Experimental analysis of organ decay and pH gradients within a carcass and the implications for phosphatization of soft tissues

Replacement of soft tissues by calcium phosphate can yield spectacular fossils. However, in the fossil record, the phosphatization of internal organs is highly selective; some internal organs, such as muscles, stomachs, and intestines, appear to preferentially phosphatize while other organs seldom phosphatize. The reasons for this are unclear but one hypothesis is that, during decay, organs create distinct chemical microenvironments and only some fall below the critical pH threshold for mineralization to occur (i.e. below the carbonic acid dissociation constant: pH 6.38). Here, we present a novel investigation using microelectrodes that record dynamic spatial and temporal pH gradients inside organs within a fish carcass in real time. Our experiments demonstrate that within a decaying fish carcass, organ-specific microenvironments are not generated. Rather, a pervasive pH environment forms within the body cavity which persists until integumentary failure. With no evidence to support the development of organ-specific microenvironments during decay our data suggest other factors must control differential organ phosphatization. We propose, that when conditions are amenable, it is tissue biochemistry that plays an important role in selective phosphatization. Tissues with high phosphate content (and those rich in collagen) are most likely to phosphatize. Internal organs that typically have lower tissue-bound phosphate, including the integuments of the stomach and intestine, may require other sources of phosphate such as ingested phosphate-rich organic matter. If tissue biochemistry is the driver behind selective phosphatization, this may provide insights into other highly selective modes of soft-tissue preservation (e.g. pyritization)

The Mazon Creek Lagerstätte: a diverse late Paleozoic ecosystem entombed within siderite concretions

One of the best records of late Paleozoic ecosystems, the Mazon Creek Lagerstätte is world famous for its striking flora and fauna preserved within siderite concretions. Distinct from other late Carboniferous concretionary Lagerstätten because of the remarkable fidelity of soft tissues and pigments that are frequently preserved, the Mazon Creek has seen a revival in investigations during the last 10 years using modern palaeontological techniques. However, many of these modern investigations build upon a literature that incorrectly interprets the palaeoenvironment of the Mazon Creek and the separate biotas: there is a lack of evidence to support a distinct freshwater fauna. Here, we present a detailed overview of the Mazon Creek Lagerstätte, including the palaeoenvironmental conditions, organisms present and the complex taphonomic processes involved in fossil formation. Investigation into the formation of siderite concretions and the complex taphonomic processes controlling soft-bodied preservation are still continuing but are reviewed in detail

Leonard Ragland to Honorable Ross Barnett, 14 September 1962

Ragland thanks Barnett for his speech of 13 September. Offers support of Oxford and Lafayette County.https://egrove.olemiss.edu/west_union_gov/1003/thumbnail.jp

Quantifying the Uncertainty in Ground-Based GNSS-Reflectometry Sea Level Measurements

Global Navigation Satellite System reflectometry (GNSS-R) tide gauges are a promising alternative to traditional tide gauges. However, the precision of GNSS-R sea-level measurements when compared to measurements from a colocated tide gauge is highly variable, with no clear indication of what causes the variability. Here, we present a modeling technique to estimate the precision of GNSS-R sea-level measurements that relies on creating and analyzing synthetic signal-to-noise-ratio (SNR) data. The modeled value obtained from the synthetic SNR data is compared to observed root mean square error between GNSS-R measurements and a colocated tide gauge at five sites and using two retrieval methods: spectral analysis and inverse modeling. We find that the inverse method is more precise than the spectral analysis method by up to 60 for individual measurements but the two methods perform similarly for daily and monthly means. We quantify the contribution of dominant effects to the variations in precision and find that noise is the dominant source of uncertainty for spectral analysis whereas the effect of the dynamic sea surface is the dominant source of uncertainty for the inverse method. Additionally, we test the sensitivity of sea-level measurements to the choice of elevation angle interval and find that the spectral analysis method is more sensitive to the choice of elevation angle interval than the inverse method due to the effect of noise, which is greater at larger elevation angle intervals. Conversely, the effect of tropospheric delay increases for lower elevation angle intervals but is generally a minor contribution

Discovery of Sexual Dimorphisms in Metabolic and Genetic Biomarkers

Metabolomic profiling and the integration of whole-genome genetic association data has proven to be a powerful tool to comprehensively explore gene regulatory networks and to investigate the effects of genetic variation at the molecular level. Serum metabolite concentrations allow a direct readout of biological processes, and association of specific metabolomic signatures with complex diseases such as Alzheimer's disease and cardiovascular and metabolic disorders has been shown. There are well-known correlations between sex and the incidence, prevalence, age of onset, symptoms, and severity of a disease, as well as the reaction to drugs. However, most of the studies published so far did not consider the role of sexual dimorphism and did not analyse their data stratified by gender. This study investigated sex-specific differences of serum metabolite concentrations and their underlying genetic determination. For discovery and replication we used more than 3,300 independent individuals from KORA F3 and F4 with metabolite measurements of 131 metabolites, including amino acids, phosphatidylcholines, sphingomyelins, acylcarnitines, and C6-sugars. A linear regression approach revealed significant concentration differences between males and females for 102 out of 131 metabolites (p-values<3.8 x 10(-4); Bonferroni-corrected threshold). Sex-specific genome-wide association studies (GWAS) showed genome-wide significant differences in beta-estimates for SNPs in the CPS1 locus (carbamoyl-phosphate synthase 1, significance level: p<3.8 x 10(-10); Bonferroni-corrected threshold) for glycine. We showed that the metabolite profiles of males and females are significantly different and, furthermore, that specific genetic variants in metabolism-related genes depict sexual dimorphism. Our study provides new important insights into sex-specific differences of cell regulatory processes and underscores that studies should consider sex-specific effects in design and interpretation

Geographic and temporal variation in racial and ethnic disparities in SARS-CoV-2 positivity between February 2020 and August 2021 in the United States.

The coronavirus pandemic has disproportionally impacted racial and ethnic minority communities in the United States. Patterns of these disparities may be changing over time as outbreaks occur in different communities. Utilizing electronic health record data from the US Department of Veterans Affairs (VA), we estimated odds ratios, stratified by time period and region, for testing positive among 1,313,402 individuals tested for SARS-CoV-2 between February 12, 2020 and August 16, 2021 at VA medical facilities. We adjusted for personal characteristics (sex, age, rural/urban residence, VA facility) and a wide range of clinical characteristics that have been evaluated in prior SARS-CoV-2 reports and could potentially explain racial/ethnic disparities in SARS-CoV-2. Our study found racial and ethnic disparities for testing positive were most pronounced at the beginning of the pandemic and decreased over time. A key finding was that the disparity among Hispanic individuals attenuated but remained elevated, while disparities among Asian individuals reversed by March 1, 2021. The variation in racial and ethnic disparities in SARS-CoV-2 positivity by time and region, independent of underlying health status and other demographic characteristics in a nationwide cohort, provides important insight for strategies to prevent further outbreaks

Triphasic production of IFNγ by innate and adaptive lymphocytes following influenza A virus infection

Interferon gamma (IFNγ) is a potent antiviral cytokine that can be produced by many innate and adaptive immune cells during infection. Currently, our understanding of which cells produce IFNγ and where they are located at different stages of an infection is limited. We have used reporter mice to investigate in vivo expression of Ifnγ mRNA in the lung and secondary lymphoid organs during and following influenza A virus (IAV) infection. We observed a triphasic production of Ifnγ expression. Unconventional T cells and innate lymphoid cells, particularly NK cells, were the dominant producers of early Ifnγ, while CD4 and CD8 T cells were the main producers by day 10 post-infection. Following viral clearance, some memory CD4 and CD8 T cells continued to express Ifnγ in the lungs and draining lymph node. Interestingly, Ifnγ production by lymph node Natural Killer (NK), NKT and innate lymphoid type 1 cells also continued to be above naïve levels, suggesting memory-like phenotypes for these cells. Analysis of the localisation of Ifnγ+ memory CD4 and CD8 T cells demonstrated that cytokine+ T cells were located near airways and in the lung parenchyma. Following a second IAV challenge, lung IAV specific CD8 T cells rapidly increased their expression of Ifnγ while CD4 T cells in the draining lymph node increased their Ifnγ response. Together, these data suggest that Ifnγ production fluctuates based on cellular source and location, both of which could impact subsequent immune responses

Babesia divergens–like Infection, Washington State

Most reported U.S. zoonotic cases of babesiosis have occurred in the Northeast and been caused by Babesia microti. In Washington State, three cases of babesiosis have been reported previously, which were caused by WA1 (for “Washington 1”)-type parasites. We investigated a case of babesiosis in Washington in an 82–year-old man whose spleen had been removed and whose parasitemia level was 41.4%. The complete 18S ribosomal RNA gene of the parasite was amplified from specimens of his whole blood by polymerase chain reaction. Phylogenetic analysis showed the parasite is most closely related, but not identical, to B. divergens (similarity score, 99.5%), a bovine parasite in Europe. By indirect fluorescent-antibody testing, his serum reacted to B. divergens but not to B. microti or WA1 antigens. This case demonstrates that babesiosis can be caused by novel parasites detectable by manual examination of blood smears but not by serologic or molecular testing for B. microti or WA1-type parasites