The horizontal gene transfer of Agrobacterium T-DNAs into the series Batatas (genus Ipomoea) genome is not confined to hexaploid sweetpotato

The discovery of the insertion of IbT-DNA1 and IbT-DNA2 into the cultivated (hexaploid) sweetpotato [Ipomoea batatas (L.) Lam.] genome constitutes a clear example of an ancient event of Horizontal Gene Transfer (HGT). However, it remains unknown whether the acquisition of both IbT-DNAs by the cultivated sweetpotato occurred before or after its speciation. Therefore, this study aims to evaluate the presence of IbT-DNAs in the genomes of sweetpotato's wild relatives belonging to the taxonomic group series Batatas. Both IbT-DNA1 and IbT-DNA2 were found in tetraploid I. batatas (L.) Lam. and had highly similar sequences and at the same locus to those found in the cultivated sweetpotato. Moreover, IbT-DNA1 was also found in I. cordatotriloba and I. tenuissima while IbT-DNA2 was detected in I. trifida. This demonstrates that genome integrated IbT-DNAs are not restricted to the cultivated sweetpotato but are also present in tetraploid I. batatas and other related species

Revisiting the Waxy Locus and the Capsicum annuum L. Complex

Waxy locus introns from 35 accessions of the species comprising the Cap­sicum annuum complex [C. annuum (7), C. frutescens (10), and C. chinense (11)1, C. baccatum (5), C. chacoense (1) and C. pubescens (1) were cloned and sequenced. These data were combined with existing GenBank waxy intron data on these same species, C. tovarii, C. ciliatum, Lycianthes heteroclita, L. lenta, and L. glandulosa in order to examine the phyloge­netic relationships within this group of plant materials, and to re-examine the strength of the delimitation of the members of the C. annuum complex provided previously by analysis of indel and transition/transversion poly­morphisms at this locus. Included in the subject materials analyzed were genotypes of C. annuum, C. chinense, and C. frutescens that possessed characteristics that were atypical for these respective species. PAUP analy­sis revealed strong support of Capsicum at the genus level. Capsicum ciliatum was the sister species to C. tovarii which was the sister species to a clade containing the five cultivated taxa and C. chacoense. The separation of C. pubescens from other cultivated Capsicum spp. was well supported. The separation of C. annuum from C. chinense and C. frutescens was less strongly supported based on bootstrap values. In contrast, no clear separa­tion of Capsicum chinense from Capsicum frutescens was observed

Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.)

Societal Impact Statement Crop wild relatives—wild species closely related to cultivated plants—are valuable genetic resources for crop improvement, but gaps in knowledge constrain their conservation and limit their further use. We develop new information on the distributions, potential breeding value, and conservation status of the 16 known wild relatives of cultivated pumpkins, squashes, zucchini, and gourds (Cucurbita L.). The taxa occur from the central USA to Central America, plus two South American species, with the greatest richness in central Mexico and the western borderlands between Mexico and the USA. We determine the majority of species are of medium priority for conservation, both with regard to collecting for ex situ maintenance, and for enhanced habitat protection. Summary Crop wild relatives are valuable genetic resources for crop improvement. Knowledge gaps, including with regard to taxonomy, distributions, and characterization for traits of interest constrain their use in plant breeding. These deficiencies also affect conservation planning, both with regard to in situ habitat protection, and further collection of novel diversity for ex situ maintenance. Here we model the potential ranges of all 16 known wild cucurbit taxa (Cucurbita L.), use ecogeographic information to infer their potential adaptations to abiotic stresses, and assess their ex situ and in situ conservation status. The taxa occur from the central USA to Central America, plus two South American species. Predicted taxon richness was highest in central Mexico and in the western borderlands between Mexico and the USA. We find substantial ecogeographic variation both across taxa and among populations within taxa, with regard to low temperatures, high and low precipitation, and other adaptations of potential interest for crop breeding. We categorize 13 of the taxa medium priority for further conservation as a combination of the ex situ and in situ assessments, two low priority, and one sufficiently conserved. Further action across the distributions of the taxa, with emphasis on taxonomic richness hotspots, is needed to comprehensively conserve wild Cucurbita populations

Genetic Diversity and Population Structure of the USDA Sweetpotato (Ipomoea batatas) Germplasm Collections Using GBSpoly

Sweetpotato (Ipomoea batatas) plays a critical role in food security and is the most important root crop worldwide following potatoes and cassava. In the United States (US), it is valued at over $700 million USD. There are two sweetpotato germplasm collections (Plant Genetic Resources Conservation Unit and US Vegetable Laboratory) maintained by the USDA, ARS for sweetpotato crop improvement. To date, no genome-wide assessment of genetic diversity within these collections has been reported in the published literature. In our study, population structure and genetic diversity of 417 USDA sweetpotato accessions originating from 8 broad geographical regions (Africa, Australia, Caribbean, Central America, Far East, North America, Pacific Islands, and South America) were determined using single nucleotide polymorphisms (SNPs) identified with a genotyping-by-sequencing (GBS) protocol, GBSpoly, optimized for highly heterozygous and polyploid species. Population structure using Bayesian clustering analyses (STRUCTURE) with 32,784 segregating SNPs grouped the accessions into four genetic groups and indicated a high degree of mixed ancestry. A neighbor-joining cladogram and principal components analysis based on a pairwise genetic distance matrix of the accessions supported the population structure analysis. Pairwise FST values between broad geographical regions based on the origin of accessions ranged from 0.017 (Far East – Pacific Islands) to 0.110 (Australia – South America) and supported the clustering of accessions based on genetic distance. The markers developed for use with this collection of accessions provide an important genomic resource for the sweetpotato community, and contribute to our understanding of the genetic diversity present within the US sweetpotato collection and the species

StarRunner: A Single-Stage-to-Orbit, Airbreathing, Hypersonic Propulsion System

40th AIAA/ASME/SAE/ASEE Joint Propulsion Conference And Exhibit Fort Lauderdale, FL, July 11-14, 2004.In response to the request for proposal (RFP) for the 2003 AIAA Undergraduate Team Engine Design Competition, the FAS Propulsion Design team from the Georgia Institute of Technology presents StarRunner: A Single-Stage-to-Orbit (SSTO), Airbreathing, Hypersonic Propulsion System. Low-cost, highly reliable access to low-Earth orbit (LEO) and the International Space Station (ISS) is an area of continuing research and debate. StarRunner is proposed to supplement a notional Crew Transfer Vehicle through the ability to deliver a 25,000 lb payload to the ISS. The horizontal takeoff/horizontal landing (HTHL) vehicle makes use of a turbine-based combined cycle (TBCC) propulsion system consisting of 14 low-bypass-ratio turbofan engines and a dual-mode ramjet/scramjet propulsion system for high-speed flight. The vehicle also takes advantage of ultra-high-temperature ceramic thermal protection materials and uses hydrogen fuel for regenerative cooling of engine components. StarRunner is compatible with standard runways, with a gross takeoff weight of approximately 1,000,000 lbs, and has a cost per pound to orbit of approximately $825/lb. This advanced, fully reusable space transport vehicle and integrated propulsion system design demonstrates student efforts to understand issues facing the space launch community. Future enabling and enhancing technologies for TBCC SSTO launch vehicles are explored and analyzed. The final StarRunner design addresses and proposes several innovative solutions to traditional problems

Author Correction: A consensus-based transparency checklist.

An amendment to this paper has been published and can be accessed via a link at the top of the paper

A consensus-based transparency checklist

We present a consensus-based checklist to improve and document the transparency of research reports in social and behavioural research. An accompanying online application allows users to complete the form and generate a report that they can submit with their manuscript or post to a public repository

Multiancestry analysis of the HLA locus in Alzheimer’s and Parkinson’s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues