyogenes and Staphylococcus aureus to carry out a dual screen in which one gene is activated while a second gene is deleted in the same cell. We analyze the quantitative effects of activation and knockout to calculate genetic interaction and directionality scores for each gene pair. Based on the results from over 100,000 perturbed gene pairs, we reconstruct a directional dependency network for human K562 leukemia cells and demonstrate how our approach allows the determination of directionality in activating genetic interactions. Our interaction network connects previously uncharacterized genes to well-studied pathways and identifies targets relevant for therapeutic intervention

Heat Shock Protein 70 Expression in Juvenile Eastern Oysters, Crassostrea virginica (Gmelin, 1791), Exposed to Anoxic Conditions

Anoxic water events in conjunction with summer high temperatures are thought to be one of the causes of declines in natural oyster reefs on the eastern shore of Mobile Bay. Work is underway to determine whether tolerance to low oxygen can be selected for in hatchery-produced oysters. As a component of this work, the expression of heat shock protein 70 (HSP 70) was examined in control (normoxia) and anoxia-challenged juvenile oysters. Parental Eastern oysters, Crassostrea virginica were collected from 2 sites, Cedar Point Reef (CP), an area considered to have normoxic conditions, and White House Reef (WH), an area suspected to experience periodic anoxia. F1 generation oysters were produced from CP and WH parents that survived an anoxic exposure of 96 h. Control F1 generation oysters from both parental stocks not exposed to anoxia were also produced. The F1 generation oysters were subsequently exposed to anoxia or control normoxic conditions, and differences in expression of HSP 70 were examined. Nitrogen was used to create the anoxic conditions for both the parental and F1 generations. Three HSP 70 isoforms—2 constitutive forms (HSC 77 and HSC 72) and 1 inducible form (HSP 69)—were expressed in both anoxia- and normoxia-exposed oysters from all groups. Although there were differences among groups of oysters from the 2 sites, there were no differences in the expression of HSC 77 and HSC 72 between the control and anoxia-treated oysters within a group. Interestingly, the expression of HSP 69 was higher in oysters exposed to normoxia than the ones from anoxia treatments. These differences are thought to reflect a combination of responses to nutritional stress in the controls and facultative anaerobiosis and metabolic arrest in the anoxia groups

New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk

To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P<5 × 10−8), of which eight were previously associated with increased overall adiposity (BMI, BF%) and four (in or near COBLL1/GRB14, IGF2BP1, PLA2G6, CRTC1) were novel associations with BF%. Seven loci showed a larger effect on BF% than on BMI, suggestive of a primary association with adiposity, while five loci showed larger effects on BMI than on BF%, suggesting association with both fat and lean mass. In particular, the loci more strongly associated with BF% showed distinct cross-phenotype association signatures with a range of cardiometabolic traits revealing new insights in the link between adiposity and disease risk

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa

West Africa is currently witnessing the most extensive Ebola virus (EBOV) outbreak so far recorded. Until now, there have been 27,013 reported cases and 11,134 deaths. The origin of the virus is thought to have been a zoonotic transmission from a bat to a two-year-old boy in December 2013 (ref. 2). From this index case the virus was spread by human-to-human contact throughout Guinea, Sierra Leone and Liberia. However, the origin of the particular virus in each country and time of transmission is not known and currently relies on epidemiological analysis, which may be unreliable owing to the difficulties of obtaining patient information. Here we trace the genetic evolution of EBOV in the current outbreak that has resulted in multiple lineages. Deep sequencing of 179 patient samples processed by the European Mobile Laboratory, the first diagnostics unit to be deployed to the epicentre of the outbreak in Guinea, reveals an epidemiological and evolutionary history of the epidemic from March 2014 to January 2015. Analysis of EBOV genome evolution has also benefited from a similar sequencing effort of patient samples from Sierra Leone. Our results confirm that the EBOV from Guinea moved into Sierra Leone, most likely in April or early May. The viruses of the Guinea/Sierra Leone lineage mixed around June/July 2014. Viral sequences covering August, September and October 2014 indicate that this lineage evolved independently within Guinea. These data can be used in conjunction with epidemiological information to test retrospectively the effectiveness of control measures, and provides an unprecedented window into the evolution of an ongoing viral haemorrhagic fever outbreak.status: publishe

New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk

To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P <5 x 10(-8)), of which eight were previously associated with increased overall adiposity (BMI, BF%) and four (in or near COBLL1/GRB14, IGF2BP1, PLA2G6, CRTC1) were novel associations with BF%. Seven loci showed a larger effect on BF% than on BMI, suggestive of a primary association with adiposity, while five loci showed larger effects on BMI than on BF%, suggesting association with both fat and lean mass. In particular, the loci more strongly associated with BF% showed distinct cross-phenotype association signatures with a range of cardiometabolic traits revealing new insights in the link between adiposity and disease risk.Peer reviewe

Publisher Correction: Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability.

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-21276-3</jats:p

Liquid culture and growth quantification of the seagrass pathogen, Labyrinthula spp.

Symptoms characteristic of wasting disease, thought to result from infection by protozoan pathogens (i.e. Labyrinthula spp.), are a common phenomenon affecting seagrass species worldwide. However relatively little is known about factors that control the survival and success of Labyrinthula in part due to the difficulty associated with quantifying the growth of this organism. Here we describe a simple and inexpensive method for measuring growth of Labyrinthula in liquid culture that takes into consideration both cell density and areal spread. The technique allows for examination of the effects of both abiotic and biotic factors on the growth of Labyrinthula apart from its seagrass host, separating the effects of environmental condition on the host from their effects on the pathogen

Impact of dispersant on early life stages of the water flea Daphnia magna

In response to the 2010 Deepwater Horizon oil spill, over 1 million gallons of dispersant were applied in Gulf of Mexico offshore waters; Corexit 9500 was the most applied dispersant. The impact on organisms in nearshore and freshwaters has received little scrutiny. Acute 48 h toxicity of Corexit 9500 and a new hyperbranched polyethylenimine (HPEI) dispersant-like compound were evaluated for the freshwater indicator organism, Daphnia magna and for larval and early spat stages of the Eastern oyster, Crassostrea virginica. For D. magna, Corexit 9500 demonstrated toxicity (EC 50 of 0.14 [0.13, 0.15] ppm) similar to the 10-kDa HPEI (EC 50 of 0.16 [0.12, 0.19] ppm). HPEI toxicity increased as a function of molecular weight (1.2 to 750 kDa). The 10 kDa size HPEI was further investigated because it dispersed crude oil with equal effectiveness as Corexit. For Corexit, 100% oyster mortality was detected for the ≤0.2-mm size classes and mortality \u3e50% for the 0.3- and 0.7-mm size classes at the two greatest concentrations (25 and 50 ppm). HPEI (10 kDa) exhibited low mortality rates (\u3c30%) for all concentrations for all oyster size classes except the 0.1-mm class. Although mortality rates for this size class were up to 60%, mortality was still less than the mortality caused by Corexit 9500. The low toxicity of HPEI polymers for C. virginica in comparison with Corexit 9500 suggests that HPEI polymers warrant further study