An Overview of University of Texas at Austin 2009-2012 Investigations of the Rogers Spring Archaeological Site

The purpose of this thesis is to examine the artifact assemblages of the Rogers Spring (41TV39) Archaeological Site excavations from the University of Texas field school in 2009-2012. These excavations were led by Fred Valdez, Jr. under Texas Antiquities Permit 5289. The Roger Springs Archaeological Site is rich in history and includes both historic and prehistoric contexts. I begin with a brief introduction to the Roger Springs Site focusing on the general site location and burned rock middens. I then discuss the historic settlement by the Roger family and all of the previous excavations at the site in 1933, 1972, and 2008. This will provide an understanding of the artifacts discussed in previous projects as well as give a general overview of which middens had already been examined prior to the 2009-2012 excavations. After establishing the background of the site, I then explain the methods of inventorying the artifacts at the Texas Archeological Research Laboratory (TARL). This also includes the process of locating additional excavation materials such as lot forms and student notes. I utilize information from these forms to create an overview of the excavation’s location and general descriptions of the units represented in the report (soil consistency, proximity to midden 5, and ash content). In the final analysis, I examine the materials uncovered during the field school and describe them within the prehistoric and historic context of Central Texas. I will focus on the typed projectile points found at the site and give an overview of the time periods that they are associated with. Based solely on the projectile points, there is evidence of human occupation from the Early Archaic through the Transitional Archaic. The final section discusses the possibility of further research with the material currently being housed at TARL.Anthropolog

Linear plasmids and the rate of sequence evolution in plant mitochondrial genomes

Includes bibliographical references (pages 373-374).The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses.Published with support from the Colorado State University Libraries Open Access Research and Scholarship Fund

Rewiring of Aminoacyl-tRNA Synthetase Localization and Interactions in Plants With Extensive Mitochondrial tRNA Gene Loss

The number of tRNAs encoded in plant mitochondrial genomes varies considerably. Ongoing loss of bacterial-like mitochondrial tRNA genes in many lineages necessitates the import of nuclear-encoded counterparts that share little sequence similarity. Because tRNAs are involved in highly specific molecular interactions, this replacement process raises questions about the identity and trafficking of enzymes necessary for the maturation and function of newly imported tRNAs. In particular, the aminoacyl-tRNA synthetases (aaRSs) that charge tRNAs are usually divided into distinct classes that specialize on either organellar (mitochondrial and plastid) or nuclear-encoded (cytosolic) tRNAs. Here, we investigate the evolution of aaRS subcellular localization in a plant lineage (Sileneae) that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts (PacBio Iso-Seq), we found predicted retargeting of many ancestrally cytosolic aaRSs to the mitochondrion and confirmed these results with colocalization microscopy assays. However, we also found cases where aaRS localization does not appear to change despite functional tRNA replacement, suggesting evolution of novel interactions and charging relationships. Therefore, the history of repeated tRNA replacement in Sileneae mitochondria reveals that differing constraints on tRNA/aaRS interactions may determine which of these alternative coevolutionary paths is used to maintain organellar translation in plant cells

Evolution by Any Other Name: Antibiotic Resistance and Avoidance of the E-Word

The word "evolution" is rarely used in papers from medical journals describing antimicrobial resistance, which may directly impact public perception of the importance of evolutionary biology in our everyday lives

PATH-38. ROSETTE-FORMING GLIONEURONAL TUMOR IS DEFINED BY FGFR1 ACTIVATING ALTERATIONS WITH FREQUENT ACCOMPANYING PI3K AND MAPK PATHWAY MUTATIONS

Abstract BACKGROUND Rosette-forming glioneuronal tumor (RGNT) is an uncommon CNS tumor originally described in the fourth ventricle characterized by a low-grade glial neoplasm admixed with a rosette-forming neurocytic component. METHODS We reviewed clinicopathologic features of 42 patients with RGNT. Targeted next-generation sequencing was performed, and genome-wide methylation profiling is underway. RESULTS The 20 male and 22 female patients had a mean age of 25 years (range 3–47) at time of diagnosis. Tumors were located within or adjacent to the lateral ventricle (n=16), fourth ventricle (15), third ventricle (9), and spinal cord (2). All 31 tumors assessed to date contained FGFR1 activating alterations, either in-frame gene fusion, kinase domain tandem duplication, or hotspot missense mutation in the kinase domain (p.N546 or p.K656). While 7 of these 31 tumors harbored FGFR1 alterations as the solitary pathogenic event, 24 contained additional pathogenic alterations within PI3-kinase or MAP kinase pathway genes: 5 with additional PIK3CA and NF1 mutations, 4 with PIK3CA mutation, 3 with PIK3R1 mutation (one of which also contained focal RAF1 amplification), 5 with PTPN11 mutation (one with additional PIK3R1 mutation), and 2 with NF1 deletion. The other 5 cases demonstrated anaplastic features including hypercellularity and increased mitotic activity. Among these anaplastic cases, 3 harbored inactivating ATRX mutations and two harbored CDKN2A homozygous deletion, in addition to the FGFR1 alterations plus other PI3-kinase and MAP kinase gene mutations seen in those RGNT without anaplasia. CONCLUSION Independent of ventricular location, RGNT is defined by FGFR1 activating mutations or rearrangements, which are frequently accompanied by mutations involving PIK3CA, PIK3R1, PTPN11, NF1, and KRAS. Whereas pilocytic astrocytoma and ganglioglioma are characterized by solitary activating MAP kinase pathway alterations (e.g. BRAF fusion or mutation), RGNT are genetically more complex with dual PI3K-Akt-mTOR and Ras-Raf-MAPK pathway activation. Rare anaplastic examples may show additional ATRX and/or CDKN2A inactivation

Gene content evolution in the arthropods

Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity

“We Used to Say Rats Fell from the Sky After a Flood:” Temporary Recovery of Muskrat Following Ice Jams in the Peace-Athabasca Delta

Elders and Indigenous land users in the Peace-Athabasca Delta (PAD) have observed a dramatic decline in the relative abundance of muskrat in recent decades (~1935–2014). The main explanation for the decline has been reduction in suitable habitat as a result of decades with reduced frequency of ice-jam flooding on the Peace River. Under favourable conditions, ice jams can cause flooding of perched basins within the PAD that would otherwise receive no recharge from floodwaters. To examine whether abundance of muskrat in the PAD is driven by flooding, we tested the predictions that the density of muskrat (estimated by winter counts of houses) (1) was inversely related to the number of years since major ice jam floods and (2) increased with water depth. An ongoing collaborative monitoring program initiated in 2011, combined with analysis of data from past surveys (1973–2015), allowed Indigenous land users and scientists to document a 10 to 100-fold increase in the density of muskrat houses in 24 basins, over the two years following ice-jam flood events in the PAD. During 1973–2015, in the periods between major floods, density of houses dropped by approximately 79% for every year after a significant flood. In 27 basins surveyed from 2011 to 2015, density of muskrat houses increased by two orders of magnitude in the two years following a flood in the spring of 2014. Density of muskrat houses had a non-linear relationship with estimated depth of water at the time of fall freeze-up; the highest densities of muskrat houses were in basins with about 60 – 250 cm of water at the time of freeze-up. The depth of snow at the time of surveys did not have a strong relationship with the density of muskrat houses. However, few houses were counted in basins with more than 20 cm of snow, likely because deeper snow made it more difficult to conduct surveys and spot houses. Factors other than an increase in the depth of water at fall freeze-up may provide the mechanisms by which flooding affects muskrat. Density of muskrat houses is clearly tied to ice-jam flooding in the PAD. However, the local mechanisms by which floods affect muskrat are best understood by Indigenous land users and remain poorly understood by Western science. Indigenous peoples continue to regard muskrat as an indicator of ecological and cultural health of the PAD. This study highlights the value of consistent ecological monitoring that includes Indigenous knowledge.Les aînés et les utilisateurs des terres autochtones du delta des rivières de la Paix et Athabasca ont observé une baisse draconienne de l’abondance du rat musqué au cours des dernières décennies (~1935-2014). La principale explication du déclin est la diminution d’abris convenables, et ce, en raison de plusieurs décennies marquées par la fréquence réduite d’inondations causées par des embâcles dans la rivière de la Paix. Dans des conditions favorables, les embâcles peuvent causer l’inondation des bassins perchés au sein du delta des rivières de la Paix et Athabasca qui autrement ne recevraient pas de recharge des eaux de crue. Afin d’examiner si l’abondance du rat musqué dans le delta des rivières de la Paix et Athabasca est favorisée par les inondations, nous avons testé des prévisions selon lesquelles la densité du rat musqué (estimée par le nombre d’abris en hiver) 1) était inversement liée au nombre d’années depuis les dernières importantes inondations causées par des embâcles et 2) augmentait avec la profondeur de l’eau. Un programme collaboratif de suivi continu lancé en 2011, combiné à l’analyse de données des relevés antérieurs (1973-2015), a permis aux utilisateurs des terres autochtones et aux scientifiques de multiplier de 10 à 100 fois la densité d’abris du rat musqué dans 24 bassins, au cours des deux années suivant des événementsd’inondation causés par des embâcles dans le delta des rivières de la Paix et Athabasca. Entre 1973 et 2015, durant les périodes se situant entre les inondations importantes, la densité d’abris a diminué d’environ 79 % chaque année suivant une inondation importante. Dans 27 bassins sondés entre 2011 et 2015, la densité d’abris du rat musqué a augmenté de deux ordres de grandeur au cours des deux années ayant suivi une inondation survenue au printemps de 2014. La densité d’abris du rat musqué avait une relation non linéaire avec la profondeur de l’eau estimée au moment de la prise des glaces en automne; les plus fortes densités d’abris du rat musqué se trouvaient dans les bassins ayant de 60 à 250 cm d’eau au moment de la prise des glaces. La profondeur de la neige au moment des relevés n’avait pas de relation solide avec la densité d’abris du rat musqué. Cependant, nous avons compté peu d’abris dans les bassins comptant plus de 20 cm de neige, probablement parce qu’il était plus difficile d’effectuer des relevés et de trouver les abris dans la neige plus épaisse. Des facteurs autres que l’augmentation de la profondeur de l’eau au moment de la prise des glaces en automne pourraient fournir les mécanismes par lesquels les inondations se répercutent sur les rats musqués. La densité d’abris du rat musqué est manifestement liée aux inondations causées par des embâcles dans le delta des rivières de la Paix et Athabasca. Toutefois, les utilisateurs des terres autochtones comprennent mieux les mécanismes locaux par lesquels les inondations se répercutent sur les rats musqués, tandis qu’ils demeurent mal compris par la science occidentale. Les peuples autochtones continuent de considérer le rat musqué comme un indicateur de la santé écologique et culturelle du delta des rivières de la Paix et Athabasca. Cette étude fait ressortir la valeur d’un suivi écologique constant qui tient compte des connaissances autochtones

Enterococcus faecalis demonstrates pathogenicity through increased attachment in an ex vivo polymicrobial pulpal infection

This study investigated the host response to a polymicrobial pulpal infection consisting of Streptococcus anginosus and Enterococcus faecalis, bacteria commonly implicated in dental abscesses and endodontic failure, using a validated ex vivo rat tooth model. Tooth slices were inoculated with planktonic cultures of S. anginosus or E. faecalis alone or in co-culture at ratios of 50:50 and 90:10 S. anginosus to E. faecalis. Attachment was semi-quantified by measuring area covered by fluorescently labelled bacteria. Host response was established by viable histological cell counts and inflammatory response using RT-qPCR and immunohistochemistry. A significant reduction in cell viability was observed for single and polymicrobial infections, with no significant differences between infection types (≈2000cells/mm2 for infected pulps compared to ≈4000cells/mm2 for uninfected pulps). E. faecalis demonstrated significantly higher levels of attachment (6.5%) compared to S. anginosus alone (2.3%) and mixed species infections (3.4% for 50:50 and 2.3% for 90:10), with a remarkable affinity to the pulpal vasculature. Infections with E. faecalis demonstrated the greatest increase in TNF-α (47.1 fold for E. faecalis, 14.6 fold for S. anginosus, 60.1 fold for 50:50 and 25.0 fold for 90:10) and IL-1β expression (54.8 fold for E. faecalis, 8.8 fold for S. anginosus, 54.5 fold for 50:50 and 39.9 fold for 90:10) when compared to uninfected samples. Immunohistochemistry confirmed this with the majority of inflammation localised to the pulpal vasculature and odontoblast regions. Interestingly, E. faecalis supernatant and heat killed E. faecalis treatment was unable to induce the same inflammatory response, suggesting E. faecalis pathogenicity in pulpitis is linked to its greater ability to attach to the pulpal vasculature

2016 Research & Innovation Day Program

A one day showcase of applied research, social innovation, scholarship projects and activities.https://first.fanshawec.ca/cri_cripublications/1003/thumbnail.jp