Production Forecasts and Information for the States of Kosrae and Pohnpei, Federated States of Micronesia

This is the first publication on !he ADAP MlS for the CoIlege of Micronesia-FSM and it reflects results of the program as conducted in Pohnpei and Kosrae. Crop production estimates for Pohnpei for the period from December 1997 to May 1999 are included. In addition, some instructions on both how to conduct field surveys and the use of the computer template are included

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean.

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad

Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis

<p>Abstract</p> <p>Background</p> <p>Extensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, the nature, timing, lineages and adaptation of local genomic rearrangement in closely related species (<it>e.g</it>., within a genus) and haplotype variation of genomic rearrangement within populations have not been well documented.</p> <p>Results</p> <p>We previously identified a hotspot for genic rearrangement and transposon accumulation in the <it>Orp </it>region of Asian rice (<it>Oryza sativa</it>, AA) by comparison with its orthologous region in sorghum. Here, we report the comparative analysis of this region with its orthologous regions in the wild progenitor species (<it>O. nivara</it>, AA) of Asian rice and African rice (<it>O. glaberrima</it>) using the BB genome <it>Oryza </it>species (<it>O. punctata</it>) as an outgroup, and investigation of transposon insertion sites and a segmental inversion event in the AA genomes at the population level. We found that <it>Orp </it>region was primarily and recently expanded in the Asian rice species <it>O. sativa </it>and <it>O. nivara</it>. LTR-retrotransposons shared by the three AA-genomic regions have been fixed in all the 94 varieties that represent different populations of the AA-genome species/subspecies, indicating their adaptive role in genome differentiation. However, LTR-retrotransposons unique to either <it>O. nivara </it>or <it>O. sativa </it>regions exhibited dramatic haplotype variation regarding their presence or absence between or within populations/subpopulations.</p> <p>Conclusions</p> <p>The LTR-retrotransposon insertion hotspot in the <it>Orp </it>region was formed recently, independently and concurrently in different AA-genome species, and that the genic rearrangements detected in different species appear to be differentially triggered by transposable elements. This region is located near the end of the short arm of chromosome 8 and contains a high proportion of LTR-retrotransposons similar to observed in the centromeric region of this same chromosome, and thus may represent a genomic region that has recently switched from euchromatic to heterochromatic states. The haplotype variation of LTR-retrotransposon insertions within this region reveals substantial admixture among various subpopulations as established by molecular markers at the whole genome level, and can be used to develop retrotransposon junction markers for simple and rapid classification of <it>O. sativa </it>germplasm.</p

What is the role of culture, diversity, and community engagement in transdisciplinary translational science?

Concepts of culture and diversity are necessary considerations in the scientific application of theory generation and developmental processes of preventive interventions; yet, culture and/or diversity are often overlooked until later stages (e.g., adaptation [T3] and dissemination [T4]) of the translational science process. Here, we present a conceptual framework focused on the seamless incorporation of culture and diversity throughout the various stages of the translational science process (T1-T5). Informed by a community-engaged research approach, this framework guides integration of cultural and diversity considerations at each phase with emphasis on the importance and value of "citizen scientists" being research partners to promote ecological validity. The integrated partnership covers the first phase of intervention development through final phases that ultimately facilitate more global, universal translation of changes in attitudes, norms, and systems. Our comprehensive model for incorporating culture and diversity into translational research provides a basis for further discussion and translational science development

The Functional Basis for Hemophagocytic Lymphohistiocytosis in a Patient with Co-inherited Missense Mutations in the Perforin (PFN1) Gene

About 30% of cases of the autosomal recessive immunodeficiency disorder hemophagocytic lymphohistiocytosis are believed to be caused by inactivating mutations of the perforin gene. We expressed perforin in rat basophil leukemia cells to define the basis of perforin dysfunction associated with two mutations, R225W and G429E, inherited by a compound heterozygote patient. Whereas RBL cells expressing wild-type perforin (67 kD) efficiently killed Jurkat target cells to which they were conjugated, the substitution to tryptophan at position 225 resulted in expression of a truncated (∼45 kD) form of the protein, complete loss of cytotoxicity, and failure to traffic to rat basophil leukemia secretory granules. By contrast, G429E perforin was correctly processed, stored, and released, but the rat basophil leukemia cells possessed reduced cytotoxicity. The defective function of G429E perforin mapped downstream of exocytosis and was due to its reduced ability to bind lipid membranes in a calcium-dependent manner. This study elucidates the cellular basis for perforin dysfunctions in hemophagocytic lymphohistiocytosis and provides the means for studying structure–function relationships for lymphocyte perforin

ULTRA-SHORT-PERIOD PLANETS IN K2 WITH COMPANIONS: A DOUBLE TRANSITING SYSTEM FOR EPIC 220674823

Two transiting planets have been identified orbiting K2 target EPIC 220674823. One object is an ultra-short-period planet (USP) with a period of just 0.57 days (13.7 hr), while the other has a period of 13.3 days. Both planets are small, with the former having a radius of R_(p1) = 1.5 R⊕ and the latter R_(p2) = 2.5 R⊕. Follow-up observations, including radial velocity (with uncertainties of 110 m s−1) and high-resolution adaptive optics imagery, show no signs of stellar companions. EPIC 220674823 is the 12th confirmed or validated planetary system in which a USP (i.e., having an orbital period less than 1 day) is accompanied by at least one additional planet, suggesting that such systems may be common and must be accounted for in models for the formation and evolution of such extreme systems

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

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

Bacterial artificial chromosome (BAC) fingerprint and end-sequenced physical maps representing the ten genome types of Oryza are presente