Thomas A. Jennings

The Buttermilk Creek Complex and the Origins of Clovis at the Debra L. Friedkin Site, Texas

A large artifact assemblage dating to 15,000 years ago lies beneath a Clovis assemblage in central Texas. Compelling archaeological evidence of an occupation older than Clovis (~12.8 to 13.1 thousand years ago) in North America is present at only a few sites, and the stone tool assemblages from these sites are small and varied. The Debra L. Friedkin site, Texas, contains an assemblage of 15,528 artifacts that define the Buttermilk Creek Complex, which stratigraphically underlies a Clovis assemblage and dates between ~13.2 and 15.5 thousand years ago. The Buttermilk Creek Complex confirms the emerging view that people occupied the Americas before Clovis and provides a large artifact assemblage to explore Clovis origins.

NS3 helicase from the hepatitis C virus can function as a monomer or oligomer depending on enzyme and substrate concentrations

Hepatitis C virus NS3 helicase can unwind double-stranded DNA and RNA and has been proposed to form oligomeric structures. Here we examine the DNA unwinding activity of monomeric NS3. Oligomerization was measured by preparing a fluorescently labeled form of NS3, which was titrated with unlabeled NS3, resulting in a hyperbolic increase in fluorescence anisotropy and providing an apparent equilibrium dissociation constant of 236 nm. To evaluate the DNA binding activity of individual subunits within NS3 oligomers, two oligonucleotides were labeled with fluorescent donor or acceptor molecules and then titrated with NS3. Upon the addition of increasing concentrations of NS3, fluorescence energy transfer was observed, which reached a plateau at a 1:1 ratio of NS3 to oligonucleotides, indicating that each subunit within the oligomeric form of NS3 binds to DNA. DNA unwinding was measured under multiple turnover conditions with increasing concentrations of NS3; however, no increase in specific activity was observed, even at enzyme concentrations greater than the apparent dissociation constant for oligomerization. An ATPase-deficient form of NS3, NS3(D290A), was prepared to explore the functional consequences of oligomerization. Under single turnover conditions in the presence of excess concentration of NS3 relative to DNA, NS3(D290A) exhibited a dominant negative effect. However, under multiple turnover conditions in which DNA concentration was in excess to enzyme concentration, NS3(D290A) did not exhibit a dominant negative effect. Taken together, these data support a model in which monomeric forms of NS3 are active. Oligomerization of NS3 occurs, but subunits can function independently or cooperatively, dependent upon the relative concentration of the DNA.

RNA unwinding activity of the hepatitis C virus NS3 helicase is modulated by the NS5B polymerase.

Hepatitis C virus (HCV) infects over 170 million persons worldwide. It is the leading cause of liver disease in the U.S. and is responsible for most liver transplants. Current treatments for this infectious disease are inadequate; therefore, new therapies must be developed. Several labs have obtained evidence for a protein complex that involves many of the nonstructural (NS) proteins encoded by the virus. NS3, NS4A, NS4B, NS5A, and NS5B appear to interact structurally and functionally. In this study, we investigated the interaction between the helicase, NS3, and the RNA polymerase, NS5B. Pull-down experiments and surface plasmon resonance data indicate a direct interaction between NS3 and NS5B that is primarily mediated through the protease domain of NS3. This interaction reduces the basal ATPase activity of NS3. However, NS5B stimulates product formation in RNA unwinding experiments under conditions of excess nucleic acid substrate. When the concentrations of NS3 and NS5B are in excess of nucleic acid substrate, NS5B reduces the rate of NS3-catalyzed unwinding. Under pre-steady-state conditions, in which NS3 and substrate concentrations are similar, product formation increased in the presence of NS5B. The increase was consistent with 1:1 complex formed between the two proteins. A fluorescently labeled form of NS3 was used to investigate this interaction through fluorescence polarization binding assays. Results from this assay support interactions that include a 1:1 complex formed between NS3 and NS5B. The modulation of NS3 by NS5B suggests that these proteins may function together during replication of the HCV genome.

Hepatitis C Virus NS3 Helicase Forms Oligomeric Structures That Exhibit Optimal DNA Unwinding Activity in Vitro

HCV NS3 helicase exhibits activity toward DNA and RNA substrates. The DNA helicase activity of NS3 has been proposed to be optimal when multiple NS3 molecules are bound to the same substrate molecule. NS3 catalyzes little or no measurable DNA unwinding under single cycle conditions in which the concentration of substrate exceeds the concentration of enzyme by 5-fold. However, when NS3 (100 nm) is equimolar with the substrate, a small burst amplitude of ∼8 nm is observed. The burst amplitude increases as the enzyme concentration increases, consistent with the idea that multiple molecules are needed for optimal unwinding. Protein-protein interactions may facilitate optimal activity, so the oligomeric properties of the enzyme were investigated. Chemical cross-linking indicates that full-length NS3 forms higher order oligomers much more readily than the NS3 helicase domain. Dynamic light scattering indicates that full-length NS3 exists as an oligomer, whereas NS3 helicase domain exists in a monomeric form in solution. Size exclusion chromatography also indicates that full-length NS3 behaves as an oligomer in solution, whereas the NS3 helicase domain behaves as a monomer. When NS3 was passed through a small pore filter capable of removing protein aggregates, greater than 95% of the protein and the DNA unwinding activity was removed from solution. In contrast, only ∼10% of NS3 helicase domain and ∼20% of the associated DNA unwinding activity was removed from solution after passage through the small pore filter. The results indicate that the optimally active form of full-length NS3 is part of an oligomeric species in vitro.

Incidence of and Risk Factors for Skin Cancer in Organ Transplant Recipients in the United States

Importance Skin cancer is the most common malignancy occurring after organ transplantation. Although previous research has reported an increased risk of skin cancer in solid organ transplant recipients (OTRs), no study has estimated the posttransplant population–based incidence in the United States. Objective To determine the incidence and evaluate the risk factors for posttransplant skin cancer, including squamous cell carcinoma (SCC), melanoma (MM), and Merkel cell carcinoma (MCC) in a cohort of US OTRs receiving a primary organ transplant in 2003 or 2008. Design, Setting, and Participants This multicenter retrospective cohort study examined 10 649 adult recipients of a primary transplant performed at 26 centers across the United States in the Transplant Skin Cancer Network during 1 of 2 calendar years (either 2003 or 2008) identified through the Organ Procurement and Transplantation Network (OPTN) database. Recipients of all organs except intestine were included, and the follow-up periods were 5 and 10 years. Main Outcomes and Measures Incident skin cancer was determined through detailed medical record review. Data on predictors were obtained from the OPTN database. The incidence rates for posttransplant skin cancer overall and for SCC, MM, and MCC were calculated per 100 000 person-years. Potential risk factors for posttransplant skin cancer were tested using multivariate Cox regression analysis to yield adjusted hazard ratios (HR). Results Overall, 10 649 organ transplant recipients (mean [SD] age, 51 [12] years; 3873 women [36%] and 6776 men [64%]) contributed 59 923 years of follow-up. The incidence rates for posttransplant skin cancer was 1437 per 100 000 person-years. Specific subtype rates for SCC, MM, and MCC were 812, 75, and 2 per 100 000 person-years, respectively. Statistically significant risk factors for posttransplant skin cancer included pretransplant skin cancer (HR, 4.69; 95% CI, 3.26-6.73), male sex (HR, 1.56; 95% CI, 1.34-1.81), white race (HR, 9.04; 95% CI, 6.20-13.18), age at transplant 50 years or older (HR, 2.77; 95% CI, 2.20-3.48), and being transplanted in 2008 vs 2003 (HR, 1.53; 95% CI, 1.22-1.94). Conclusions and Relevance Posttransplant skin cancer is common, with elevated risk imparted by increased age, white race, male sex, and thoracic organ transplantation. A temporal cohort effect was present. Understanding the risk factors and trends in posttransplant skin cancer is fundamental to targeted screening and prevention in this population.

PRE-CLOVIS LITHIC TECHNOLOGY AT THE DEBRA L. FRIEDKIN SITE, TEXAS: COMPARISONS TO CLOVIS THROUGH SITE-LEVEL BEHAVIOR, TECHNOLOGICAL TRAIT-LIST, AND CLADISTIC ANALYSES

Abstract Humans first left Siberia and colonized the Americas perhaps around 16,000 years ago, and the Clovis archaeological complex in North America has traditionally been linked to this migratory pulse. Archaeologists searching for evidence of Clovis technological antecedents have focused their attention on the Beringian and Siberian archaeological records. Growing evidence for the pre-Clovis occupation of North America provides a possible alternative source for the origins of Clovis. In this paper, we present new data on the pre-Clovis lithic assemblage from the Debra L. Friedkin site, Texas, and compare Clovis and pre-Clovis lithic technological signatures. We show that while Clovis and pre-Clovis share some important technological traits, they also differ in important ways. We conclude that the pre-Clovis assemblage from Debra L. Friedkin cannot be called “Clovis,” but it could represent a technological antecedent of Clovis.

TESTING FOR EVIDENCE OF PALEOINDIAN RESPONSES TO ENVIRONMENTAL CHANGES DURING THE YOUNGER DRYAS CHRONOZONE IN GEORGIA

Abstract For the Southeast, it has been proposed that climate changes during the Younger Dryas period triggered a human population decline and/or substantial reorganization. We use the Georgia point record in the Paleoindian Database of the Americas to test for evidence of changes in landscape use through the Paleoindian period and consider these changes in the context of the Georgia paleoenvironmental record spanning the Younger Dryas. Based on differences in point frequencies, distributions, raw material types, and transport distances and directions, we conclude that significant changes in landscape use occurred during the Paleoindian period, and these correspond to destabilization of the immediate coastal zone due to fluctuations in sea level.

Paleoindian unifacial stone tool 'spurs': intended accessories or incidental accidents?

Paleoindian unifacial stone tools frequently exhibit distinct, sharp projections, known as “spurs”. During the last two decades, a theoretically and empirically informed interpretation–based on individual artifact analysis, use-wear, tool-production techniques, and studies of resharpening–suggested that spurs were sometimes created intentionally via retouch, and other times created incidentally via resharpening or knapping accidents. However, more recently Weedman strongly criticized the inference that Paleoindian spurs were ever intentionally produced or served a functional purpose, and asserted that ethnographic research “demonstrates that the presence of so called ‘graver’ spurs does not have a functional significance.” While ethnographic data cannot serve as a direct test of the archaeological record, we used Weedman’s ethnographic observations to create two quantitative predictions of the Paleoindian archaeological record in order to directly examine the hypothesis that Paleoindian spurs were predominantly accidents occurring incidentally via resharpening and reshaping. The first prediction is that the frequency of spurs should increase as tool reduction proceeds. The second prediction is that the frequency of spurs should increase as tool breakage increases. An examination of 563 unbroken tools and 629 tool fragments from the Clovis archaeological record of the North American Lower Great Lakes region showed that neither prediction was consistent with the notion that spurs were predominately accidents. Instead, our results support the prevailing viewpoint that spurs were sometimes created intentionally via retouch, and other times, created incidentally via resharpening or knapping accidents. Behaviorally, this result is consistent with the notion that unifacial stone tools were multifunctional implements that enhanced the mobile lifestyle of Pleistocene hunter-gatherers.

The Impact of Stone Supply Stress on the Innovation of a Cultural Variant: The Relationship of Folsom and Midland

Multiple hypotheses have been proposed to explain the relationship between fully fluted Folsom points and unfluted Midland points. One hypothesis, proposed by Hofman (1992, “Recognition and interpretation of Folsom technological variability on the southern plains.” In Ice Age Hunters of the Rockies, edited by D. J. Stanford, and J. S. Day, 193–229. Boulder: University Press of Colorado), is that mobile Folsom bands shifted from making Folsom points, which often fatally broke during the production process, to less risky Midland points as stone supplies dwindled. In cultural evolutionary terms, this hypothesis proposes that an increase in local, site-scale functional controls, specifically stone supply stress, resulted in the modification of the existing Folsom point production recipe and led to the adoption of a new cultural variant, the Midland point. After testing archaeological implications of Hofmans hypothesis, I conclude that it is empirically supported and does explain the innovation of the Midland cultural variant. I then use assemblage-scale measures to reconstruct Folsom/Midland mobility patterns in the southern Plains.

Exploring late Paleoindian and early Archaic unfluted lanceolate point classification in the Southern Plains

During the late Paleoindian and early Archaic periods, the Southern Plains witnessed a diversification in unfluted lanceolate point styles. The classification of these points into distinct and meaningful typological groups continues to play a fundamental role in building an understanding of cultural changes at the end of the last Ice Age. In this study, we analyze a sample of points from the Hogeye site, Texas to explore unfluted lanceolate point classifications. The results suggest the presence of at least three late Paleoindian/early Archaic point hafting traditions in the Southern Plains, an Angostura/Thrall Tradition, a Dalton/Golondrina Tradition, and a Plainview/St. Marys Hall Tradition.