Characterization of Growth for the Subcluster B5 Mycobacteriophage Donny Using Optical Density Measurements

The mycobacteriophage Donny was discovered in Dahlonega, GA in 2016 as part of the SEA-PHAGES Program and is currently only one of seven verified phages in subcluster B5. Through various protocols for phage DNA purification and amplification, gene expression can be observed during lysis of its host, Mycobacterium smegmatis using real time PCR. Bacteriophages provide inherently novel subjects for genetic analyses as they are a highly diverse and ubiquitous group. There is little published research on phage from Cluster B which are a large yet genetically distinct group compared to other clusters or singletons. In order to begin analyzing gene expression during the phage life cycle, observation of Donny’s unique burst time is required so that optimal time frames can be selected for RNA extraction. Using absorbance data obtained from Optical Density (OD) measurements at a wavelength of 600nm, a potential time frame for RNA extraction during early, middle, and late infection was determined. This project contributes to the overall goal of characterizing the genes expressed during Donny\u27s lytic cycle using primers designed from sequence analysis of all 96 genes

Alaska Peninsula Stable Isotope and Radioisotope Chemistry: A Study in Temporal and Adaptive Diversity

Purified bone collagen from a small suite of human remains recovered at three sites on the Alaska Peninsula (Port Moller, Brooks River, and Mink Island) were analyzed for stable carbon and nitrogen isotope chemistry and were accelerator radiocarbon dated. Because samples sizes were small and faunal isotope chemistry lacking, results should be considered preliminary. However, these data indicate that each locality was represented by a somewhat different suite of subsistence strategies and covered a distinct temporal span. Port Moller burials (n = 7) from the Hot Springs site date to a calibrated 2σ range of 3547–1388 BP. Although marine foods clearly made the greatest contribution to these diets, individuals were not as heavily reliant on high-trophic-level marine taxa as eastern Aleutian groups to the west, given their intake of salmon and evidence of caribou hunting. Brooks River burials (n = 9) expressed an inland foraging focus with significant reliance on caribou and spawning salmon and covered a calibrated 2σ range of 1484–381 BP. In contrast, individuals from Mink Island (n = 7), dating to cal. 666–292 BP, were heavily reliant on high-trophic-level marine prey similar to but not as enriched isotopically as the Aleut, perhaps a consequence of limited access to caribou and greater reliance on invertebrates. This pattern suggests that prehistoric economic strategies on the Alaska Peninsula were diverse, characterized by fine-tuned adaptations to local ecological settings, perhaps mediated by ethnic factors and territorial and social pressures. Pay-Per-View Download To access this article as a PDF pay-per-view download via BioOne, please click here

Temporal and Dietary Reconstruction of Past Aleut Populations: Stable- and Radio-Isotope Evidence Revisited

A recent accelerator radiocarbon study of Eastern Aleutian human remains that Ales Hrdlicka collected in the 1930s contradicts his long-standing assertion that brachycranic Neo-Aleut people, moving west along the island chain at ca. 1000 BP, replaced the dolichocranic Paleo-Aleut population. Radiocarbon dates for Paleo-Aleut individuals ranged from ca. 3400 to 400 cal BP, covering the entire temporal span of the study and indicating that Paleo-Aleuts coexisted in the study area with Neo-Aleuts from ca. AD 1000 until well into the 16th century. Shortly after publication of that study, the curating institution informed the authors that a small number of cataloguing errors with respect to cranial category had come to their attention. Subsequent corrections made to cranial categories have strengthened temporal patterning characteristic of this data set. Mortuary practices and genetic and dietary patterning also distinguish Paleo-Aleut from Neo-Aleut groups. The stable isotope chemistry of their diets indicates that Neo-Aleuts relied on higher-trophic-level marine taxa than Paleo-Aleuts and, within that category of taxa, on more offshore rather than nearshore-feeding pinnipeds.Une étude récente réalisée au moyen d’un accélérateur pour la datation par le carbone 14 visant des dépouilles mortelles d’Aléoutes de l’Est recueillies par Ales Hrdlicka dans les années 1930 vient contredire son affirmation de longue date selon laquelle le peuple néo-aléoute brachycrâne, se déplaçant vers l’ouest le long de l’arc insulaire vers l’an 1000 BP, a remplacé la population paléo-aléoute dolichocrâne. La datation par le carbone 14 pour les individus paléo-aléoutes variait environ entre 3400 et 400 cal. BP, ce qui recouvrait toute la durée temporelle de l’étude et indiquait que les Paléo-Aléoutes ont coexisté avec les Néo-Aléoutes dans la région visée par l’étude d’environ 1000 AD jusqu’au XVIe siècle avancé. Peu après la publication de cette étude, l’établissement responsable de la conservation a signalé aux auteurs qu’un petit nombre d’erreurs de catalogage avaient été décelées relativement à la catégorie crânienne. Les corrections qui ont été subséquemment apportées aux catégories crâniennes se sont trouvé à renforcer les caractéristiques de typification temporelle de cet ensemble de données. Les pratiques mortuaires de même que les caractéristiques génétiques et alimentaires ont également permis de distinguer les Paléo-Aléoutes des Néo-Aléoutes. La chimie des isotopes stables de leurs alimentations indique que les Néo-Aléoutes dépendaient de taxons marins de niveau trophique plus élevé que les Paléo-Aléoutes et, au sein de cette catégorie de taxon, qu’ils dépendaient davantage de pinnipèdes extracôtiers que côtiers

Measures of Center of Pressure and Lower Leg Muscle Electromyography during Landing before and after Plantar flexor Stretch

Static stretching of the plantar flexor muscles is reported to modify neuromuscular responses to external stimuli. However, it is not known how these muscles respond to external loading in an applied task, such as single-leg drops. Further, if mechanical laxity in the plantar flexor muscles is present after stretching of it is unclear how this laxity will influence the muscle activation and movement patterns of the lower extremities. PURPOSE: This study is intended to further explore the response of the lower extremities to plantar flexor muscle stretch in an effort to understand its impact on potential injury. METHODS: Five participants (20.6 ± 1.1 yrs: 1.78 ± 0.1 m:, 80.6 ± 9.9 kg) performed drop landings from a 30 cm box onto a force platform before and immediately after 10 min of passive plantar flexor stretch. Surface electromyography (EMG) was collected from tibialis anterior (TA), medial gastrocnemius (MG), lateral gastrocnemius (LG), peroneus longus (PL), and soleus (SOL) muscles. Maximal isometric plantar and dorsi flexion efforts were performed before and after 10 minutes on passive plantar flexor stretch. EMG were normalized (NEMG) to maximum values during the maximal isometric efforts. Variables of interest were NEMG at landing and center of pressure (COP) measures. NEMG were assessed 300 ms prior to and after landing onto the force platform. An inertia measurement unit (IMU) was fixed to the tibia to record landing. Comparisons were performed at landing for NEMG and COP/COP velocity up to 5 sec after landing to measure COP/COP velocity variability. Alpha was set at 0.05. RESULTS: NEMG signals differed over time for all muscle from -300 to 300 ms (all p \u3c 0.01). Significant differences in NEMG amplitude were present in MG (0.44 ± 0.5 vs 0.36 ± 0.4), LG (0.28 ± 0.3 vs 0.24 ± 0.3), and SOL (0.40 ± 0.5 vs 0.32 ± 0.3) muscles (all p \u3c 0.05) before and after stretch. COPx (pre: -Δ29.8% post: -Δ56.4%) and COPy (pre: -Δ58.8%, post: -Δ 53.5%) variability measures were significant reduced over time (p \u3c 001). A significant time x condition interaction was present for COPx velocity variability (F6,308 = 2.135, p \u3c 0.049). CONCLUSION: Passive prolonged stretching of the plantarflexor muscles can modify a functional dynamic activity, such as single-leg drop landings. Although COP was not different between the landing before and after static stretch, the control of the balance at landing was different

Hrdlič̌ka's Aleutian population-replacement hypothesis: a radiometric evaluation

Journal ArticleIn a 1945 monograph, Hrdlička argued that, at 1,000 BP, Paleo-Aleut people on Umnak Island were replaced by Neo-Aleut groups moving west along the island chain. His argument was based on cranial measurements of skeletal remains from Chaluka Midden and mummified remains from Kagamil and Ship Rock burial caves. By the 1980s, researchers had concluded that the transition demonstrated by Hrdlička, from a high oblong to a low-vaulted wide face, was merely one example of a global trend in cranial morphology and therefore population replacement had not occurred

AZIMUTH 3D: A Tool for Publishing and Annotating Rich Historical 3D Reconstructions on the Web

Despite continuing innovations in the real time display of 3D models inside web browsers, scholarly 3D historical reconstructions still have yet to make a major impact on the digital humanities landscape. This presentation will demonstrate the completed features from the first edition of Azimuth 3D, a tool developed at the University of Nebraska-Lincoln to allow humanities scholars to easily publish, annotate, and combine 3D reconstructions with other 3D data sets. As a result researchers can create persistent, richly annotated, collaborative 3d environments that can grow over time, all viewable in any web browser. Azimuth 3D is comprised of a web application that runs as a shell around 3D scenes constructed with Unity, an industry leading free and customizable online game engine. Azimuth is designed to allow the greatest degree of detail and customization while preserving the workflows of both 3D artists and digital humanities scholars. Creators can import completed content in any major 3D format into the Unity editor, and then need only to tag parts of the scene as Azimuth objects before exporting them to the Azimuth web app. In Azimuth, a creator can link a published 3D scene to any standard MySQL database, and then assign scene objects custom metadata, chronological information, annotate them, and link them to primary documents used in the reconstruction. Chronologically tagged objects will appear, evolve, and disappear as users move a timeline slider. After the initial setup of the scene objects, creators will be able to continue to enrich Azimuth scenes by connecting other digital humanities data in traditional formats. Azimuth will allow for the uploading of spatial data with standard geographic coordinates, including CSV and KML files, plotting the points live in the 3D space. Any associated or linked information to those spatial points will be viewable in the user interface. Import features will also support data in vector graphics formats like SVG, as well as georeferenced maps that users can match to the topography of the terrain. Azimuth will also include a tool for matching the perspective of imported historical photographs with the scene view. Additionally, Azimuth features a tool with which users can annotate either scene space or individual objects. Each of these annotations will also be saved as separate layers, allowing for collaboration between scholars, three dimensional peer review, and community contributions to scenes. Each imported data set will be listed as a separate layer which users may toggle on and off. Azimuth will provide scholars with great freedom to bring different kinds of humanities data together in a single 3D environment. This will allow for different sets of humanities data to contextualize one another without forcing researchers to learn to work in unfamiliar formats, or convert large sets of existing data. Because Azimuth is based on Unity, the platform will automatically incorporate updates and advances in the underlying game engine, freeing scene creators to focus on advancements in the display of humanities content, without having to worry about incorporating improvements in graphics technology