Genomic duplication and translocation of reactivation transactivator and bZIP-homolog genes is a conserved event in alcelaphine herpesvirus 1.

Alcelaphine herpesvirus 1 (AlHV-1) is a gammaherpesvirus carried asymptomatically by wildebeest. Upon cross-species transmission, AlHV-1 induces malignant catarrhal fever (MCF), a fatal lymphoproliferative disease of ruminants, including cattle. The strain C500 has been cloned as an infectious, pathogenic bacterial artificial chromosome (BAC) that is used to study MCF. Although AlHV-1 infection can be established in cell culture, multiple passages in vitro cause a loss of virulence associated with rearrangements of the viral genome. Here, sequencing of the BAC clone showed that the long unique region (LUR) of the genome is nearly identical to that of the previously sequenced strain from which the BAC was derived, and identified the duplication and translocation of a region from within LUR, containing the entire coding sequences of ORF50-encoding reactivation transactivator Rta and A6-encoding bZIP protein genes. The duplicated region was further located to a position within the terminal repeat (TR) and its deletion resulted in lower ORF50 expression levels and reduced viral fitness. Finally, the presence of a similar but not identical duplication and translocation containing both genes was found in AlHV-1 strain WC11. These results indicate that selection pressure for enhanced viral fitness may drive the duplication of ORF50 and A6 in AlHV-1.Peer reviewe

Floristics and physical structure of five Amazon plots in Ecuador and Peru

The Amazon contains some of the most important forested ecosystems on earth and so we need to know the nature and degree of their similarities and differences.  Therefore, I compared the floristics and physical structure of five common Amazonian forest-types (terra firme, palm and white sand [all unflooded], várzea and igapó [both flooded]) with data from separate one ha plots in the Ecuadorean and Peruvian Amazon.  I found (1) the most abundant families were Arecaceae, Fabaceae, and Clusiaceae and those families along with Euphorbiaceae were the only families found in all five plots, (2) the highest stem density, the greatest number of large stems and the most closed canopy were in várzea and terra firme, (3) palm had the most median stems and the smallest average stem size, and (4) igapó had the smallest basal area and above-ground biomass.  Ordination on the five plots then suggested that Arecaceae and Clusiaceae best defined the floristic data, and total stems and smallest stem size class best defined the physical structure data.  Cluster analysis after ordination (1) based on floristics, showed that terra firme, várzea and igapó formed a cluster and both palm and white sand were in separate clusters by themselves, and (2) based on physical structure, showed that terra firme and palm formed a cluster, white sand and igapó formed a cluster and várzea was in a cluster by itself.  While results suggest that soil characteristics are important in determining the floristic composition of Amazon forests and flooding characteristics are important in determining their physical structure, they can only set-up hypotheses to test by future sampling of these forest-types elsewhere in the Amazon.

Ten Thousand Years of Population Relationships at the Prairie-Woodland Interface: Cranial Morphology in the Upper Midwest and Contiguous Areas of Manitoba and Ontario

Prehistoric Minnesota was characterized by significant cultural and environmental diversity. Throughout much of its 10,000 year history, this region has witnessed the interaction of human populations with their physical environment, developing adaptive strategies to effectively utilize the resources distinctive to this area. Archaeological research has focused on reconstructing the culture history and the nature and extent of relationships between contemporaneous archaeological manifestations and across major environmental biomes. The research presented here applies a bioarchaeological perspective to the investigation of past population relationships through the integration of archaeological and osteological data. This approach facilitates a more holistic understanding of human interaction in this region during the past 10,000 years of human history. A multivariate discriminant function analysis was conducted on a large sample of human crania recovered from sites dating from the Early Prehistoric to the Historic period in Minnesota and surrounding border areas in Ontario, Manitoba, North Dakota, South Dakota, Nebraska, and Iowa. A series of 41 measurements, representing the major cranio-facial functional complexes, was taken on 380 crania. Interpretation of results provided insight into the degree of genetic continuity among groups, biological homogeneity of defined archaeological cultures and burial complexes, and evaluation of proposed transformation models. Results indicate overall biological continuity between Paleoindian, Archaic and Initial Woodland groups. Significant biological discontinuity between Late Woodland groups and the populations of the Middle Missouri Initial variant, Oneota, and Mississippi traditions suggests in-migration of various populations during this time. The Late Woodland Blackduck phase and the Arvilla and Devils Lake - Sourisford burial complexes exhibit significant biological heterogeneity while the Oneota, Mississippi, and Middle Missouri traditions are more homogeneous. This distinction is most likely due to the more sedentary settlement-subsistence pattern of the southern horticulturalists and the continuation of the more mobile lifestyles of the northern groups despite documented increases in population sizes, intensive collection and reliance on wild rice, and other socio-political practices characteristic of transformation to a tribal pattern of sociopolitical organization. Results further indicate no definitive ancestor - descendant relationships between late prehistoric archaeological manifestations and resident historic tribal groups. These results may reflect the coalescence of many different tribal communities as a result of the effects of European colonization including disease, forced relocation to military forts and reservations, and manipulation by fur-trade companies to better pursue their own economic interests

A Refined Methodology for Defining Plant Communities Using Postagricultural Data from the Neotropics

How best to define and quantify plant communities was investigated using long-term plot data sampled from a recovering pasture in Puerto Rico and abandoned sugarcane and banana plantations in Ecuador. Significant positive associations between pairs of old field species were first computed and then clustered together into larger and larger species groups. I found that (1) no pasture or plantation had more than 5% of the possible significant positive associations, (2) clustering metrics showed groups of species participating in similar clusters among the five pasture/plantations over a gradient of decreasing association strength, and (3) there was evidence for repeatable communities—especially after banana cultivation—suggesting that past crops not only persist after abandonment but also form significant associations with invading plants. I then showed how the clustering hierarchy could be used to decide if any two pasture/plantation plots were in the same community, that is, to define old field communities. Finally, I suggested a similar procedure could be used for any plant community where the mechanisms and tolerances of species form the “cohesion” that produces clustering, making plant communities different than random assemblages of species

Soil chemical signatures of past activities on historic farmsteads in the Upland South

This study was an attempt to document the usefulness of chemical analysis for activity detection and soil identification on late nineteenth and early twentieth century historic farmstead sites in the Upland South. Five historic house sites in Knox County, Tennessee were selected for study. These included the Mabry site (40KN86) in West Knoxville, and four sites in Tooele Bend; the Oliver site (40KN103), the Bart Toole House site (no number), the Horace Jones House site (40KN105), and the John Jones House site (no number). Research concentrated on defining building dimensions and function, locating and assessing areas of past activities through the identification of soil chemical signatures, and testing a yard proxemics model developed by Moir (1987).Total carbon, pH, and twenty chemical elements, assayed by anInductively Coupled Plasma Optical Emission Spectrometer,were used in the analysis. Through ethnographic and ethnohistorical research of activities common to historic farms in the Upland South nine analytical categories were constructed. These categories represented the specific chemical portions of the possible activities. Using the background off-site soil as a control standard, the magnitude of soil chemical anomalies within these categories were mapped at each site sampling location. It was the spatially distinct co-occurrence of soil chemical anomalies in the different categories that pointed to the detection and identification of soil activities. chemical signatures of past The confirmation of the dimensions of the houses or cabins that were no longer standing at the Mabry, Oliver, and the John Jones House sites was adequate. However, the less specific identification of the interior versus the exterior was more satisfactory. Functionally, the standing outbuildings at the Horace Jones House site were speculated as industrial storage or multi-use structures. Soil chemical anomalies were found on all the sites and were often spatially distinct. Soil chemical signatures could be determined and were directly related to specific areas of past activities. Possible smokehouses were identified on the Mabry and Oliver sites. In addition, one or many agricultural/industrial buildings were postulated on the Mabry site. Areas of generalized sheet midden deposition were found at many of the sites. The yard proxemics model derived from Moir\u27s (1987) work on free tenant farmers in the Upland South holds up fairly well on these sites, including Mabry, a slave plantation site. On all sites except Oliver, the Immediate Active Yard (within 6 m of the domicile) was fairly clean of soil chemical anomalies--at least in the front yard. Confirmation of the proxemics model in the back yard was more mixed. For Example, soil chemical anomalies were found in the Immediate Active Yard on the Bart Toole and John Jones House sites. Despite the less than complete confirmation of Moir\u27s (1987) proxemics model, it appears that the spatial arrangement of activities was similar around these house sites. This arrangement was fairly consistent across farmsteads in the Upland South during this time. The results of this study showed that, though still in its infancy, the application of soil chemical research can be a valid, consistent complement to traditional object- orientated methods of activity area analysis

Ten Thousand Years of Population Relationships at the Prairie-Woodland Interface: Cranial Morphology in the Upper Midwest and Contiguous Areas of Manitoba and Ontario

Prehistoric Minnesota was characterized by significant cultural and environmental diversity. Throughout much of its 10,000 year history, this region has witnessed the interaction of human populations with their physical environment, developing adaptive strategies to effectively utilize the resources distinctive to this area. Archaeological research has focused on reconstructing the culture history and the nature and extent of relationships between contemporaneous archaeological manifestations and across major environmental biomes. The research presented here applies a bioarchaeological perspective to the investigation of past population relationships through the integration of archaeological and osteological data. This approach facilitates a more holistic understanding of human interaction in this region during the past 10,000 years of human history. A multivariate discriminant function analysis was conducted on a large sample of human crania recovered from sites dating from the Early Prehistoric to the Historic period in Minnesota and surrounding border areas in Ontario, Manitoba, North Dakota, South Dakota, Nebraska, and Iowa. A series of 41 measurements, representing the major cranio-facial functional complexes, was taken on 380 crania. Interpretation of results provided insight into the degree of genetic continuity among groups, biological homogeneity of defined archaeological cultures and burial complexes, and evaluation of proposed transformation models. Results indicate overall biological continuity between Paleoindian, Archaic and Initial Woodland groups. Significant biological discontinuity between Late Woodland groups and the populations of the Middle Missouri Initial variant, Oneota, and Mississippi traditions suggests in-migration of various populations during this time. The Late Woodland Blackduck phase and the Arvilla and Devils Lake - Sourisford burial complexes exhibit significant biological heterogeneity while the Oneota, Mississippi, and Middle Missouri traditions are more homogeneous. This distinction is most likely due to the more sedentary settlement-subsistence pattern of the southern horticulturalists and the continuation of the more mobile lifestyles of the northern groups despite documented increases in population sizes, intensive collection and reliance on wild rice, and other socio-political practices characteristic of transformation to a tribal pattern of socio-political organization. Results further indicate no definitive ancestor - descendant relationships between late prehistoric archaeological manifestations and resident historic tribal groups. These results may reflect the coalescence of many different tribal communities as a result of the effects of European colonization including disease, forced relocation to military forts and reservations, and manipulation by fur-trade companies to better pursue their own economic interests