Figuring Out Gas & Galaxies in Enzo (FOGGIE). III. The Mocky Way:Investigating Biases in Observing the Milky Way's Circumgalactic Medium

The circumgalactic medium (CGM) of the Milky Way is mostly obscured by nearby gas in position-velocity space because we reside inside the Galaxy. Substantial biases exist in most studies on the Milky Way's CGM that focus on easier-to-detect high-velocity gas. With mock observations on a Milky-Way analog from the FOGGIE simulation, we investigate four observational biases related to the Milky Way's CGM. First, QSO absorption-line studies probe a limited amount of the CGM mass: only 35% of the mass is at high Galactic latitudes $|b|>20$ degrees, of which only half is moving at $|v_{\rm LSR}|\gtrsim100$ km s$^{-1}$. Second, the inflow rate ($\dot{M}$) of the cold gas observable in HI 21cm is reduced by a factor of $\sim10$ as we switch from the local standard of rest to the galaxy's rest frame; meanwhile $\dot{M}$ of the cool and warm gas does not change significantly. Third, OVI and NV are promising ions to probe the Milky Way's outer CGM ($r\gtrsim$15 kpc), but CIV may be less sensitive. Lastly, the scatter in ion column density is a factor of 2 higher if the CGM is observed from inside-out than from external views because of the gas radial density profile. Our work highlights that observations of the Milky Way's CGM, especially those using HI 21cm and QSO absorption lines, are highly biased. We demonstrate that these biases can be quantified and calibrated through synthetic observations with simulated Milky-Way analogs.Comment: ApJ in pres

Figuring Out Gas & Galaxies In Enzo (FOGGIE). IV. The Stochasticity of Ram Pressure Stripping in Galactic Halos

We study ram pressure stripping in simulated Milky Way-like halos at z>=2 from the Figuring Out Gas & Galaxies In Enzo (FOGGIE) project. These simulations reach exquisite resolution in their circumgalactic medium (CGM) gas owing to FOGGIE's novel refinement scheme. The CGM of each halo spans a wide dynamic range in density and velocity over its volume---roughly 6 dex and 1000 km/s, respectively---translating into a 5 dex range in ram pressure imparted to interacting satellites. The ram pressure profiles of the simulated CGM are highly stochastic, owing to kpc-scale variations of the density and velocity fields of the CGM gas. As a result, the efficacy of ram pressure stripping depends strongly on the specific path a satellite takes through the CGM. The ram-pressure history of a single satellite is generally unpredictable and not well correlated with its approach vector with respect to the host galaxy. The cumulative impact of ram pressure on the simulated satellites is dominated by only a few short strong impulses---on average, 90% of the total surface momentum gained through ram pressure is imparted in 20% or less of the total orbital time. These results reveal an erratic mode of ram pressure stripping in Milky-Way like halos at high redshift---one that is not captured by a smooth spherically-averaged model of the circumgalactic medium.Comment: 18 pages, 10 figures. Submitted to Ap

Electrical impedance tomography with fuzzy logic classification in lung image reconstruction

Electrical Impedance Tomography (EIT) estimates the electrical impedance distribution within a medium and produces cross-sectional images of an admittivity distribution inside an electrically conducting object. EIT in biomedicine application was first applied in lung due to it being large organs that allow large conductivity changes and is a promising technique since it allows continuous monitoring of the ventilation distribution. This study aims to explore the potential EIT technique in medical applications, with strategies to enhance the image reconstruction of the lung images. Performance of the enhanced image reconstruction is analyzed through simulation on the thorax Finite Element Model (FEM) based on a thorax CT image generated using NETGEN Mesher. To integrate and simulate EIT image of the thorax model, data are obtained from the forward and inverse model. Graz consensus Reconstruction algorithm for EIT (GREIT) technique is then applied as the consensus linear reconstruction algorithm for lung EIT images. Subsequently, the involvement of 3D imaging opens the opportunity to explore more electrode placement strategies for enhancement in image reconstruction. Performance of the reconstructed images based on electrode numbers and placement strategies are analyzed using the five figures of merits and classified into poor, average and good using Fuzzy Logic (FL). From the analysis, planar-offset configuration with 16-electrodes outperforms all others while planar configuration with 16-electrodes followed closely

HERON: Demonstrating a Novel Biological Platform for Small Satellite Missions

Long-duration deep space missions pose a significant health risk for both humans and their resident microorganisms. The GeneSat, PharmaSat and O/OREOS missions have previously explored biological questions regarding the effects of spaceflight on S. cerevisiase, B. subtilis, and E. coli. However, there currently exists both a knowledge and an accessibility gap in small satellite biological experiments. These payloads require precise instrumentation and complex platforms that are usually reserved for large research organizations. This makes it difficult for smaller organizations to perform biological research in low Earth orbit (LEO). To address these challenges, the University of Toronto Aerospace Team (UTAT) Space Systems Division is currently developing the HERON CubeSat. HERON houses a payload platform which measures the effects of the LEO environment on the gene expression and drug resistance of Candida albicans, a yeast commonly found in the human gut microbiome. Previous research has suggested that C. albicans might display increased pathogenicity and drug resistance in response to microgravity, which has important implications for long-duration human spaceflight. The yeast cells are housed in custom acrylic microfluidics chips containing 32 wells with channels for media and drug delivery. A measurement printed circuit board (PCB) contains custom optics capable of measuring minute changes in cell fluorescence. The entire payload stack is then housed in a temperature- and humidity-controlled 2U pressure vessel. Space Systems as a whole is an undergraduate student-led and student-funded design team, dedicated to the development of small satellite missions with a focus on education and undergraduate learning. HERON is scheduled to launch Q1 2022 into a Sun-synchronous orbit via a SpaceX Falcon 9 rocket at an altitude of approximately 550 km. Our platform is open-source and can serve as a low-cost template for future biological CubeSat missions. This paper serves as a technical and scientific description of the platform, along with the lessons learned during the payload design, assembly, and validation processes

Inspiring the Next Generation: Challenges and Strategies for Onboarding and Retention in an Undergraduate CubeSat Design Team

The University of Toronto Aerospace Team (UTAT) Space Systems Division is a fully student levy-funded, student-led undergraduate design team that develops CubeSats with research-oriented payloads. UTAT’s mission is to provide undergraduate students with unique opportunities to develop engineering design skills outside of the classroom, and therefore has a distinct focus on member growth and education. As an undergraduate student team, UTAT faces a unique set of challenges in onboarding members and maintaining a strong knowledge base on the team. These challenges include onboarding members with limited technical experience, equipping them with satellite design skills, and maintaining high interest levels among volunteer members with limited time to contribute. The team has implemented a wide range of strategies related to onboarding and member development over the past two years. Notable examples include hosting workshops and regular work sessions, and employing practice projects for technical skill development. This paper presents these practices in depth and evaluates their impacts using both quantitative and qualitative metrics of team success including retention rates, team demographic data, and individual perceptions of team dynamics. It also evaluates these practices against scientifically backed models, while evaluating the effectiveness of these models in the student team environment. Lessons learned include the importance of emphasizing a culture of inclusivity and psychological safety as well as utilizing workshops and skill-building modules both in the onboarding phase and throughout the year to generate and maintain interest in the team. The practices presented here are relevant and transferable to similar organizations including student teams, industry projects, and research initiatives

A grapevine anthocyanin acyltransferase, transcriptionally regulated by VvMYBA, can produce most acylated anthocyanins present in grape skins

Anthocyanins are flavonoid compounds responsible for red/purple colors in the leaves, fruit, and flowers of many plant species. They are produced through a multistep pathway that is controlled by MYB transcription factors. VvMYBA1 and VvMYBA2 activate anthocyanin biosynthesis in grapevine (Vitis vinifera) and are nonfunctional in white grapevine cultivars. In this study, transgenic grapevines with altered VvMYBA gene expression were developed, and transcript analysis was carried out on berries using a microarray technique. The results showed that VvMYBA is a positive regulator of the later stages of anthocyanin synthesis, modification, and transport in cv Shiraz. One up-regulated gene, ANTHOCYANIN 3-O-GLUCOSIDE-6″-O-ACYLTRANSFERASE (Vv3AT), encodes a BAHD acyltransferase protein (named after the first letter of the first four characterized proteins: BEAT [for acetyl CoA:benzylalcohol acetyltransferase], AHCT [for anthocyanin O-hydroxycinnamoyltransferase], HCBT [for anthranilate N-hydroxycinnamoyl/benzoyltransferase], and DAT [for deacetylvindoline 4-O-acetyltransferase]), belonging to a clade separate from most anthocyanin acyltransferases. Functional studies (in planta and in vitro) show that Vv3AT has a broad anthocyanin substrate specificity and can also utilize both aliphatic and aromatic acyl donors, a novel activity for this enzyme family found in nature. In cv Pinot Noir, a red-berried grapevine mutant lacking acylated anthocyanins, Vv3AT contains a nonsense mutation encoding a truncated protein that lacks two motifs required for BAHD protein activity. Promoter activation assays confirm that Vv3AT transcription is activated by VvMYBA1, which adds to the current understanding of the regulation of the BAHD gene family. The flexibility of Vv3AT to use both classes of acyl donors will be useful in the engineering of anthocyanins in planta or in vitro

Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels

Large-scale meta-analyses of genome-wide association studies (GWAS) have identified >175 loci associated with fasting cholesterol levels, including total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). With differences in linkage disequilibrium (LD) structure and allele frequencies between ancestry groups, studies in additional large samples may detect new associations. We conducted staged GWAS meta-analyses in up to 69,414 East Asian individuals from 24 studies with participants from Japan, the Philippines, Korea, China, Singapore, and Taiwan. These meta-analyses identified (P < 5 × 10-8) three novel loci associated with HDL-C near CD163-APOBEC1 (P = 7.4 × 10-9), NCOA2 (P = 1.6 × 10-8), and NID2-PTGDR (P = 4.2 × 10-8), and one novel locus associated with TG near WDR11-FGFR2 (P = 2.7 × 10-10). Conditional analyses identified a second signal near CD163-APOBEC1. We then combined results from the East Asian meta-analysis with association results from up to 187,365 European individuals from the Global Lipids Genetics Consortium in a trans-ancestry meta-analysis. This analysis identified (log10Bayes Factor ≥6.1) eight additional novel lipid loci. Among the twelve total loci identified, the index variants at eight loci have demonstrated at least nominal significance with other metabolic traits in prior studies, and two loci exhibited coincident eQTLs (P < 1 × 10-5) in subcutaneous adipose tissue for BPTF and PDGFC. Taken together, these analyses identified multiple novel lipid loci, providing new potential therapeutic targets

Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels.

Elevated serum urate levels cause gout and correlate with cardiometabolic diseases via poorly understood mechanisms. We performed a trans-ancestry genome-wide association study of serum urate in 457,690 individuals, identifying 183 loci (147 previously unknown) that improve the prediction of gout in an independent cohort of 334,880 individuals. Serum urate showed significant genetic correlations with many cardiometabolic traits, with genetic causality analyses supporting a substantial role for pleiotropy. Enrichment analysis, fine-mapping of urate-associated loci and colocalization with gene expression in 47 tissues implicated the kidney and liver as the main target organs and prioritized potentially causal genes and variants, including the transcriptional master regulators in the liver and kidney, HNF1A and HNF4A. Experimental validation showed that HNF4A transactivated the promoter of ABCG2, encoding a major urate transporter, in kidney cells, and that HNF4A p.Thr139Ile is a functional variant. Transcriptional coregulation within and across organs may be a general mechanism underlying the observed pleiotropy between urate and cardiometabolic traits.The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Variant annotation was supported by software resources provided via the Caché Campus program of the InterSystems GmbH to Alexander Teumer

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.

BACKGROUND: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes