READING THE BONES: A TAPHONOMIC INVESTIGATION OF ARCHAEOFAUNAL REMAINS RECOVERED FROM SITE 48PA551, NORTHWEST WYOMING

This is a preliminary taphonomy study of archaeofaunal remains found at site 48PA551, more commonly known as the Dead Indian Creek Site. 48PA551 is a well-known and commonly cited example of a McKean Complex occupation dating to between 3,800 and 4,800 B.P. The University of Montana held a field school at the site conducting small test excavations under the supervision of Dr. Anna Marie Prentiss in 2018. In the course of this testing a highly fragmentary bone bed consisting mostly of mammalian bone, cervids largely, was discovered eroding into the nearby creek. Ten 50 x 50 cm quadrants were excavated and a large number of faunal remains recovered. This study seeks to reconstruct taphonomic site history specifically focusing on what taphonomic agents and processes have created and impacted the data recovered from the Cut Bank. Using well established statistical methods, I test for both human and non-human processes that may have biasing effects on the data. In doing so patterns in the data emerge that build upon and reinforce interpretations from previous studies at this site. Implications for the importance of the contribution of this site to the greater understanding of the socio-economic changes that were taking place during the McKean complex are offered, as well as recommendations for future research and the need for further data recovery

Changes in Alternative Splicing as Pharmacodynamic Markers for Sudemycin D6

Objective: The aim of the study was to define pharmacodynamic markers for sudemycin D6, an experimental cancer drug that changes alternative splicing in human blood. Methods: Blood samples from 12 donors were incubated with sudemycin D6 for up to 24 hours, and at several time points total RNA from lymphocytes was prepared and the pre-messenger RNA (mRNA) splicing patterns were analyzed with reverse transcription-polymerase chain reaction. Results: Similar to immortalized cells, blood lymphocytes change alternative splicing due to sudemycin D6 treatment. However, lymphocytes in blood respond slower than immortalized cultured cells. Conclusions: Exon skipping in the DUSP11 and SRRM1 pre-mRNAs are pharmacodynamic markers for sudemycin D6 treatment and show effects beginning at 9 hours after treatment

Specific inhibition of complement activation significantly ameliorates autoimmune blistering disease in mice

Epidermolysis bullosa acquisita (EBA) is an antibody-mediated blistering skin disease associated with tissue-bound and circulating autoantibodies to type VII collagen (COL7). Transfer of antibodies against COL7 into mice results in a subepidermal blistering phenotype, strictly depending on the complement component C5. Further, activation predominantly by the alternative pathway is required to induce experimental EBA, as blistering was delayed and significantly ameliorated only in factor B−/− mice. However, C5 deficiency not only blocked the activation of terminal complement components and assembly of the membrane attack complex (MAC) but also eliminated the formation of C5a. Therefore, in the present study, we first aimed to elucidate which molecules downstream of C5 are relevant for blister formation in this EBA model and could be subsequently pharmaceutically targeted. For this purpose, we injected mice deficient in C5a receptor 1 (C5aR1) or C6 with antibodies to murine COL7. Importantly, C5ar1−/− mice were significantly protected from experimental EBA, demonstrating that C5a–C5aR1 interactions are critical intermediates linking pathogenic antibodies to tissue damage in this experimental model of EBA. By contrast, C6−/− mice developed widespread blistering disease, suggesting that MAC is dispensable for blister formation in this model. In further experiments, we tested the therapeutic potential of inhibitors of complement components which were identified to play a key role in this experimental model. Complement components C5, factor B (fB), and C5aR1 were specifically targeted using complement inhibitors both prophylactically and in mice that had already developed disease. All complement inhibitors led to a significant improvement of the blistering phenotype when injected shortly before anti-COL7 antibodies. To simulate a therapeutic intervention, anti-fB treatment was first administered in full-blown EBA (day 5) and induced significant amelioration only in the final phase of disease evolution, suggesting that early intervention in disease development may be necessary to achieve higher efficacy. Anti-C5 treatment in incipient EBA (day 2) significantly ameliorated disease during the whole experiment. This finding is therapeutically relevant, since the humanized anti-C5 antibody eculizumab is already successfully used in patients. In conclusion, in this study, we have identified promising candidate molecules for complement-directed therapeutic intervention in EBA and similar autoantibody-mediated diseases

Qualitative insights into the feelings, knowledge, and impact of SUDEP: A narrative synthesis

People with epilepsy (PWE) have a two- to threefold increased chance of premature death due to the condition. Interested in exploring the first-person perspective on this topic, we conducted a narrative synthesis to present the qualitative insight of PWE, their family, friends, and healthcare providers (HCPs) in relation to epilepsy-related death. A comprehensive electronic search of all peer-reviewed qualitative studies was conducted through databases using relevant keywords and Medical Subject Headings (MeSH) terms. Handsearching and exploration of pertinent gray literature was conducted thereafter. After a comprehensive literature search, the decisions of inclusion of literature were discussed and confirmed between the two authors. A total of 20 peer-reviewed papers were included. Within this, 17 were qualitative or mixed methods studies, and three were gray literature and guidelines/recommendations in discussing sudden unexpected death in epilepsy (SUDEP) with PWE and their families. The resultant main categories were the following: a) understanding of SUDEP and b) discussion of SUDEP. Findings show that there is an overall lack of understanding of unexpected epilepsy-related death for PWE and their relations. The literature focused on the education of PWE and their family in relation to SUDEP, and therefore, there is a lack of discussion on the general topic of epilepsy-related death. Findings show the conflicting perceptions, feelings, and thought processes that occur in learning about and deciding to discuss SUDEP as a HCP, PWE, or family/friend of a PWE. The literature suggests that it would be appropriate and necessary to discuss the topic of SUDEP with patients and their family members upon diagnosis

The burden of premature mortality of epilepsy in high-income countries: A systematic review from the Mortality Task Force of the International League Against Epilepsy

Since previous reviews of epidemiologic studies of premature mortality among people with epilepsy were completed several years ago, a large body of new evidence about this subject has been published. We aim to update prior reviews of mortality in epilepsy and to reevaluate and quantify the risks, potential risk factors, and causes of these deaths. We systematically searched the Medline and Embase databases to identify published reports describing mortality risks in cohorts and populations of people with epilepsy. We reviewed relevant reports and applied criteria to identify those studies likely to accurately quantify these risks in representative populations. From these we extracted and summarized the reported data. All population-based studies reported an increased risk of premature mortality among people with epilepsy compared to general populations. Standard mortality ratios are especially high among people with epilepsy aged <50 years, among those whose epilepsy is categorized as structural/metabolic, those whose seizures do not fully remit under treatment, and those with convulsive seizures. Among deaths directly attributable to epilepsy or seizures, important immediate causes include sudden unexpected death in epilepsy (SUDEP), status epilepticus, unintentional injuries, and suicide. Epilepsy-associated premature mortality imposes a significant public health burden, and many of the specific causes of death are potentially preventable. These require increased attention from healthcare providers, researchers, and public health professionals

An expansive human regulatory lexicon encoded in transcription factor footprints.

Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency

Tissue microarray methodology identifies complement pathway activation and dysregulation in progressive multiple sclerosis

BACKGROUND: The complement pathway has potential contributions to both white (WM) and grey matter (GM) pathology in Multiple Sclerosis (MS). A quantitative assessment of complement involvement is lacking. OBJECTIVE: Tissue MicroArray methodology was used in conjunction with immunohistochemistry to investigate the localization of complement pathway proteins in progressive MS cortical GM and subcortical WM. METHODS: Antibodies targeting complement proteins C1q, C3b, regulatory proteins C1 inhibitor (C1INH), complement receptor 1 (CR1), clusterin, factor H (FH) and the C5a anaphylatoxin receptor (C5aR) were utilised alongside standard markers of tissue pathology. All stained slides were digitised for quantitative analysis. RESULTS: Numbers of cells immunolabelled for HLA-DR, GFAP, C5aR, C1q and C3b were increased in WM lesions (WML) and GM lesions (GML) compared to normal appearing WM (NAWM) and GM (NAGM), respectively. The complement regulators C1INH, CR1, FH and clusterin were more abundant in WM lesions, while the number of C1q+ neurons were increased and the number of C1INH+, clusterin+, FH+ and CR1+ neurons decreased in GM lesions. The number of complement component positive cells (C1q, C3b) correlated with complement regulator expression in WM, but there was no statistical association between complement activation and regulator expression in the GM. CONCLUSION: Tissue microarray methodology and quantitative analysis provides evidence of complement dysregulation in MS GML, including an association of the numerical density of C1q+ cells with tissue lesions. Our work confirms that complement activation and dysregulation occur in all cases of progressive MS and suggest that complement may provide potential biomarkers of the disease.

Purification and characterization of cytochrome P450 2E2 from hepatic microsomes of neonatal rabbits

The alcohol-inducible P450 2E subfamily in the rabbit has two known members that differ in only 16 amino acid residues scattered throughout the polypeptide chain. P450 2E1 has been thoroughly characterized, and is known to have diverse inducers and substrates. Little is known, however, about the properties of P450 2E2, since efforts to isolate this isozyme from adult rabbits have been unsuccessful. In the present study, 2E2 was purified to electrophoretic homogeneity from liver microsomes of neonatal rabbits with the use of 4-methylpyrazole as a stabilizing agent. The purified cytochrome was identified as 2E2 by NH2-terminal amino acid sequence analysis as well as by immunoblot analysis with three different antibodies to 2E1. Purified 2E2, in contrast to 2E1, is predominantly low-spin in the presence of 20% glycerol, but is in a mixed high- and low-spin state as the concentration of glycerol is decreased. The catalytic properties of purified 2E1 and 2E2 were compared in the reconstituted system with a variety of substrates, including alcohols, ethers nitrosamines, and aromatic compounds. Differences between the two enzymes in catalytic activity and in the interaction with cytochrome b5 were observed with some but not all of the substrates tested. Purified 2E1 and 2E2 both consume molecular oxygen relatively rapidly during NADPH oxidation in the absence of an added substrate, and stoichiometric determinations indicated that only about 20% of the O2 was reduced to H2O2, with the remainder apparently undergoing four-electron reduction to water.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29002/1/0000031.pd

The accessible chromatin landscape of the human genome

DNaseI hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers, and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ~2.9 million DHSs that encompass virtually all known experimentally-validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation, and regulatory factor occupancy patterns. We connect ~580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is choreographed with dozens to hundreds of co-activated elements, and the trans-cellular DNaseI sensitivity pattern at a given region can predict cell type-specific functional behaviors. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation

Surviving Mousepox Infection Requires the Complement System

Poxviruses subvert the host immune response by producing immunomodulatory proteins, including a complement regulatory protein. Ectromelia virus provides a mouse model for smallpox where the virus and the host's immune response have co-evolved. Using this model, our study investigated the role of the complement system during a poxvirus infection. By multiple inoculation routes, ectromelia virus caused increased mortality by 7 to 10 days post-infection in C57BL/6 mice that lack C3, the central component of the complement cascade. In C3−/− mice, ectromelia virus disseminated earlier to target organs and generated higher peak titers compared to the congenic controls. Also, increased hepatic inflammation and necrosis correlated with these higher tissue titers and likely contributed to the morbidity in the C3−/− mice. In vitro, the complement system in naïve C57BL/6 mouse sera neutralized ectromelia virus, primarily through the recognition of the virion by natural antibody and activation of the classical and alternative pathways. Sera deficient in classical or alternative pathway components or antibody had reduced ability to neutralize viral particles, which likely contributed to increased viral dissemination and disease severity in vivo. The increased mortality of C4−/− or Factor B−/− mice also indicates that these two pathways of complement activation are required for survival. In summary, the complement system acts in the first few minutes, hours, and days to control this poxviral infection until the adaptive immune response can react, and loss of this system results in lethal infection