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Foraminifera as a Model of Eukaryotic Genome Dynamism
Get PDFIn contrast to the canonical view that genomes cycle only between haploid and diploid states, many eukaryotes have dynamic genomes that change content throughout an individual’s life cycle. However, the few detailed studies of microeukaryotic life cycles render our understanding of eukaryotic genome dynamism incomplete. Foraminifera (Rhizaria) are an ecologically important, yet understudied, clade of microbial eukaryotes with complex life cycles that include changes in ploidy and genome organization. Here, we apply fluorescence microscopy and image analysis techniques to over 2,800 nuclei in 110 cells to characterize the life cycle of Allogromia laticollaris strain Cold Spring Harbor (CSH), one of few cultivable foraminifera species. We show that haploidy and diploidy are brief moments in the A. laticollaris life cycle and that A. laticollaris nuclei endoreplicate up to 12,000 times the haploid genome size. We find that A. laticollaris reorganizes a highly endoreplicated nucleus into thousands of haploid genomes through a non-canonical mechanism called Zerfall, in which the nuclear envelope degrades and extrudes chromatin into the cytoplasm. Based on these findings, along with changes in nuclear architecture across the life cycle, we believe that A. laticollaris uses spatio-temporal mechanisms to delineate germline and somatic DNA within a single nucleus. The analyses here extend our understanding of the genome dynamics across the eukaryotic tree of life.
IMPORTANCEIn traditional depictions of eukaryotes (i.e., cells with nuclei), life cycles alternate only between haploid and diploid phases, overlooking studies of diverse microeukaryotic lineages (e.g., amoebae, ciliates, and flagellates) that show dramatic variation in DNA content throughout their life cycles. Endoreplication of genomes enables cells to grow to large sizes and perhaps to also respond to changes in their environments. Few microeukaryotic life cycles have been studied in detail, which limits our understanding of how eukaryotes regulate and transmit their DNA across generations. Here, we use microscopy to study the life cycle of Allogromia laticollaris strain CSH, an early-diverging lineage within the Foraminifera (an ancient clade of predominantly marine amoebae). We show that DNA content changes significantly throughout their life cycle and further describe an unusual process called Zerfall, by which this species reorganizes a large nucleus with up to 12,000 genome copies into hundreds of small gametic nuclei, each with a single haploid genome. Our results are consistent with the idea that all eukaryotes demarcate germline DNA to pass on to offspring amidst more flexible somatic DNA and extend the known diversity of eukaryotic life cycles
Denise Levertov’s “Histrionics”
No full textThis essay argues that Denise Levertov’s antiwar poetry challenges contemporary assumptions about the limits of bearing witness to war. Contrary to George Oppen’s intimation that she should limit her writing to “authentic” accounts of her own domestic experience, Levertov wrote about her uneven relationship with the “here” of the Cold War homefront and the “there” of the Vietnam War’s violence. In grappling with these two seemingly disparate domains, she exposes the Cold War security state’s reliance on gendered household motifs to justify state-sponsored violence across geographic and temporal divides. Levertov treats wartime witnessing as an imaginative and critical encounter with racial and gendered violence—one that relies less on narrating discrete and directly observed events and more on challenging the permissibility of perpetual war itself
Neighborhood Eviction Trajectories and Odds of Moderate and Serious Psychological Distress During Pregnancy Among African American Women
Get PDFAfrican American mothers are unjustly burdened both by residential evictions and psychological distress. We quantified associations between trajectories of neighborhood evictions over time, and odds of moderate and serious psychological distress (MPD and SPD, respectively) during pregnancy among African American women. We linked publicly available neighborhood eviction filing and judgement rate data to preconception and during pregnancy addresses from the Life-course Influences on Fetal Environments Study (2009-2011, n=808). Multinomial logistic regression estimated odds of MPD and SPD during pregnancy associated with eviction filing and judgement rate trajectories incorporating preconception and during pregnancy addresses (each categorized as low/medium/high, with two 9-category trajectory measures). Psychological distress was measured with the Kessler (K6) scale (scores between 5-12 = MPD, and ≥ 13 = SPD). MPD was reported in 60% and SPD in 8% of the sample. Higher neighborhood eviction filing and judgement rates, compared to low/low in the preconception and pregnancy periods was associated with between 2- and 4-fold higher odds of both MDP and SPD during pregnancy among African American women, in adjusted models. Future studies should identify mechanisms of these findings to inform timely community-based interventions and effective policy solutions to ensure the basic human right to housing for all
Effects of Ear Canal Geometry on Normative Adult Wideband Acoustic Immittance (WAI) Measurements
No full textWideband Acoustic Immittance (WAI) measurement is recognized as an objective, noninvasive diagnostic tool for middle-ear pathologies causing conductive hearing losses. Power absorbance (absorbance) in the WAI family requires calculating with the ear-canal cross-sectional area at the measurement location. Traditionally, researchers and FDA-approved WAI instruments, such as Mimosa’s Hear-ID, have relied on the simplifying assumption that the ear canal is a uniformly cylindrical structure with a constant cross-sectional area. This assumption overlooks the complex, variable nature of real ear canal geometry. Therefore, the objective of this work is to investigate the effects of varying cross-sectional areas and different probe locations on normative adult WAI measurements. In this thesis work, an experimental platform is developed to facilitate WAI measurements on subject-specific, 3D-printed ear canal models derived from high-resolution CT scans, and detailed procedures for conducting leak-free absorbance measurements with minimized intrasubject variability are elaborated. Ear canals from eight subjects aged 40 to 50 were 3D printed and coupled to a 3D-printed artificial middle ear for absorbance measurements using a Hear-ID probe. Results show: (1) Absorbance depends on probe location in some canals, especially above 2000 Hz, and the effect of probe position on absorbance might rely on a combination of how quickly the area changes along the canal and how much the canal curves; and (2) variations in ear-canal cross-sectional area become systematically more significant as the canal area increases beyond the assumed 44 mm2. Larger canal areas lead to lower absorbance below about 3000 Hz
Enacting Data Context: Fixing Meaning in Transparency Data Initiatives
Get PDFThis article documents the “context cultures” underpinning efforts to develop regulations for collecting and reporting data in a United States public database known as Open Payments. Open Payments is a dataset published annually by the US Center for Medicare and Medicaid Services that documents the transfers of value from pharmaceutical and medical device manufacturers to physicians, prescribing non-physicians, and teaching hospitals. In the article, I show context became a manifold concern as differentially-situated actors engaged in modes of public advocacy and social action around not only what data meant, but also what it meant to make data meaningful. I show how “context” took on multiple meanings as it was brought into relationship with certain concepts (such as “light,” “transparency,” and “interpretation”) and as stakeholders developed arguments for where they believed meaning should originate. In presenting this case, I call for further ethnographic attention to the ways in which meaning-making is enacted in relation to datasets—particularly those datasets intended to hold institutions accountable. I conclude the article meditating on the political significance of attending to various “context cultures” when putting data signification in context, along with the implications for how critical data studies scholars historicize big data epistemologies and rhetoric
Many Direct-To-Consumer Canine Genetic Tests Can Identify the Breed of Purebred Dogs
Get PDFOBJECTIVE To compare pedigree documentation and genetic test results to evaluate whether user-provided photographs influence the breed ancestry predictions of direct-to-consumer (DTC) genetic tests for dogs.
ANIMALS 12 registered purebred pet dogs representing 12 different breeds. METHODS Each dog owner submitted 6 buccal swabs, 1 to each of 6 DTC genetic testing companies. Experimenters registered each sample per manufacturer instructions. For half of the dogs, the registration included a photograph of the DNA donor. For the other half of the dogs, photographs were swapped between dogs. DNA analysis and breed ancestry prediction were conducted by each company. The effect of condition (ie, matching vs shuffled photograph) was evaluated for each company’s breed predictions. As a positive control, a convolutional neural network was also used to predict breed based solely on the photograph. RESULTS Results from 5 of the 6 tests always included the dog’s registered breed. One test and the convolutional neural network were unlikely to identify the registered breed and frequently returned results that were more similar to the photograph than the DNA. Additionally, differences in the predictions made across all tests underscored the challenge of identifying breed ancestry, even in purebred dogs.
CLINICAL RELEVANCE Veterinarians are likely to encounter patients who have conducted DTC genetic testing and may be asked to explain the results of genetic tests they did not order. This systematic comparison of commercially available tests provides context for interpreting results from consumer-grade DTC genetic testing kits
The JWST Early Release Science Program for Direct Observations of Exoplanetary Systems. IV. NIRISS Aperture Masking Interferometry Performance and Lessons Learned
Get PDFWe present a performance analysis for the aperture masking interferometry (AMI) mode on board the James Webb Space Telescope Near Infrared Imager and Slitless Spectrograph (JWST/NIRISS). Thanks to self-calibrating observables, AMI accesses inner working angles down to and even within the classical diffraction limit. The scientific potential of this mode has recently been demonstrated by the Early Release Science (ERS) 1386 program with a deep search for close-in companions in the HIP 65426 exoplanetary system. As part of ERS 1386, we use the same data set to explore the random, static, and calibration errors of NIRISS AMI observables. We compare the observed noise properties and achievable contrast to theoretical predictions. We explore possible sources of calibration errors and show that differences in charge migration between the observations of HIP 65426 and point-spread function calibration stars can account for the achieved contrast curves. Lastly, we use self-calibration tests to demonstrate that with adequate calibration NIRISS F380M AMI can reach contrast levels of ~9-10 mag at ≥λ/D. These tests lead us to observation planning recommendations and strongly motivate future studies aimed at producing sophisticated calibration strategies taking these systematic effects into account. This will unlock the unprecedented capabilities of JWST/NIRISS AMI, with sensitivity to significantly colder, lower-mass exoplanets than lower-contrast ground-based AMI setups, at orbital separations inaccessible to JWST coronagraphy
MS-ESI Analysis of Glyoxal, Methyl Glyoxal, and Hydroxy Acetone - Salt Systems to Model Atmospheric Product Formation
No full textSecondary organic aerosols (SOA) are a significant component of total atmospheric organic particulate matter. Yet a lot of uncertainty remains regarding the composition of SOA formed through cloud processing and other aqueous reactions. We conducted aqueous phase ESI-MS experiments of glyoxal, methylglyoxal, and hydroxy acetone with a variety of ammonium salts to simulate these reaction conditions. Statistical analysis was conducted to identify chemical compositional trends across the samples. I also report the identification of the formation of a biological cofactor under abiotic conditions. Pyridoxal, also known as vitamin B6, was identified to be a major contributor to the 300-400 nm absorbance band and observed in mixtures of methyl glyoxal/ hydroxy acetone and ammonium salts. Future statistical analyses methods were additionally proposed for further study
