Hopewell Archeology: Volume 2 , Number 1, October 1996

1. From the Editor, Mark J. Lynott We apologize for the delay in getting this issue of the Newsletter together. The government furlough put all of us in the National Park Service behind, and we are still trying to catch up. Despite the delay, we hope you will find this issue of interest. The focus of this issue is on the value of archeology as an education tool. During the last three summers, the Midwest Archeological Center has worked with the Milton Hersey School in Hersey, Pennsylvania to offer high school students the opportunity to participate in an archeological project. This valuable experience (both for the students and for National Park Service archeologists) has been possible, because the organizer for the Milton Hersey School is also a former employee of the Midwest Archeological Center. I met Randy Farmer in 1983 when he enrolled with fifteen other students in a fieldschool we offered through the Department of Anthropology, University of Nebraska-Lincoln. The fieldschool was held at Ozark National Scenic Riverways in southeast Missouri, and most of the students were enthralled by the scenery and the thrill of archeology. Following that summer, Randy came to work at the Midwest Archeological Center on a part-time basis until he finished his B.A. in Anthropology. He then worked with us as a full-time employee, until he decided to return to school and fulfill the requirements for his teaching certificate. 2. The National Park Service and High School Archeology By Randy Farmer I became a social studies teacher for three reasons. One, I believed in the importance of understanding and appreciating history and prehistory. Two, I believed in the idea that hands on and innovative ways of teaching were critical to the future of our young people. Three, I wanted to show more people the value of archaeological research in the world today. This article describes a program I have developed to satisfy my need to improve public understanding and support for archeological study and preservation. 3.Toolesboro Mounds, Iowa, National Historic Landmark Study A recent study by the Office of the State Archaeologist of Iowa with the support of the State Historical Society of Iowa and funds provided by the National Park Service, has resulted in a new report on the Middle Woodland mounds at Toolesboro, Louisa County, Iowa. This report includes a history of the mound investigations conducted primarily by the Davenport Academy of Natural Sciences in 1875 and 1886, an analysis of the 89 extant artifacts from the mounds currently curated by the Putnam Museum in Davenport (successor to the Davenport Academy), and interpretations regarding mortuary behavior and related activities based on surviving archival evidence. 4. Current Research on the Goodall Focus On August 23, 1996, Mark Schurr hosted an informal workshop on the Goodall focus at the Archaeology Laboratory, University of Notre Dame. The meeting was held in the recently remodeled laboratories and classrooms assigned to the archaeology program at the University of Notre Dame. 5. Reviews By Bret J. Ruby, National Park Service, Hopewell Culture National Historical Park. Exploring Prehistoric Mounds on the Rix Mills-High Hill Divide: The Archaeology of the Wilds and Vicinity, Southeastern Muskingum County, Ohio. Jeff Carskadden, Jeff Brown and Gary Felumlee. Published by The Muskingum Valley Archaeological Survey, Zanesville, Ohio, in cooperation with The International Center for the Preservation of Wild Animals, 1995; 102 pp., 49 photographs, 10 maps, 4 tables, references; $20.00 (paper). 6. Meeting Calendar Midwest Archaeological Conference, Beloit College, Beloit, Wisconsin, October 9-12, 1996, contact Robert J. Salzer, Beloit College, (608) 363-2616. Southeastern Archaeological Conference, Sheraton Civic Center, Birmingham, AL, November 6- 9, 1996, contact Ian Brown, (205) 348-9742. Society for Historical Archaeology Conference, Corpus Christi, Texas, January 8-12, 1997, contact David Carlson and Shawn Carlson, Texas A&M University, (409) 847-9248. Society for American Archaeology, Annual Meeting, Nashville, Tennessee, April 2-6, 1997, contact Society for American Archaeology, (202) 789-8200. Ohio Archaeological Council, Fall Meeting, Ohio Historical Center, Columbus, OH, November 15, 1996. Ohio Archaeological Council, Spring Meeting, Symposium on Adena, Chillicothe Comfort Inn, May 9-10, 1997

The Legume Information System (LIS): an integrated information resource for comparative legume biology

The Legume Information System (LIS) (http://www.comparative-legumes.org), developed by the National Center for Genome Resources in cooperation with the USDA Agricultural Research Service (ARS), is a comparative legume resource that integrates genetic and molecular data from multiple legume species enabling cross-species genomic and transcript comparisons. The LIS virtual plant interface allows simplified and intuitive navigation of transcript data from Medicago truncatula, Lotus japonicus, Glycine max and Arabidopsis thaliana. Transcript libraries are represented as images of plant organs in different developmental stages, which are selected to query the analyzed and annotated data. Complex queries can be accomplished by adding modifiers, keywords and sequence names. The LIS also contains annotated genomic data featuring transcript alignments to validate gene predictions as well as motif and similarity analyses. The genomic browser supports comparative analysis via novel dynamic functional annotation comparisons. CMap, developed as part of the GMOD project (http://www.gmod.org/cmap/index.shtml), has been incorporated to support comparative analyses of community linkage and physical map data. LIS is being expanded to incorporate gene expression and biochemical pathways which will be seamlessly integrated forming a knowledge discovery framework

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence

Background: The Soybean Consensus Map 4.0 facilitated the anchoring of 95.6% of the soybean whole genome sequence developed by the Joint Genome Institute, Department of Energy, but its marker density was only sufficient to properly orient 66% of the sequence scaffolds. The discovery and genetic mapping of more single nucleotide polymorphism (SNP) markers were needed to anchor and orient the remaining genome sequence. To that end, next generation sequencing and high-throughput genotyping were combined to obtain a much higher resolution genetic map that could be used to anchor and orient most of the remaining sequence and to help validate the integrity of the existing scaffold builds. Results: A total of 7,108 to 25,047 predicted SNPs were discovered using a reduced representation library that was subsequently sequenced by the Illumina sequence-by-synthesis method on the clonal single molecule array platform. Using multiple SNP prediction methods, the validation rate of these SNPs ranged from 79% to 92.5%. A high resolution genetic map using 444 recombinant inbred lines was created with 1,790 SNP markers. Of the 1,790 mapped SNP markers, 1,240 markers had been selectively chosen to target existing un-anchored or un-oriented sequence scaffolds, thereby increasing the amount of anchored sequence to 97%. Conclusion: We have demonstrated how next generation sequencing was combined with high-throughput SNP detection assays to quickly discover large numbers of SNPs. Those SNPs were then used to create a high resolution genetic map that assisted in the assembly of scaffolds from the 8× whole genome shotgun sequences into pseudomolecules corresponding to chromosomes of the organism

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation.</p> <p>Results</p> <p>The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the <it>Glycine max </it>genome.</p> <p>Conclusions</p> <p>This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of <it>Glycine max </it>can be explored at <url>http://www.soybase.org/soyseq</url>.</p

Gene expression patterns are correlated with genomic and genic structure in soybean

Studies have indicated that exon and intron size and intergenic distance are correlated with gene expression levels and expression breadth. Previous reports on these correlations in plants and animals have been conflicting. In this study, next-generation sequence data, which has been shown to be more sensitive than previous expression profiling technologies, were generated and analyzed from 14 tissues. Our results revealed a novel dichotomy. At the low expression level, an increase in expression breadth correlated with an increase in transcript size because of an increase in the number of exons and introns. No significant changes in intron or exon sizes were noted. Conversely, genes expressed at the intermediate to high expression levels displayed a decrease in transcript size as their expression breadth increased. This was due to smaller exons, with no significant change in the number of exons. Taking advantage of the known gene space of soybean, we evaluated the positioning of genes and found significant clustering of similarly expressed genes. Identifying the correlations between the physical parameters of individual genes could lead to uncovering the role of regulation owing to nucleotide composition, which might have potential impacts in discerning the role of the noncoding regions

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

Background: The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) of soybean (Glycine max (L.) Merrill) has a striking effect on seed protein content. Results: A soybean near-isogenic line (NIL) pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix® Soy GeneChip and high-throughput Illumina® whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region. Conclusions: This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome

Cognitive and autonomic dysfunction measures in normal controls, white coat and borderline hypertension

<p>Abstract</p> <p>Background</p> <p>White coat hypertension (WCHT) is a significant clinical condition with haemodynamic differences and presence of functional changes. We aim to compare cognitive and autonomic dysfunction variables (heart rate variability) between subjects with normal blood pressure (controls), WCHT, and borderline hypertension (BLH).</p> <p>Methods</p> <p>We performed a cross-sectional study in a cohort of 69 subjects (mean age ± SD; 38.2 ±10.8 years) comprising comparable number of normal controls, WCHT, and BLH. We measured clinic and 24-hour ambulatory blood pressure monitoring (ABPM), cognitive function parameters, and heart rate variability (HRV). All subjects underwent 24-hour ambulatory electrocardiography monitoring which was analyzed for HRV measurements. We performed a routine echocardiography (ECHO) for all subjects.</p> <p>Results</p> <p>Multiple comparison between the three groups revealed significant (p < 0.04) differences in mean day-time ABPM (systolic and diastolic). In the state anxiety inventory (SAI), both subjects with WCHT and BLH had significantly (p < 0.006) higher anxiety levels than the control group. In memory tasks WCHT subjects scored significantly (p < 0.004) lower in comparison with the other two groups. WCHT significantly (p < 0.001) performed less in memory tests, whereas BLH subjects had significantly (p < 0.001) lower reaction time. We found a significant (p < 0.05) difference in the 24-hour RMSSD and SDNN between the three groups. There was significant correlation between 24-hour RMSSD and computer CANTAB scores. The Echocardiography assessment revealed no significant differences in LV mass indices and diastolic function.</p> <p>Conclusions</p> <p>WCHT and BLH subjects showed lower cognitive performance and higher levels of anxiety when compared to controls. Autonomic function reflected by HRV indices was lower in WCHT and BLH in contrast to control, though not significantly. Our results suggest that WCHT may not be a benign condition as it may contribute to the overall risk for cardiovascular disease and LV damage. Longitudinal studies of patients with WCHT should clarify the transient, persistent or the progressive nature of this condition.</p

Variation in carbon and nitrogen concentrations among peatland categories at the global scale

Publisher Copyright: © 2022 This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.Peatlands account for 15 to 30% of the world's soil carbon (C) stock and are important controls over global nitrogen (N) cycles. However, C and N concentrations are known to vary among peatlands contributing to the uncertainty of global C inventories, but there are few global studies that relate peatland classification to peat chemistry. We analyzed 436 peat cores sampled in 24 countries across six continents and measured C, N, and organic matter (OM) content at three depths down to 70 cm. Sites were distinguished between northern (387) and tropical (49) peatlands and assigned to one of six distinct broadly recognized peatland categories that vary primarily along a pH gradient. Peat C and N concentrations, OM content, and C:N ratios differed significantly among peatland categories, but few differences in chemistry with depth were found within each category. Across all peatlands C and N concentrations in the 10-20 cm layer, were 440 ± 85.1 g kg-1 and 13.9 ± 7.4 g kg-1, with an average C:N ratio of 30.1 ± 20.8. Among peatland categories, median C concentrations were highest in bogs, poor fens and tropical swamps (446-532 g kg-1) and lowest in intermediate and extremely rich fens (375-414 g kg-1). The C:OM ratio in peat was similar across most peatland categories, except in deeper samples from ombrotrophic tropical peat swamps that were higher than other peatlands categories. Peat N concentrations and C:N ratios varied approximately two-fold among peatland categories and N concentrations tended to be higher (and C:N lower) in intermediate fens compared with other peatland types. This study reports on a unique data set and demonstrates that differences in peat C and OM concentrations among broadly classified peatland categories are predictable, which can aid future studies that use land cover assessments to refine global peatland C and N stocks.Peer reviewe

3 years of liraglutide versus placebo for type 2 diabetes risk reduction and weight management in individuals with prediabetes: a randomised, double-blind trial

Background: Liraglutide 3·0 mg was shown to reduce bodyweight and improve glucose metabolism after the 56-week period of this trial, one of four trials in the SCALE programme. In the 3-year assessment of the SCALE Obesity and Prediabetes trial we aimed to evaluate the proportion of individuals with prediabetes who were diagnosed with type 2 diabetes. Methods: In this randomised, double-blind, placebo-controlled trial, adults with prediabetes and a body-mass index of at least 30 kg/m2, or at least 27 kg/m2 with comorbidities, were randomised 2:1, using a telephone or web-based system, to once-daily subcutaneous liraglutide 3·0 mg or matched placebo, as an adjunct to a reduced-calorie diet and increased physical activity. Time to diabetes onset by 160 weeks was the primary outcome, evaluated in all randomised treated individuals with at least one post-baseline assessment. The trial was conducted at 191 clinical research sites in 27 countries and is registered with ClinicalTrials.gov, number NCT01272219. Findings: The study ran between June 1, 2011, and March 2, 2015. We randomly assigned 2254 patients to receive liraglutide (n=1505) or placebo (n=749). 1128 (50%) participants completed the study up to week 160, after withdrawal of 714 (47%) participants in the liraglutide group and 412 (55%) participants in the placebo group. By week 160, 26 (2%) of 1472 individuals in the liraglutide group versus 46 (6%) of 738 in the placebo group were diagnosed with diabetes while on treatment. The mean time from randomisation to diagnosis was 99 (SD 47) weeks for the 26 individuals in the liraglutide group versus 87 (47) weeks for the 46 individuals in the placebo group. Taking the different diagnosis frequencies between the treatment groups into account, the time to onset of diabetes over 160 weeks among all randomised individuals was 2·7 times longer with liraglutide than with placebo (95% CI 1·9 to 3·9, p&lt;0·0001), corresponding with a hazard ratio of 0·21 (95% CI 0·13–0·34). Liraglutide induced greater weight loss than placebo at week 160 (–6·1 [SD 7·3] vs −1·9% [6·3]; estimated treatment difference −4·3%, 95% CI −4·9 to −3·7, p&lt;0·0001). Serious adverse events were reported by 227 (15%) of 1501 randomised treated individuals in the liraglutide group versus 96 (13%) of 747 individuals in the placebo group. Interpretation: In this trial, we provide results for 3 years of treatment, with the limitation that withdrawn individuals were not followed up after discontinuation. Liraglutide 3·0 mg might provide health benefits in terms of reduced risk of diabetes in individuals with obesity and prediabetes. Funding: Novo Nordisk, Denmark