An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants.

Soybean (Glycine max L.) is a major crop providing an important source of protein and oil, which can also be converted into biodiesel. A major milestone in soybean research was the recent sequencing of its genome.

Exploring the concordance of Aspergillus fumigatus pathogenicity in mice and Toll-deficient flies.

The pathogenicity of six mutants of Aspergillus fumigatus that had been previously characterized in mice was assessed in Toll-deficient Drosophila melanogaster flies. Four out of six mutants of A. fumigatus, which displayed attenuated virulence in mice due to defects in siderophore biosynthesis (DeltasidA, DeltasidD), PABA metabolism (H515), and starvation stress response (DeltacpcA), also had attenuated virulence in the fly model.

Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping.

Tragopogon miscellus (Asteraceae) is an evolutionary model for the study of natural allopolyploidy, but until now has been under-resourced as a genetic model. Using 454 and Illumina expressed sequence tag sequencing of the parental diploid species of T. miscellus, we identified 7782 single nucleotide polymorphisms that differ between the two progenitor genomes present in this allotetraploid.

Soybean root hairs: a valuable system to investigate plant biology at the cellular level.

Plant organs and tissues are composed of many differentiated cell types. Most functional genomic studies sample whole tissues, which dilutes the signals that may arise from individual cells within the population. The result is an averaging of the cellular response.

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.

Prediction of novel miRNAs and associated target genes in Glycine max.

Background: Small non-coding RNAs (21 to 24 nucleotides) regulate a number of developmental processes in plants and animals by silencing genes using multiple mechanisms. Among these, the most conserved classes are microRNAs (miRNAs) and small interfering RNAs (siRNAs), both of which are produced by RNase III-like enzymes called Dicers. Many plant miRNAs play critical roles in nutrient homeostasis, developmental processes, abiotic stress and pathogen responses.

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.

Correlating multimodal physical sensor information with biological analysis in ultra endurance cycling.

The sporting domain has traditionally been used as a testing ground for new technologies which subsequently make their way into the public domain. This includes sensors. In this article a range of physical and biological sensors deployed in a 64 hour ultra-endurance non-stop cycling race are described.

Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection.

Nodulation is the result of a mutualistic interaction between legumes and symbiotic soil bacteria (e.g. soybean [Glycine max] and Bradyrhizobium japonicum) initiated by the infection of plant root hair cells by the symbiont.

Evolution of digit identity in the three-toed Italian skink Chalcides chalcides: a new case of digit identity frame shift.

Digit identity in the avian wing is a classical example of conflicting anatomical and embryological evidence regarding digit homology. Anatomical in conjunction with phylogenetic evidence supports the hypothesis that the three remaining digits in the bird wing are digits 1, 2, and 3. At the same time, various lines of embryological evidence support the notion that these digits develop in positions that normally produce digits 2, 3, and 4.

SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services.

Background: SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies.

Results: There are currently over 2400 resources published in SSWAP.

Distributing free fresh fruit and vegetables at school: results of a pilot outcome evaluation.

Objectives: Consumption of fruit and vegetables among children is generally below recommended levels. This evaluation addressed two questions: (1) To what extent did children's attitudes toward, familiarity with, and preferences for fruit and vegetables change during the school year? and (2) To what extent did children's consumption of fruit and vegetables change during the school year?

Methods: During the 2004-2005 school year, the Mississippi Department of Education, Child Nutrition Programs initiated a pilot program to distribute free fruit and vegetables to students (kindergarten through 12th grade) during the school day. Data were collected in 2004-2005 within a one-group pretest/posttest design using a self-report questionnaire (n=725) and 24-hour dietary recalls (n=207) with a sample of students from five schools in Mississippi.

Thalidomide for the treatment of chronic gastrointestinal bleeding from angiodysplasias: a case series.

Background: Mucosal angiodysplasias, either inherited or acquired, can cause gastrointestinal bleeding, sometimes refractory to treatment. From earlier case reports, thalidomide has been described to possess some benefits in this disease, but its benefits and risks nevertheless remain unclear.

Objectives: This pilot study assesses the efficacy, safety, and side-effect of thalidomide in the treatment of patients with chronic gastrointestinal bleeding from angiodysplasias.

Infection with "escaped" virus variants impairs control of simian immunodeficiency virus SIVmac239 replication in Mamu-B*08-positive macaques.

An understanding of the mechanism(s) by which some individuals spontaneously control human immunodeficiency virus (HIV)/simian immunodeficiency virus replication may aid vaccine design. Approximately 50% of Indian rhesus macaques that express the major histocompatibility complex (MHC) class I allele Mamu-B*08 become elite controllers after infection with simian immunodeficiency virus SIVmac239. Mamu-B*08 has a binding motif that is very similar to that of HLA-B27, a human MHC class I allele associated with the elite control of HIV, suggesting that SIVmac239-infected Mamu-B*08-positive (Mamu-B*08+) animals may be a good model for the elite control of HIV.

Endophytic Fusarium verticillioides reduces disease severity caused by Ustilago maydis on maize.

Endophytic fungi represent diverse taxa that inhabit plant hosts without causing disease symptoms. We used endophytic isolates of Fusarium verticillioides (Sacc.) Nirenberg to understand how endophytic fungi interact with pathogens, in this case, the corn smut pathogen, Ustilago maydis DC (Corda).

Next-generation sequencing technologies and their implications for crop genetics and breeding.

Using next-generation sequencing technologies it is possible to resequence entire plant genomes or sample entire transcriptomes more efficiently and economically and in greater depth than ever before. Rather than sequencing individual genomes, we envision the sequencing of hundreds or even thousands of related genomes to sample genetic diversity within and between germplasm pools. Identification and tracking of genetic variation are now so efficient and precise that thousands of variants can be tracked within large populations.

Improved long-term survival after intra-operative single high-dose ATG-Fresenius induction in renal transplantation: a single centre experience.

Background: In organ grafts donor-specific sensitization is initiated immediately after revascularization. Therefore, in 1990 we introduced the intra-operative single high-dose ATG-Fresenius (ATG-F) induction in addition to standard triple drug therapy (TDT) consisting of steroids, azathioprine and cyclosporin. A total of 778 first renal transplantations from deceased donors, performed between 1987 and 1998, were included in this evaluation.

Novel translation products from simian immunodeficiency virus SIVmac239 Env-encoding mRNA contain both Rev and cryptic T-cell epitopes.

Understanding the correlates of immune protection against human immunodeficiency virus and simian immunodeficiency virus (SIV) will require defining the entire cellular immune response against the viruses. Here, we define two novel translation products from the SIV env mRNA that are targeted by the T-cell response in SIV-infected rhesus macaques. The shorter product is a subset of the larger product, which contains both the first exon of the Rev protein and a translated portion of the rev intron.

Fungal-fungal associations affect the assembly of endophyte communities in maize (Zea mays).

Many factors can affect the assembly of communities, ranging from species pools to habitat effects to interspecific interactions. In microbial communities, the predominant focus has been on the well-touted ability of microbes to disperse and the environment acting as a selective filter to determine which species are present. In this study, we investigated the role of biotic interactions (e.

Comparative performance of uncoated, self-expanding metal biliary stents of different designs in 2 diameters: final results of an international multicenter, randomized, controlled trial.

Background: The Wallstent has remained the industry standard for biliary self-expanding metal stents (SEMSs). Recently, stents of differing designs, compositions, and diameters have been developed.

Objective: To compare the new nitinol 6-mm and 10-mm Zilver stents with the 10-mm stainless steel Wallstent and determine the mechanism of obstruction.